ARS Scientists working on Antibiotic Resistance June 2016

Prepared as supplementary material for the

Presidential Advisory Council on Combating Antibiotic Resistant

Bacteria (PACCARB) public meeting

Surveillance and USG Activities Panel

June 22nd 2016 in Washington DC

Compiled by Lisa Durso lisadursoarsusdagov 402‐472‐9622

ARS Agricultural Antibiotic Resistance (AgAR) Advisory TeamJune 2016

Heather AllenAmes IA

Mark IbekweRiverside CA

Kim CookAthens GA

Dan MillerLincoln NE

Rob DunganKimberly ID

Tom DuceyFlorence SC

Lisa DursoLincoln NE

John BrooksMississippi State MS

Terry WhiteheadPeoria IL

Clinton WilliamsMaricopa AZ

Tom MoormanAmes IA

Heather AllenResearch Microbiologist

HeatherAllenarsusdagov

515-337-7207

Current Projectsbull Comparison of swine gut microbiotas with antibiotic

and non‐antibiotic feed additives in a heat stress model

bull Characterization of functional gene diversity (antibiotic resistance genes and butyrate transferasegenes) in sequence‐based and functional metagenomic analyses

Selected Publicationsbull Allen H K 2014 Antibiotic resistance gene discovery in

food‐producing animals Curr Opin Microbiol 1925‐29 bull Looft T H K Allen B L Cantarel U Y Levine D O

Bayles D P Alt B Henrissat and T Stanton 2014 Bacteria phages and pigs The effects of in‐feed antibiotics on the microbiome at different gut locations ISME J doi 101038ismej201412

bull Allen H K T Looft D O Bayles S Humphrey U Y Levine D Alt and T Stanton 2011 Antibiotics in feed induce prophages in swine fecal microbiomes mBio 26 e00260‐11

bull Allen H K J J Donato H Huimi Wang K A Cloud‐Hansen J Davies and J Handelsman 2010 Call of the wild antibiotic resistance genes in natural environments Nat Rev Microbiol 8(4) 251‐259

National Animal Disease CenterFood Safety and Enteric Pathogens Research Unit

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Jan 2016 Intestinal Microbial Ecology and Metagenomic Strategies to Reduce Antibiotic Resistance and Foodborne Pathogens

Production Systems StudiedSwine

Laboratory and Field Expertisebull Bacteriophage isolationbull Metagenomic analysesbull 16S rRNA gene sequence

analysesbull PCR and qPCRbull Bioinformaticsbull Anaerobic and aerobic bacterial

culturing

Research Interestsbull Determine the effects of industry‐relevant antibiotics

such as carbadox and chlortetracycline on swine gut bacterial community membership antibiotic resistance gene carriage and prophage induction

bull Develop and test probiotic bacteria including butyrate‐producing bacteria as an alternative to in‐feed antibiotics

Robin AndersonResearch Microbiologist

RobinAndersonarsusdagov

979-260-9317

Current Projectsbull Determine the role of gastrointestinal hydrogen ecology

on virulence gene expression in E coli Salmonella and Campylobacter

bull Develop prebiotic feed additives for pathogen control in swine and cattle

Selected Publicationsbull Petrujkić BT Sedej I Beier RC Anderson RC Harvey

RB Epps SVR Stipanovic RD Krueger NA and Nisbet DJ Ex vivo absorption of thymol and thymol‐β‐D‐glucopyranoside in piglet everted jejunal segments Journal of Agricultural and Food Chemistry 613757‐3762 2013

bull Anderson RC Harvey RB Wickersham TA MacDonald JC Ponce CH Brown M Pinchak WE Osterstock JB Krueger NA and Nisbet DJ Effect of distillers feedstuffs and lasalocid on Campylobactercarriage in feedlot cattle Journal of Food Protection 771968‐1975 2014

bull Epps SVR Petrujkić BT Sedej I Harvey RB Beier RC Stanton TB Phillips TD Hume ME Anderson RC and Nisbet DJ Comparison of anti‐Campylobacteractivity of free thymol and thymol‐β‐D‐glucopyranoside in absence or presence of β‐glycoside‐hydrolyzing gut bacteria Food Chemistry 17392‐98 2015

Food and Feed Safety Research Unit

Mailing AddressSouthern Plains Agricultural Research CtrFood amp Feed Safety Research Unit2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedBeef and dairy cattle swine and sheep

Laboratory and Field Expertisebull Rumen and gastrointestinal

microbiologybull Cultivation of anaerobesbull Bacterial physiology and

metabolismbull Preharvest food safety

Research Interestsbull Develop interventions to reduce the carriage of

foodborne pathogens in food animals and their production environments

bull Identify ecological factors impacting attachment and energy metabolism of enteropathogens within the gut

bull Identify selective factors impacting antimicrobial resistance acquisition dissemination and persistence

Terry ArthurResearch Microbiologist

TerranceArthurarsusdagov

402-762-4227

Current Projectsbull Effects of mass CTC treatment of calves entering feedlot

on animal health and AMR bacterial populationsbull Longitudinal study of antimicrobial‐resistant bacterial

populations in cattle feedlotbull Antimicrobial‐Resistant Fecal Bacteria from Ceftiofur‐

Treated and Non‐Antimicrobial‐Treated Co‐mingled Beef Cows at a Cow‐Calf Operation

Selected Publicationsbull Agga GE Arthur TM Brichta‐Harhay DM Durso

LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

bull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coli and Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Animal and environmental

sampling at cattle feedlots and beef processing facilities

bull Culture and molecular characterization of antimicrobial‐resistant bacterial populations

Research Interestsbull Comparison of AMR bacterial populations in livestock

and non‐livestock environmentsbull Impact of antimicrobial selection vs nutrient

supplementation on increases in environmental AMR bacterial populations

bull Mitigation of AMR bacterial populations associated with animal agriculture

Bradley BearsonMicrobiologist

BradBearsonarsusdagov

515-294-0209

Selected Publicationsbull Bearson BL and BW Brunelle Fluoroquinolone

Induction of Phage‐mediated Gene Transfer in Multidrug‐resistant Salmonella Int J Antimicrob Agents 46(2)201‐204 2015

bull Bearson B L Allen H K Brunelle B W Lee I S Casjens S R and Stanton T B The agricultural antibiotic carbadox induces phage‐mediated gene transfer in Salmonella Front Microbiol 552 2014

bull Bearson B L Bearson S M D Kich J D and Lee I S An rfaHmutant of Salmonella enterica serovar Typhimurium is attenuated in swine and reduces intestinal colonization fecal shedding and disease severity due to virulent Salmonella Typhimurium Front Vet Sci 19 2014

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Boulevard NLAEAmes IA 50011

National Program101 ndash Animal Production (Pending)

CRIS Project (terminated)Animal and Manure Management for Sustainable Production and Reduced Environmental Impact

Production Systems StudiedSwine and Turkeys

Laboratory and Field Expertisebull Bacterial strain construction

using classical genetics and recombineering

bull Antibiotic induced phage‐mediated gene transfer in Salmonella

bull Salmonella challenge models for swine and turkeys to investigate pathogenesis colonization and vaccine efficacy

bull PCR Salmonella genetics bacterial transformation and transduction modification of media for selection and differentiation of Salmonella

Research Interestsbull Development of alternatives to antibiotics such as

vaccines and other targeted interventionsbull Investigation of antibiotic resistance gene transfer

among microorganisms in the host and in the environment including multidrug‐resistant Salmonella

Current Projectsbull Validation of a Salmonella vaccine in swine and turkeys

to protect animal health and enhance food safetybull Identification of multidrug‐resistant Salmonella serovars

containing prophage capable of antibiotic‐induced gene transfer

bull Transcriptional analysis of phage genes following Salmonella exposure to antibiotics

bull Identification of antibiotics that induce phage‐mediated gene transfer in Salmonella

Shawn BearsonResearch Microbiologist

Current Projectsbull Characterizing novel porcine‐microbiota‐Salmonella

interactions as potential targets to reduce Salmonellacolonization and persistence in the intestinal tract

bull Developing alternatives to antibioticsbull Cross‐protective vaccine development against Salmonella serovars in food animals

bull Biotherapeutic immunostimulants for treatment of swine colonized with Salmonella

Selected Publicationsbull Knetter SM et al 2015 Salmonella enterica serovar

Typhimurium‐infected pigs with different shedding levels exhibit distinct clinical peripheral cytokine and transcriptomic immune response phenotypes Innate Immun 21227‐241

bull Bearson SM et al 2013 Polynucleotide phosphorylase (PNPase) is required for Salmonella enterica serovar Typhimurium colonization in swine Microb Pathog 6563‐66

bull Bearson SM et al 2013 Profiling the gastrointestinal microbiota in response to Salmonella low versus high Salmonella shedding in the natural porcine host Infect Genet Evol 16330‐340

Food Safety and Enteric Pathogens Research Unit

Mailing AddressNational Animal Disease Center1920 Dayton Ave1403Ames IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Title here

Second Title here if applicable

Production Systems StudiedSwine and Turkey

Laboratory and Field Expertisebull Molecular microbiologybull Salmonella geneticsbull Host transcriptomicsbull Salmonella colonization and

persistence in food animals

ShawnBearsonarsusdagov

515-337-7455

Research InterestsMy current research efforts are characterizing the effects of antibiotics on MDR Salmonella and identifying antibiotic alternatives to decrease Salmonella on the farm reduce antibiotic dependence promote animal health and provide the public with a safe food supply My research investigations focus on three factors that influence Salmonella colonization and persistence in food animals virulence mechanisms of Salmonella the tactical response from the host and interactions with the host microbiota residing within the gastrointestinal tract

Ross C BeierResearch Chemist

RossBeierarsusdagov

979-260-9411

Current Projectsbull Conduct disinfectant susceptibility tests on 145

Salmonella strains from feed lot water‐sprinkled cattlebull Synthesize thymol‐‐D‐cellobioside for use in delivering

the antibacterial thymol to the lower swine gutbull Conduct disinfectant susceptibility tests on 134

Campylobacter coli and jejuni from swine cecal samples meat products and feces

Selected Publicationsbull Beier RC E Franz JL Bono RE Mandrell PM

Fratamico TR Callaway K Andrews TL Poole TL Crippen CL Sheffield RC Anderson and DJ Nisbet Disinfectant and antimicrobial susceptibility profiles of the big six non‐O157 Shiga toxin‐producing Escherichia coli from food animals and humans J Food Protect 2016 (In press)

bull Crippen TL CL Sheffield JA Byrd JF Esquivel RC Beier and K Yeater Poultry litter and the environment Physiochemical properties of litter and soil during successive flock rotations and after remote site deposition Sci Total Environ 553650661 2016

bull Beier RC SE Duke RL Ziprin RB Harvey ME Hume TL Poole HM Scott LD Highfield WQ Alali K Andrews RC Anderson and DJ Nisbet Antibiotic and disinfectant susceptibility profiles of vancomycin‐resistant Enterococcus faecium (VRE) isolated from community wastewater in Texas Bull Environ Contam Toxicol 80188194 2008

Food and Feed SafetyResearch Unit

Mailing AddressSouthern Plains AgriculturalResearch Center

Food and Feed SafetyResearch Unit

2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedFocus is on bacterial isolates in beef swine and poultry

Laboratory and Field Expertisebull Microbroth dilution

antimicrobial susceptibility testing

bull Microbroth dilution disinfectant susceptibility testing

bull PCRbull Gas Chromatographybull High‐Performance Liquid

Chromatographybull TLC HPTLCbull Chemical Synthesis

Research Interestsbull Establish a knowledge base for disinfectant susceptibility

in foodborne pathogensbull Identify disinfectant and antimicrobial co‐resistancebull Evaluate the impact of disinfectant resistance genes

Elaine BerryResearch Microbiologist

ElaineBerryarsusdagov

402-762-4204

Current Projectsbull Evaluate the influence of spatiotemporal environmental

and wildlife factors on pathogen and antibiotic resistance occurrence and transmission dynamics in cattle and waterways in a pasture‐based production system

bull Determine phenotypic and genotypic factors associated with persistence of E coli O157H7 in cattle production

bull Determine the effect of calcium hydroxide application to feedlot pens on E coli O157H7 total E coli and antibiotic resistance on feedlot pen surfaces and in cattle

Selected Publicationsbull Berry ED JE Wells JL Bono BL Woodbury N

Kalchayanand KN Norman TV Suslow G Lόpez‐Velasco and PD Millner Effect of proximity to a cattle feedlot on Escherichia coli O157H7 contamination of leafy greens and evaluation of the potential for airborne transmission Appl Environ Microbiol 811101‐1110 2015

bull Wells JE ED Berry N Kalchayanand LA Rempel M Kim and WT Oliver Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Assessment of Genotypic and Phenotypic Factors for Foodborne Pathogen Transmission and Development of Intervention Strategies

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Sampling and analyses for

bacterial pathogens in manures soils and other environmental and complex sample matrices

bull Treatment and intervention processes to reduce pathogens in cattle swine and their manure

Research Interestsbull Understanding and reducing the transmission and

persistence of zoonotic pathogens and antibiotic resistance in livestock and preharvest production environments

bull Reducing pathogen and antibiotic resistance transmission from animal production to produce water and the environment

Carl BolsterResearch Hydrologist

CarlBolsterarsusdagov

270-781-2632 ext 244

Current Projectsbull Evaluating effects of manure application rate and

timing on the leaching and runoff potential of antibiotic resistant bacteria and their associated genes as part of a National Pork Board funded project

bull Incorporating uncertainty estimates in model predictions of phosphorus loss from agricultural fields

bull Comparing predictions from annual and daily time‐step phosphorus transport models as part of a National Conservation Innovation Grant project

Selected Publicationsbull Abit SM Bolster CH Cantrell KB Flores JQ and SL

Walker 2014 Transport of Escherichia coli Salmonella typhimurium and microspheres in biochar‐amended soils with different textures J of Environ Qual 43371‐378

bull Bolster CH and Abit SM 2012 Biochar pyrolyzed at two temperatures impacts E coli transport through a sandy soil J of Environ Qual 41124‐133

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville RD ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Management

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental QualitySecond Title here if applicable

Production Systems StudiedPoultry and swine

Laboratory and Field Expertisebull Conducting laboratory‐scale

flow through experimentsbull Developing and using numerical

models for describing bacteria and solute fate and transport in the environment

bull Quantifying uncertainties in observed and modeled data

Research Interestsbull Understanding the factors controlling microbial

transport through biochar‐amended soilsbull Evaluating transport of antibiotic resistant bacteria

through soilsbull Improving modeling tools for describing fate and

transport of phosphorus in the environment

Brian BrunelleResearch Microbiologist

BrianBrunellearsusdagov

515-337-7612

Current Projectsbull Comparing transcriptional differences between

antibiotics that induce invasion in multidrug‐resistant Salmonella and those that have no effect

bull Genome sequencing of novel multidrug‐resistant Salmonella isolates

bull Assessing antibiotics that can enhance resistance in multidrug‐resistant Salmonella

Selected Publicationsbull Brunelle BW Bearson BL Bearson SMD 2015

Chloramphenicol and tetracycline decrease motility and increase invasion and attachment gene expression in specific isolates of multidrug‐resistant Salmonella entericaserovar Typhimurium Front Microbiol 5801

bull Brunelle BW Bearson SMD Bearson BL 2013 Tetracycline accelerates the temporally‐regulated invasion response in specific isolates of multidrug‐resistant Salmonella enterica serovar Typhimurium BMC Microbiology 13 202

Food Safety and Enteric Pathogen Research Unit

Mailing AddressNational Animal Disease Center1920 Dayton AvePO Box 70Ames IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Analysis of Virulence and Antibiotic Resistance Mechanisms of Salmonella and Development of Intervention Strategies

Production Systems StudiedSwine

Laboratory and Field Expertisebull Analysis of bacterial

transcription using real‐time PCR and RNA‐seq

bull Characterization of antibiotic resistance levels and associated genes

bull Conducting assays to measure different virulence phenotypes (cellular invasion motility etc)

Research Interestsbull Investigating the impact antibiotic usage has on

influencing multidrug‐resistant Salmonella virulence phenotypes

bull Identifying genes and regulation pathways associated with phenotypic differences in multidrug‐resistant Salmonella isolates exposed to antibiotics

John P BrooksResearch Microbiologist

JohnBrooksarsusdagov

662-320-7411

7

Current Projectsbull The effect of degraded antibiotic on soil microbial

ecology and antibacterial microbiomebull Aerosol carriage of antibiotic resistant genes and

bacteria from land application of poultry litterbull Antibiotic resistant bacteria and genes in naiumlve

broiler CAFOs

Selected Publicationsbull Brooks JP MR McLaughlin A Adeli DM Miles 2016

Cultivation and qPCR detection of pathogenic and antibiotic‐resistant bacterial establishment in naiumlve broiler houses J Environ Qual 45958‐966

bull Brooks JP Adeli A McLaughlin MR 2014 Microbial ecology bacterial pathogens and antibiotic resistant genes in swine manure as influenced by three swine management systems Water Res 5796‐103

bull Brooks JP McLaughlin MR Scheffler B and Miles DM 2010 Microbial and antibiotic resistant constituents associated with biological aerosols and poultry litter within a commercial poultry house Sci Tot Environ 4084770‐4777

Genetics and Sustainable Agriculture Research Unit

Mailing Address810 Highway 12 East PO Box 5367Mississippi State MS 39762

National Program(s)216 ndash Agricultural System Competitiveness and Sustainability

CRIS Project(s)Integration of Site‐Specific Crop Production Practices amp Industrial amp Animal Ag Byproducts to Improve Ag Competitiveness amp Sustainability

Production Systems StudiedSwine Poultry Forage amp Row Crop

Laboratory and Field Expertisebull Detection amp enumeration of

pathogens and antibacterial resistant genes and bacteria

bull Sampling soil water air amp CAFO environments

bull Quantitative microbial risk assessment of pathogens amp antibacterial resistant bacteria in the environment

Research Interestsbull Identify the movement and fate of pathogens and

antibacterial resistant genesbacteria through the environment and CAFO environments

bull Apply quantitative microbial risk assessment to anthropogenic impacted environments

bull Determine the impact of row crop agriculture on the soil microbial and antibacterial resistant biome

Tucker BurchResearch Agricultural

Engineer

TuckerBurcharsusdagov

715-387-3670

Current Projectsbull Occurrence and Distribution of Antibiotic Resistance

Genes (ARGs) in Groundwater of Kewaunee County Wisconsin

Selected Publicationsbull Burch TR Sadowsky MJ LaPara TM 2016 Modeling the

fate of antibiotic resistance genes and class 1 integronsduring thermophilic anaerobic digestion of municipal wastewater solids Appl Microbiol Biotechnol 100(3) 1437‐1444

bull Burch TR Sadowsky MJ LaPara TM 2014 Fate of antibiotic resistance genes and class 1 integrons in soil microcosms following the application of treated residual municipal wastewater solids Environ Sci Technol 48(10) 5620‐5627

bull Burch TR Sadowsky MJ LaPara TM 2013 Air‐drying beds reduce the quantities of antibiotic resistance genes and class 1 integrons in residual municipal wastewater solids Environ Sci Technol 47(17) 9965‐9971

bull Burch TR Sadowsky MJ LaPara TM 2013 Aerobic digestion reduces the quantity of antibiotic resistance genes in residual municipal wastewater solids Front Microbiol 4(Feb)

Dairy Forage Research CenterEnvironmentally Integrated Dairy Management Research Unit

Mailing Address2615 Yellowstone DriveMarshfield WI 54449

National Program(s)212 ndash Soil and Air

CRIS Project(s)Improving Nutrient Use Efficiency and Mitigating Nutrient and Pathogen Losses from Dairy Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull qPCRbull Bioaerosol samplingbull Quantitative microbial risk

assessment

Research Interestsbull Environmental distribution and transmission of

antibiotic resistance genes (ARGs)bull Quantitative microbial risk assessment

Todd CallawayResearch Microbiologist

ToddCallawayarsusdagov

979-260-9374 7

Current Projectsbull Effects of organic acids on the microbiome of food

animals and impact on foodborne pathogensbull Dietary impacts on foodborne pathogenic bacteria

and the microbial ecosystembull Phytochemicals and their ability to alter composition

of the gastrointestinal microbiome

Selected Publicationsbull Callaway T R T S Edrington and D J Nisbet 2014

Isolation of E coli O157H7 and Salmonella from migratory brown‐headed cowbirds (Molothrus ater) common grackles (Quiscalus quiscula) and cattle egrets (Bubulcus ibis) Foodborne Path Dis 11791‐794

bull Broadway P R J A Carroll J C Brooks J R Donaldson N C Burdick‐Sanchez T B Schmidt T R Brown and T R Callaway 2015 Salmonella transfer to the lymph nodes and synovial fluid of experimentally orally inoculated swine Agric Food Anal Bacteriol (In Press)

bull Grilli E F Foresti B Tugnoli M Fustini M G Zanoni P Pasquali T R Callaway A Piva and G L Alborali 2015 Microencapsulated sorbic acid and pure botanicals affect Salmonella Typhimurium shedding in pigs a close‐up look from weaning to slaughter in controlled and field conditions Foodborne Path Dis (In Press)

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedBeef Cattle Dairy Cattle Swine and Poultry

Laboratory and Field Expertisebull Microbial Physiologybull Microbial Ecologybull Continuous culturebull Mixed culture environmental

simulationsbull Environmental impacts on

survival of foodborne pathogenic bacteria

bull Animal model challengesbull Development of pre‐harvest

intervention strategiesbull Feedlot and dairy procedures

Research Interestsbull Understanding how the microbial ecosystem interacts

with foodborne pathogens at a functional nicheguild level

bull Developing non‐antibiotic methods of reducing foodborne pathogenic bacteria in the gut of food animals

Kimberly CookResearch Microbiologist

KimCookarsusdagov

270-781-2579 ext 232

Current Projectsbull Capture and identify mobile genetic elements

associated with bacteria in soils with applied poultry litter effect of application method

bull Evaluate persistence and concentration of antibiotics and bacteria with AR genes in waste treatment systems and soils with application manures

bull Transport and adhesion of bacteria with AR genesbull Evaluate AR properties of E coli and enterococci

isolates from agricultural ecosystems

Selected Publicationsbull Durso LM and KL Cook 2014 Impacts of antibiotic

use in agriculture what are the benefits and risks CurrOpinion Microbiol 1937‐44 2014

bull Cook KL AMP Netthisinghe and RA Gilfillen 2014 Detection of Pathogens Indicators and Antibiotic Resistance Genes after Land Application of Poultry Litter J Environ Qual 43 1546‐1558

bull Netthisinghe AMP KL Cook C Rice RA Gilfillen and KR Sistani 2013 Soil Nutrients Bacteria Populations and Veterinary Pharmaceuticals across a Backgrounding Beef Feedlot J Environ Qual 42 532‐544

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville Red ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Research

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental Quality

Production Systems StudiedPoultry Swine Beef

Laboratory and Field Expertisebull Soils manure and waste

treatment systemsbull PCR Quantitiative real‐time

PCRbull Culture and antimicrobial

susceptibilitybull Isolation and characterization of

mobile genetic elements carrying genes for antibiotic resistance

Research Interestsbull Characterizing persistence and transmission of

antibiotics antibiotic resistance (AR) genes and AR bacteria through agroecosystems

bull Capture and characterize mobile genetic elements carrying AR genes between microbial populations in soils with applied manures

bull Strain level differences in resistance transport and adhesion properties of bacteria with AR genes

Annie DonoghueResearch Leader (Physiologist)

AnnieDonoghuearsusdagov479-575-2413

7

Current Projectsbull Use of natural remedies to alleviate enteric

pathogens in organic and conventionally raised poultry

bull Alternatives to antibiotics for controlling Salmonella and Campylobacter in poultry and poultry products

Selected Publicationsbull Donoghue AM Venkitanarayanan K Arsi K Woo‐

Ming A Upadhyaya I Kollanoor‐Johny A Darre MJ Upadhyay A Fanatico A and Donoghue DJ 2015 Organic Poultry Developing Natural Solutions for Reducing Pathogens and Improving Production Organic Agriculture Research Symp in press

bull Arsi K Donoghue AM Woo‐Ming A Blore PJ and Donoghue DJ 2015 Intracloacal inoculation an effective screening method for determining the efficacy of probiotic bacterial isolates against Campylobactercolonization in broiler chickens J Food Prot 78 209‐213

bull Arsi K Donoghue AM Venkitanarayanan K Kollanoor‐Johny A Fanatico AC Blore PJ and Donoghue DJ2014 The efficacy of the natural plant extracts thymol and carvacrol against Campylobacter colonization in broiler chickens J Food Safety 34 321ndash325

Poultry Production and Products Safety Research Unit

Mailing AddressUniversity Of ArkansasPOSC O‐303Fayetteville AR 72701

National Program(s)108 ndash Food Safety103 ndash Animal Health

CRIS Project(s)Alternative Intervention and Control Strategies for Foodborne Pathogens in Poultry and Poultry Products

Novel Therapeutic Diagnostic and Management Strategies to Reduce Antibiotic Use in Poultry Production

Production Systems StudiedPoultry

Laboratory and Field ExpertiseLab uses traditional microbiological culture and molecular biological techniques to study food borne pathogens Organic and conventional practices for poultry production

Research Interestsbull developing alternatives to antibiotic use in poultry bull developing strategies to reduce or eliminate pathogen

contamination with a focus on Campylobacter and Salmonella

bull developing sustainable and organic farming practices for poultry producers

David DonavanResearch Molecular Biologist

DavidDonovanarsusdagov

Ce 443-690-4251 Office 301-504-9150

Current Projectsbull Mastitis a cow‐side diagnosticbull Mastitis treatment with triple‐acting antimicrobialsbull Clostridium perfringens novel endolysins that are heat‐resistantbull Yeast expressed endolysins as an alternative to antibiotics in animal feedbull CRISPRCas9 genomic engineering of cow and pig embryos

Selected Publicationsbull Rodriacuteguez‐Rubio L Martiacutenez B Rodriacuteguez A Donovan DM Goumltz F et al The

phage lytic proteins from the Staphylococcus aureus bacteriophage vB_SauS‐phiIPLA88 display multiple active catalytic domains and do not trigger staphylococcal resistance PloS one 2013 8(5)e64671

bull Singh PK Donovan DM Kumar A Intravitreal injection of the chimeric phage endolysin Ply187 protects mice from Staphylococcus aureus endophthalmitis Antimicrobial agents and chemotherapy 2014 58(8)4621‐9

bull Swift SM Seal BS Garrish JK Oakley BB Hiett K et al A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens‐Specific Cell Wall Binding Domain Creates an Anti‐Clostridium Antimicrobial with Improved Thermostability Viruses 2015 7(6)3019‐34

Link to all publications httpwwwncbinlmnihgovsitesmyncbi1jOJlsCcVSxQTbibliography41565643publicsort=dateampdirection=ascending

Animal Biosciences and Biotechnology Laboratory

Mailing AddressRoom 104 10300 Baltimore AveBLDG 230 BARC‐EastBeltsville MD 20705

National ProgramNP101 Food Animal Production

CRIS Project TitleDeveloping Genetic Biotechnologies for Increased Food Animal Production including Novel Antimicrobials for Improved Health and Product Safety

Production Systems StudiedDairy cattle Swine poultry Aquaculture

Laboratory and Field Expertisebull Molecular biologist with

transgenic and knockout mouse background

bull Heterologous gene expression in yeast bacteria mice and cell culture

bull Induced Pluripotent Stem cell production via lentiviral transduction

bull Mouse colony animal husbandry and embryo transfer

Research InterestsDavid M Donovan PhD Research Scientist (Molecular Biologist) at the US Department of Agriculture received his PhD in 1987 in molecular genetics of the yeast Saccharomyces cerevisiae and has 22 years experience in heterologous gene expression He spent 15 years at the NIH culminating in Section Chief Transgenic and Knockout Mouse lab NIA In 2002 he joined the USDA where he has been developing antimicrobials for the treatment of mastitis pathogens including Staphylococcus aureus His enzyme antimicrobials harbor three unique synergistic lytic domains and a protein transduction domain to target intracellular pathogens and have been shown to be highly refractory to resistance development His constructs eradicate both extracellular S aureus [in a rat nasal colonization model and murine systemic infections] and intracellular pathogens ex vivo in bovine mammary epithelial cells and in both a mouse model of mastitis and osteomyelitis He is working to identify protein feed additives as alternative to antibiotic growth promotants

Thomas F DuceyMicrobiologist

ThomasDuceyarsusdagov

843-669-5203 x112

Current Projectsbull Microbial responses to wetland restoration as a part

of the Mid‐Atlantic Region Conservation Effects Assessment Project

bull Response of the microbial rhizosphere and arbuscular mycorrhizae fungi to clover cover crop and conservation tillage in cotton production

bull Isolation of E coli and Enterococcus species from swine wastewater poultry litter and agriculturally‐impacted groundwater for the determination of baseline antibiotic resistance levels in agricultural production systems

Selected Publicationsbull Ducey et al Soil physicochemical conditions

denitrification rates and nosZ abundance in NC coastal plain restored wetlands 2015 J Environ Qual 44 1011‐1022

bull Ducey et al Microbial community analysis of swine wastewater anaerobic lagoons by next‐generation DNA sequencing 2013 Anaerobe 2150‐57

Coastal Plain Soil Water and Plant Research Center

Mailing Address2611 West Lucas StreetFlorence SC 29501

National Program(s)211 ndash Water Availability and Water Management212 ndash Climate Change Soils and Emissions214 ndash Agricultural and Industrial Byproducts

CRIS Project(s)Managing Water Availability and Quality (NP 211)Improving Chemical Physical and Biological Properties of Degraded Sandy Soils (NP 212)Innovative Bioresource Management Technologies (NP 214)

Production Systems StudiedCrops Poultry and Swine

Laboratory and Field Expertisebull Classical Microbiology

bull DetectionEnumerationIsolationbull New species identification

bull Molecular Biologybull T‐RFLPARISAbull qPCRReal Time PCRbull High‐throughput DNA Sequencing

(Ion Torrent)

Research Interestsbull Southeastern US coastal plain wetland restoration

and its effect on microbial community composition and function

bull Animal wastewater treatment systems with a particular focus on pathogen reduction and antibiotic resistance gene elimination

bull Microbial community analysis and response to crop conservation and cover cropping management practices

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

ARS Agricultural Antibiotic Resistance (AgAR) Advisory TeamJune 2016

Heather AllenAmes IA

Mark IbekweRiverside CA

Kim CookAthens GA

Dan MillerLincoln NE

Rob DunganKimberly ID

Tom DuceyFlorence SC

Lisa DursoLincoln NE

John BrooksMississippi State MS

Terry WhiteheadPeoria IL

Clinton WilliamsMaricopa AZ

Tom MoormanAmes IA

Heather AllenResearch Microbiologist

HeatherAllenarsusdagov

515-337-7207

Current Projectsbull Comparison of swine gut microbiotas with antibiotic

and non‐antibiotic feed additives in a heat stress model

bull Characterization of functional gene diversity (antibiotic resistance genes and butyrate transferasegenes) in sequence‐based and functional metagenomic analyses

Selected Publicationsbull Allen H K 2014 Antibiotic resistance gene discovery in

food‐producing animals Curr Opin Microbiol 1925‐29 bull Looft T H K Allen B L Cantarel U Y Levine D O

Bayles D P Alt B Henrissat and T Stanton 2014 Bacteria phages and pigs The effects of in‐feed antibiotics on the microbiome at different gut locations ISME J doi 101038ismej201412

bull Allen H K T Looft D O Bayles S Humphrey U Y Levine D Alt and T Stanton 2011 Antibiotics in feed induce prophages in swine fecal microbiomes mBio 26 e00260‐11

bull Allen H K J J Donato H Huimi Wang K A Cloud‐Hansen J Davies and J Handelsman 2010 Call of the wild antibiotic resistance genes in natural environments Nat Rev Microbiol 8(4) 251‐259

National Animal Disease CenterFood Safety and Enteric Pathogens Research Unit

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Jan 2016 Intestinal Microbial Ecology and Metagenomic Strategies to Reduce Antibiotic Resistance and Foodborne Pathogens

Production Systems StudiedSwine

Laboratory and Field Expertisebull Bacteriophage isolationbull Metagenomic analysesbull 16S rRNA gene sequence

analysesbull PCR and qPCRbull Bioinformaticsbull Anaerobic and aerobic bacterial

culturing

Research Interestsbull Determine the effects of industry‐relevant antibiotics

such as carbadox and chlortetracycline on swine gut bacterial community membership antibiotic resistance gene carriage and prophage induction

bull Develop and test probiotic bacteria including butyrate‐producing bacteria as an alternative to in‐feed antibiotics

Robin AndersonResearch Microbiologist

RobinAndersonarsusdagov

979-260-9317

Current Projectsbull Determine the role of gastrointestinal hydrogen ecology

on virulence gene expression in E coli Salmonella and Campylobacter

bull Develop prebiotic feed additives for pathogen control in swine and cattle

Selected Publicationsbull Petrujkić BT Sedej I Beier RC Anderson RC Harvey

RB Epps SVR Stipanovic RD Krueger NA and Nisbet DJ Ex vivo absorption of thymol and thymol‐β‐D‐glucopyranoside in piglet everted jejunal segments Journal of Agricultural and Food Chemistry 613757‐3762 2013

bull Anderson RC Harvey RB Wickersham TA MacDonald JC Ponce CH Brown M Pinchak WE Osterstock JB Krueger NA and Nisbet DJ Effect of distillers feedstuffs and lasalocid on Campylobactercarriage in feedlot cattle Journal of Food Protection 771968‐1975 2014

bull Epps SVR Petrujkić BT Sedej I Harvey RB Beier RC Stanton TB Phillips TD Hume ME Anderson RC and Nisbet DJ Comparison of anti‐Campylobacteractivity of free thymol and thymol‐β‐D‐glucopyranoside in absence or presence of β‐glycoside‐hydrolyzing gut bacteria Food Chemistry 17392‐98 2015

Food and Feed Safety Research Unit

Mailing AddressSouthern Plains Agricultural Research CtrFood amp Feed Safety Research Unit2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedBeef and dairy cattle swine and sheep

Laboratory and Field Expertisebull Rumen and gastrointestinal

microbiologybull Cultivation of anaerobesbull Bacterial physiology and

metabolismbull Preharvest food safety

Research Interestsbull Develop interventions to reduce the carriage of

foodborne pathogens in food animals and their production environments

bull Identify ecological factors impacting attachment and energy metabolism of enteropathogens within the gut

bull Identify selective factors impacting antimicrobial resistance acquisition dissemination and persistence

Terry ArthurResearch Microbiologist

TerranceArthurarsusdagov

402-762-4227

Current Projectsbull Effects of mass CTC treatment of calves entering feedlot

on animal health and AMR bacterial populationsbull Longitudinal study of antimicrobial‐resistant bacterial

populations in cattle feedlotbull Antimicrobial‐Resistant Fecal Bacteria from Ceftiofur‐

Treated and Non‐Antimicrobial‐Treated Co‐mingled Beef Cows at a Cow‐Calf Operation

Selected Publicationsbull Agga GE Arthur TM Brichta‐Harhay DM Durso

LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

bull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coli and Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Animal and environmental

sampling at cattle feedlots and beef processing facilities

bull Culture and molecular characterization of antimicrobial‐resistant bacterial populations

Research Interestsbull Comparison of AMR bacterial populations in livestock

and non‐livestock environmentsbull Impact of antimicrobial selection vs nutrient

supplementation on increases in environmental AMR bacterial populations

bull Mitigation of AMR bacterial populations associated with animal agriculture

Bradley BearsonMicrobiologist

BradBearsonarsusdagov

515-294-0209

Selected Publicationsbull Bearson BL and BW Brunelle Fluoroquinolone

Induction of Phage‐mediated Gene Transfer in Multidrug‐resistant Salmonella Int J Antimicrob Agents 46(2)201‐204 2015

bull Bearson B L Allen H K Brunelle B W Lee I S Casjens S R and Stanton T B The agricultural antibiotic carbadox induces phage‐mediated gene transfer in Salmonella Front Microbiol 552 2014

bull Bearson B L Bearson S M D Kich J D and Lee I S An rfaHmutant of Salmonella enterica serovar Typhimurium is attenuated in swine and reduces intestinal colonization fecal shedding and disease severity due to virulent Salmonella Typhimurium Front Vet Sci 19 2014

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Boulevard NLAEAmes IA 50011

National Program101 ndash Animal Production (Pending)

CRIS Project (terminated)Animal and Manure Management for Sustainable Production and Reduced Environmental Impact

Production Systems StudiedSwine and Turkeys

Laboratory and Field Expertisebull Bacterial strain construction

using classical genetics and recombineering

bull Antibiotic induced phage‐mediated gene transfer in Salmonella

bull Salmonella challenge models for swine and turkeys to investigate pathogenesis colonization and vaccine efficacy

bull PCR Salmonella genetics bacterial transformation and transduction modification of media for selection and differentiation of Salmonella

Research Interestsbull Development of alternatives to antibiotics such as

vaccines and other targeted interventionsbull Investigation of antibiotic resistance gene transfer

among microorganisms in the host and in the environment including multidrug‐resistant Salmonella

Current Projectsbull Validation of a Salmonella vaccine in swine and turkeys

to protect animal health and enhance food safetybull Identification of multidrug‐resistant Salmonella serovars

containing prophage capable of antibiotic‐induced gene transfer

bull Transcriptional analysis of phage genes following Salmonella exposure to antibiotics

bull Identification of antibiotics that induce phage‐mediated gene transfer in Salmonella

Shawn BearsonResearch Microbiologist

Current Projectsbull Characterizing novel porcine‐microbiota‐Salmonella

interactions as potential targets to reduce Salmonellacolonization and persistence in the intestinal tract

bull Developing alternatives to antibioticsbull Cross‐protective vaccine development against Salmonella serovars in food animals

bull Biotherapeutic immunostimulants for treatment of swine colonized with Salmonella

Selected Publicationsbull Knetter SM et al 2015 Salmonella enterica serovar

Typhimurium‐infected pigs with different shedding levels exhibit distinct clinical peripheral cytokine and transcriptomic immune response phenotypes Innate Immun 21227‐241

bull Bearson SM et al 2013 Polynucleotide phosphorylase (PNPase) is required for Salmonella enterica serovar Typhimurium colonization in swine Microb Pathog 6563‐66

bull Bearson SM et al 2013 Profiling the gastrointestinal microbiota in response to Salmonella low versus high Salmonella shedding in the natural porcine host Infect Genet Evol 16330‐340

Food Safety and Enteric Pathogens Research Unit

Mailing AddressNational Animal Disease Center1920 Dayton Ave1403Ames IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Title here

Second Title here if applicable

Production Systems StudiedSwine and Turkey

Laboratory and Field Expertisebull Molecular microbiologybull Salmonella geneticsbull Host transcriptomicsbull Salmonella colonization and

persistence in food animals

ShawnBearsonarsusdagov

515-337-7455

Research InterestsMy current research efforts are characterizing the effects of antibiotics on MDR Salmonella and identifying antibiotic alternatives to decrease Salmonella on the farm reduce antibiotic dependence promote animal health and provide the public with a safe food supply My research investigations focus on three factors that influence Salmonella colonization and persistence in food animals virulence mechanisms of Salmonella the tactical response from the host and interactions with the host microbiota residing within the gastrointestinal tract

Ross C BeierResearch Chemist

RossBeierarsusdagov

979-260-9411

Current Projectsbull Conduct disinfectant susceptibility tests on 145

Salmonella strains from feed lot water‐sprinkled cattlebull Synthesize thymol‐‐D‐cellobioside for use in delivering

the antibacterial thymol to the lower swine gutbull Conduct disinfectant susceptibility tests on 134

Campylobacter coli and jejuni from swine cecal samples meat products and feces

Selected Publicationsbull Beier RC E Franz JL Bono RE Mandrell PM

Fratamico TR Callaway K Andrews TL Poole TL Crippen CL Sheffield RC Anderson and DJ Nisbet Disinfectant and antimicrobial susceptibility profiles of the big six non‐O157 Shiga toxin‐producing Escherichia coli from food animals and humans J Food Protect 2016 (In press)

bull Crippen TL CL Sheffield JA Byrd JF Esquivel RC Beier and K Yeater Poultry litter and the environment Physiochemical properties of litter and soil during successive flock rotations and after remote site deposition Sci Total Environ 553650661 2016

bull Beier RC SE Duke RL Ziprin RB Harvey ME Hume TL Poole HM Scott LD Highfield WQ Alali K Andrews RC Anderson and DJ Nisbet Antibiotic and disinfectant susceptibility profiles of vancomycin‐resistant Enterococcus faecium (VRE) isolated from community wastewater in Texas Bull Environ Contam Toxicol 80188194 2008

Food and Feed SafetyResearch Unit

Mailing AddressSouthern Plains AgriculturalResearch Center

Food and Feed SafetyResearch Unit

2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedFocus is on bacterial isolates in beef swine and poultry

Laboratory and Field Expertisebull Microbroth dilution

antimicrobial susceptibility testing

bull Microbroth dilution disinfectant susceptibility testing

bull PCRbull Gas Chromatographybull High‐Performance Liquid

Chromatographybull TLC HPTLCbull Chemical Synthesis

Research Interestsbull Establish a knowledge base for disinfectant susceptibility

in foodborne pathogensbull Identify disinfectant and antimicrobial co‐resistancebull Evaluate the impact of disinfectant resistance genes

Elaine BerryResearch Microbiologist

ElaineBerryarsusdagov

402-762-4204

Current Projectsbull Evaluate the influence of spatiotemporal environmental

and wildlife factors on pathogen and antibiotic resistance occurrence and transmission dynamics in cattle and waterways in a pasture‐based production system

bull Determine phenotypic and genotypic factors associated with persistence of E coli O157H7 in cattle production

bull Determine the effect of calcium hydroxide application to feedlot pens on E coli O157H7 total E coli and antibiotic resistance on feedlot pen surfaces and in cattle

Selected Publicationsbull Berry ED JE Wells JL Bono BL Woodbury N

Kalchayanand KN Norman TV Suslow G Lόpez‐Velasco and PD Millner Effect of proximity to a cattle feedlot on Escherichia coli O157H7 contamination of leafy greens and evaluation of the potential for airborne transmission Appl Environ Microbiol 811101‐1110 2015

bull Wells JE ED Berry N Kalchayanand LA Rempel M Kim and WT Oliver Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Assessment of Genotypic and Phenotypic Factors for Foodborne Pathogen Transmission and Development of Intervention Strategies

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Sampling and analyses for

bacterial pathogens in manures soils and other environmental and complex sample matrices

bull Treatment and intervention processes to reduce pathogens in cattle swine and their manure

Research Interestsbull Understanding and reducing the transmission and

persistence of zoonotic pathogens and antibiotic resistance in livestock and preharvest production environments

bull Reducing pathogen and antibiotic resistance transmission from animal production to produce water and the environment

Carl BolsterResearch Hydrologist

CarlBolsterarsusdagov

270-781-2632 ext 244

Current Projectsbull Evaluating effects of manure application rate and

timing on the leaching and runoff potential of antibiotic resistant bacteria and their associated genes as part of a National Pork Board funded project

bull Incorporating uncertainty estimates in model predictions of phosphorus loss from agricultural fields

bull Comparing predictions from annual and daily time‐step phosphorus transport models as part of a National Conservation Innovation Grant project

Selected Publicationsbull Abit SM Bolster CH Cantrell KB Flores JQ and SL

Walker 2014 Transport of Escherichia coli Salmonella typhimurium and microspheres in biochar‐amended soils with different textures J of Environ Qual 43371‐378

bull Bolster CH and Abit SM 2012 Biochar pyrolyzed at two temperatures impacts E coli transport through a sandy soil J of Environ Qual 41124‐133

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville RD ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Management

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental QualitySecond Title here if applicable

Production Systems StudiedPoultry and swine

Laboratory and Field Expertisebull Conducting laboratory‐scale

flow through experimentsbull Developing and using numerical

models for describing bacteria and solute fate and transport in the environment

bull Quantifying uncertainties in observed and modeled data

Research Interestsbull Understanding the factors controlling microbial

transport through biochar‐amended soilsbull Evaluating transport of antibiotic resistant bacteria

through soilsbull Improving modeling tools for describing fate and

transport of phosphorus in the environment

Brian BrunelleResearch Microbiologist

BrianBrunellearsusdagov

515-337-7612

Current Projectsbull Comparing transcriptional differences between

antibiotics that induce invasion in multidrug‐resistant Salmonella and those that have no effect

bull Genome sequencing of novel multidrug‐resistant Salmonella isolates

bull Assessing antibiotics that can enhance resistance in multidrug‐resistant Salmonella

Selected Publicationsbull Brunelle BW Bearson BL Bearson SMD 2015

Chloramphenicol and tetracycline decrease motility and increase invasion and attachment gene expression in specific isolates of multidrug‐resistant Salmonella entericaserovar Typhimurium Front Microbiol 5801

bull Brunelle BW Bearson SMD Bearson BL 2013 Tetracycline accelerates the temporally‐regulated invasion response in specific isolates of multidrug‐resistant Salmonella enterica serovar Typhimurium BMC Microbiology 13 202

Food Safety and Enteric Pathogen Research Unit

Mailing AddressNational Animal Disease Center1920 Dayton AvePO Box 70Ames IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Analysis of Virulence and Antibiotic Resistance Mechanisms of Salmonella and Development of Intervention Strategies

Production Systems StudiedSwine

Laboratory and Field Expertisebull Analysis of bacterial

transcription using real‐time PCR and RNA‐seq

bull Characterization of antibiotic resistance levels and associated genes

bull Conducting assays to measure different virulence phenotypes (cellular invasion motility etc)

Research Interestsbull Investigating the impact antibiotic usage has on

influencing multidrug‐resistant Salmonella virulence phenotypes

bull Identifying genes and regulation pathways associated with phenotypic differences in multidrug‐resistant Salmonella isolates exposed to antibiotics

John P BrooksResearch Microbiologist

JohnBrooksarsusdagov

662-320-7411

7

Current Projectsbull The effect of degraded antibiotic on soil microbial

ecology and antibacterial microbiomebull Aerosol carriage of antibiotic resistant genes and

bacteria from land application of poultry litterbull Antibiotic resistant bacteria and genes in naiumlve

broiler CAFOs

Selected Publicationsbull Brooks JP MR McLaughlin A Adeli DM Miles 2016

Cultivation and qPCR detection of pathogenic and antibiotic‐resistant bacterial establishment in naiumlve broiler houses J Environ Qual 45958‐966

bull Brooks JP Adeli A McLaughlin MR 2014 Microbial ecology bacterial pathogens and antibiotic resistant genes in swine manure as influenced by three swine management systems Water Res 5796‐103

bull Brooks JP McLaughlin MR Scheffler B and Miles DM 2010 Microbial and antibiotic resistant constituents associated with biological aerosols and poultry litter within a commercial poultry house Sci Tot Environ 4084770‐4777

Genetics and Sustainable Agriculture Research Unit

Mailing Address810 Highway 12 East PO Box 5367Mississippi State MS 39762

National Program(s)216 ndash Agricultural System Competitiveness and Sustainability

CRIS Project(s)Integration of Site‐Specific Crop Production Practices amp Industrial amp Animal Ag Byproducts to Improve Ag Competitiveness amp Sustainability

Production Systems StudiedSwine Poultry Forage amp Row Crop

Laboratory and Field Expertisebull Detection amp enumeration of

pathogens and antibacterial resistant genes and bacteria

bull Sampling soil water air amp CAFO environments

bull Quantitative microbial risk assessment of pathogens amp antibacterial resistant bacteria in the environment

Research Interestsbull Identify the movement and fate of pathogens and

antibacterial resistant genesbacteria through the environment and CAFO environments

bull Apply quantitative microbial risk assessment to anthropogenic impacted environments

bull Determine the impact of row crop agriculture on the soil microbial and antibacterial resistant biome

Tucker BurchResearch Agricultural

Engineer

TuckerBurcharsusdagov

715-387-3670

Current Projectsbull Occurrence and Distribution of Antibiotic Resistance

Genes (ARGs) in Groundwater of Kewaunee County Wisconsin

Selected Publicationsbull Burch TR Sadowsky MJ LaPara TM 2016 Modeling the

fate of antibiotic resistance genes and class 1 integronsduring thermophilic anaerobic digestion of municipal wastewater solids Appl Microbiol Biotechnol 100(3) 1437‐1444

bull Burch TR Sadowsky MJ LaPara TM 2014 Fate of antibiotic resistance genes and class 1 integrons in soil microcosms following the application of treated residual municipal wastewater solids Environ Sci Technol 48(10) 5620‐5627

bull Burch TR Sadowsky MJ LaPara TM 2013 Air‐drying beds reduce the quantities of antibiotic resistance genes and class 1 integrons in residual municipal wastewater solids Environ Sci Technol 47(17) 9965‐9971

bull Burch TR Sadowsky MJ LaPara TM 2013 Aerobic digestion reduces the quantity of antibiotic resistance genes in residual municipal wastewater solids Front Microbiol 4(Feb)

Dairy Forage Research CenterEnvironmentally Integrated Dairy Management Research Unit

Mailing Address2615 Yellowstone DriveMarshfield WI 54449

National Program(s)212 ndash Soil and Air

CRIS Project(s)Improving Nutrient Use Efficiency and Mitigating Nutrient and Pathogen Losses from Dairy Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull qPCRbull Bioaerosol samplingbull Quantitative microbial risk

assessment

Research Interestsbull Environmental distribution and transmission of

antibiotic resistance genes (ARGs)bull Quantitative microbial risk assessment

Todd CallawayResearch Microbiologist

ToddCallawayarsusdagov

979-260-9374 7

Current Projectsbull Effects of organic acids on the microbiome of food

animals and impact on foodborne pathogensbull Dietary impacts on foodborne pathogenic bacteria

and the microbial ecosystembull Phytochemicals and their ability to alter composition

of the gastrointestinal microbiome

Selected Publicationsbull Callaway T R T S Edrington and D J Nisbet 2014

Isolation of E coli O157H7 and Salmonella from migratory brown‐headed cowbirds (Molothrus ater) common grackles (Quiscalus quiscula) and cattle egrets (Bubulcus ibis) Foodborne Path Dis 11791‐794

bull Broadway P R J A Carroll J C Brooks J R Donaldson N C Burdick‐Sanchez T B Schmidt T R Brown and T R Callaway 2015 Salmonella transfer to the lymph nodes and synovial fluid of experimentally orally inoculated swine Agric Food Anal Bacteriol (In Press)

bull Grilli E F Foresti B Tugnoli M Fustini M G Zanoni P Pasquali T R Callaway A Piva and G L Alborali 2015 Microencapsulated sorbic acid and pure botanicals affect Salmonella Typhimurium shedding in pigs a close‐up look from weaning to slaughter in controlled and field conditions Foodborne Path Dis (In Press)

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedBeef Cattle Dairy Cattle Swine and Poultry

Laboratory and Field Expertisebull Microbial Physiologybull Microbial Ecologybull Continuous culturebull Mixed culture environmental

simulationsbull Environmental impacts on

survival of foodborne pathogenic bacteria

bull Animal model challengesbull Development of pre‐harvest

intervention strategiesbull Feedlot and dairy procedures

Research Interestsbull Understanding how the microbial ecosystem interacts

with foodborne pathogens at a functional nicheguild level

bull Developing non‐antibiotic methods of reducing foodborne pathogenic bacteria in the gut of food animals

Kimberly CookResearch Microbiologist

KimCookarsusdagov

270-781-2579 ext 232

Current Projectsbull Capture and identify mobile genetic elements

associated with bacteria in soils with applied poultry litter effect of application method

bull Evaluate persistence and concentration of antibiotics and bacteria with AR genes in waste treatment systems and soils with application manures

bull Transport and adhesion of bacteria with AR genesbull Evaluate AR properties of E coli and enterococci

isolates from agricultural ecosystems

Selected Publicationsbull Durso LM and KL Cook 2014 Impacts of antibiotic

use in agriculture what are the benefits and risks CurrOpinion Microbiol 1937‐44 2014

bull Cook KL AMP Netthisinghe and RA Gilfillen 2014 Detection of Pathogens Indicators and Antibiotic Resistance Genes after Land Application of Poultry Litter J Environ Qual 43 1546‐1558

bull Netthisinghe AMP KL Cook C Rice RA Gilfillen and KR Sistani 2013 Soil Nutrients Bacteria Populations and Veterinary Pharmaceuticals across a Backgrounding Beef Feedlot J Environ Qual 42 532‐544

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville Red ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Research

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental Quality

Production Systems StudiedPoultry Swine Beef

Laboratory and Field Expertisebull Soils manure and waste

treatment systemsbull PCR Quantitiative real‐time

PCRbull Culture and antimicrobial

susceptibilitybull Isolation and characterization of

mobile genetic elements carrying genes for antibiotic resistance

Research Interestsbull Characterizing persistence and transmission of

antibiotics antibiotic resistance (AR) genes and AR bacteria through agroecosystems

bull Capture and characterize mobile genetic elements carrying AR genes between microbial populations in soils with applied manures

bull Strain level differences in resistance transport and adhesion properties of bacteria with AR genes

Annie DonoghueResearch Leader (Physiologist)

AnnieDonoghuearsusdagov479-575-2413

7

Current Projectsbull Use of natural remedies to alleviate enteric

pathogens in organic and conventionally raised poultry

bull Alternatives to antibiotics for controlling Salmonella and Campylobacter in poultry and poultry products

Selected Publicationsbull Donoghue AM Venkitanarayanan K Arsi K Woo‐

Ming A Upadhyaya I Kollanoor‐Johny A Darre MJ Upadhyay A Fanatico A and Donoghue DJ 2015 Organic Poultry Developing Natural Solutions for Reducing Pathogens and Improving Production Organic Agriculture Research Symp in press

bull Arsi K Donoghue AM Woo‐Ming A Blore PJ and Donoghue DJ 2015 Intracloacal inoculation an effective screening method for determining the efficacy of probiotic bacterial isolates against Campylobactercolonization in broiler chickens J Food Prot 78 209‐213

bull Arsi K Donoghue AM Venkitanarayanan K Kollanoor‐Johny A Fanatico AC Blore PJ and Donoghue DJ2014 The efficacy of the natural plant extracts thymol and carvacrol against Campylobacter colonization in broiler chickens J Food Safety 34 321ndash325

Poultry Production and Products Safety Research Unit

Mailing AddressUniversity Of ArkansasPOSC O‐303Fayetteville AR 72701

National Program(s)108 ndash Food Safety103 ndash Animal Health

CRIS Project(s)Alternative Intervention and Control Strategies for Foodborne Pathogens in Poultry and Poultry Products

Novel Therapeutic Diagnostic and Management Strategies to Reduce Antibiotic Use in Poultry Production

Production Systems StudiedPoultry

Laboratory and Field ExpertiseLab uses traditional microbiological culture and molecular biological techniques to study food borne pathogens Organic and conventional practices for poultry production

Research Interestsbull developing alternatives to antibiotic use in poultry bull developing strategies to reduce or eliminate pathogen

contamination with a focus on Campylobacter and Salmonella

bull developing sustainable and organic farming practices for poultry producers

David DonavanResearch Molecular Biologist

DavidDonovanarsusdagov

Ce 443-690-4251 Office 301-504-9150

Current Projectsbull Mastitis a cow‐side diagnosticbull Mastitis treatment with triple‐acting antimicrobialsbull Clostridium perfringens novel endolysins that are heat‐resistantbull Yeast expressed endolysins as an alternative to antibiotics in animal feedbull CRISPRCas9 genomic engineering of cow and pig embryos

Selected Publicationsbull Rodriacuteguez‐Rubio L Martiacutenez B Rodriacuteguez A Donovan DM Goumltz F et al The

phage lytic proteins from the Staphylococcus aureus bacteriophage vB_SauS‐phiIPLA88 display multiple active catalytic domains and do not trigger staphylococcal resistance PloS one 2013 8(5)e64671

bull Singh PK Donovan DM Kumar A Intravitreal injection of the chimeric phage endolysin Ply187 protects mice from Staphylococcus aureus endophthalmitis Antimicrobial agents and chemotherapy 2014 58(8)4621‐9

bull Swift SM Seal BS Garrish JK Oakley BB Hiett K et al A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens‐Specific Cell Wall Binding Domain Creates an Anti‐Clostridium Antimicrobial with Improved Thermostability Viruses 2015 7(6)3019‐34

Link to all publications httpwwwncbinlmnihgovsitesmyncbi1jOJlsCcVSxQTbibliography41565643publicsort=dateampdirection=ascending

Animal Biosciences and Biotechnology Laboratory

Mailing AddressRoom 104 10300 Baltimore AveBLDG 230 BARC‐EastBeltsville MD 20705

National ProgramNP101 Food Animal Production

CRIS Project TitleDeveloping Genetic Biotechnologies for Increased Food Animal Production including Novel Antimicrobials for Improved Health and Product Safety

Production Systems StudiedDairy cattle Swine poultry Aquaculture

Laboratory and Field Expertisebull Molecular biologist with

transgenic and knockout mouse background

bull Heterologous gene expression in yeast bacteria mice and cell culture

bull Induced Pluripotent Stem cell production via lentiviral transduction

bull Mouse colony animal husbandry and embryo transfer

Research InterestsDavid M Donovan PhD Research Scientist (Molecular Biologist) at the US Department of Agriculture received his PhD in 1987 in molecular genetics of the yeast Saccharomyces cerevisiae and has 22 years experience in heterologous gene expression He spent 15 years at the NIH culminating in Section Chief Transgenic and Knockout Mouse lab NIA In 2002 he joined the USDA where he has been developing antimicrobials for the treatment of mastitis pathogens including Staphylococcus aureus His enzyme antimicrobials harbor three unique synergistic lytic domains and a protein transduction domain to target intracellular pathogens and have been shown to be highly refractory to resistance development His constructs eradicate both extracellular S aureus [in a rat nasal colonization model and murine systemic infections] and intracellular pathogens ex vivo in bovine mammary epithelial cells and in both a mouse model of mastitis and osteomyelitis He is working to identify protein feed additives as alternative to antibiotic growth promotants

Thomas F DuceyMicrobiologist

ThomasDuceyarsusdagov

843-669-5203 x112

Current Projectsbull Microbial responses to wetland restoration as a part

of the Mid‐Atlantic Region Conservation Effects Assessment Project

bull Response of the microbial rhizosphere and arbuscular mycorrhizae fungi to clover cover crop and conservation tillage in cotton production

bull Isolation of E coli and Enterococcus species from swine wastewater poultry litter and agriculturally‐impacted groundwater for the determination of baseline antibiotic resistance levels in agricultural production systems

Selected Publicationsbull Ducey et al Soil physicochemical conditions

denitrification rates and nosZ abundance in NC coastal plain restored wetlands 2015 J Environ Qual 44 1011‐1022

bull Ducey et al Microbial community analysis of swine wastewater anaerobic lagoons by next‐generation DNA sequencing 2013 Anaerobe 2150‐57

Coastal Plain Soil Water and Plant Research Center

Mailing Address2611 West Lucas StreetFlorence SC 29501

National Program(s)211 ndash Water Availability and Water Management212 ndash Climate Change Soils and Emissions214 ndash Agricultural and Industrial Byproducts

CRIS Project(s)Managing Water Availability and Quality (NP 211)Improving Chemical Physical and Biological Properties of Degraded Sandy Soils (NP 212)Innovative Bioresource Management Technologies (NP 214)

Production Systems StudiedCrops Poultry and Swine

Laboratory and Field Expertisebull Classical Microbiology

bull DetectionEnumerationIsolationbull New species identification

bull Molecular Biologybull T‐RFLPARISAbull qPCRReal Time PCRbull High‐throughput DNA Sequencing

(Ion Torrent)

Research Interestsbull Southeastern US coastal plain wetland restoration

and its effect on microbial community composition and function

bull Animal wastewater treatment systems with a particular focus on pathogen reduction and antibiotic resistance gene elimination

bull Microbial community analysis and response to crop conservation and cover cropping management practices

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Heather AllenResearch Microbiologist

HeatherAllenarsusdagov

515-337-7207

Current Projectsbull Comparison of swine gut microbiotas with antibiotic

and non‐antibiotic feed additives in a heat stress model

bull Characterization of functional gene diversity (antibiotic resistance genes and butyrate transferasegenes) in sequence‐based and functional metagenomic analyses

Selected Publicationsbull Allen H K 2014 Antibiotic resistance gene discovery in

food‐producing animals Curr Opin Microbiol 1925‐29 bull Looft T H K Allen B L Cantarel U Y Levine D O

Bayles D P Alt B Henrissat and T Stanton 2014 Bacteria phages and pigs The effects of in‐feed antibiotics on the microbiome at different gut locations ISME J doi 101038ismej201412

bull Allen H K T Looft D O Bayles S Humphrey U Y Levine D Alt and T Stanton 2011 Antibiotics in feed induce prophages in swine fecal microbiomes mBio 26 e00260‐11

bull Allen H K J J Donato H Huimi Wang K A Cloud‐Hansen J Davies and J Handelsman 2010 Call of the wild antibiotic resistance genes in natural environments Nat Rev Microbiol 8(4) 251‐259

National Animal Disease CenterFood Safety and Enteric Pathogens Research Unit

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Jan 2016 Intestinal Microbial Ecology and Metagenomic Strategies to Reduce Antibiotic Resistance and Foodborne Pathogens

Production Systems StudiedSwine

Laboratory and Field Expertisebull Bacteriophage isolationbull Metagenomic analysesbull 16S rRNA gene sequence

analysesbull PCR and qPCRbull Bioinformaticsbull Anaerobic and aerobic bacterial

culturing

Research Interestsbull Determine the effects of industry‐relevant antibiotics

such as carbadox and chlortetracycline on swine gut bacterial community membership antibiotic resistance gene carriage and prophage induction

bull Develop and test probiotic bacteria including butyrate‐producing bacteria as an alternative to in‐feed antibiotics

Robin AndersonResearch Microbiologist

RobinAndersonarsusdagov

979-260-9317

Current Projectsbull Determine the role of gastrointestinal hydrogen ecology

on virulence gene expression in E coli Salmonella and Campylobacter

bull Develop prebiotic feed additives for pathogen control in swine and cattle

Selected Publicationsbull Petrujkić BT Sedej I Beier RC Anderson RC Harvey

RB Epps SVR Stipanovic RD Krueger NA and Nisbet DJ Ex vivo absorption of thymol and thymol‐β‐D‐glucopyranoside in piglet everted jejunal segments Journal of Agricultural and Food Chemistry 613757‐3762 2013

bull Anderson RC Harvey RB Wickersham TA MacDonald JC Ponce CH Brown M Pinchak WE Osterstock JB Krueger NA and Nisbet DJ Effect of distillers feedstuffs and lasalocid on Campylobactercarriage in feedlot cattle Journal of Food Protection 771968‐1975 2014

bull Epps SVR Petrujkić BT Sedej I Harvey RB Beier RC Stanton TB Phillips TD Hume ME Anderson RC and Nisbet DJ Comparison of anti‐Campylobacteractivity of free thymol and thymol‐β‐D‐glucopyranoside in absence or presence of β‐glycoside‐hydrolyzing gut bacteria Food Chemistry 17392‐98 2015

Food and Feed Safety Research Unit

Mailing AddressSouthern Plains Agricultural Research CtrFood amp Feed Safety Research Unit2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedBeef and dairy cattle swine and sheep

Laboratory and Field Expertisebull Rumen and gastrointestinal

microbiologybull Cultivation of anaerobesbull Bacterial physiology and

metabolismbull Preharvest food safety

Research Interestsbull Develop interventions to reduce the carriage of

foodborne pathogens in food animals and their production environments

bull Identify ecological factors impacting attachment and energy metabolism of enteropathogens within the gut

bull Identify selective factors impacting antimicrobial resistance acquisition dissemination and persistence

Terry ArthurResearch Microbiologist

TerranceArthurarsusdagov

402-762-4227

Current Projectsbull Effects of mass CTC treatment of calves entering feedlot

on animal health and AMR bacterial populationsbull Longitudinal study of antimicrobial‐resistant bacterial

populations in cattle feedlotbull Antimicrobial‐Resistant Fecal Bacteria from Ceftiofur‐

Treated and Non‐Antimicrobial‐Treated Co‐mingled Beef Cows at a Cow‐Calf Operation

Selected Publicationsbull Agga GE Arthur TM Brichta‐Harhay DM Durso

LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

bull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coli and Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Animal and environmental

sampling at cattle feedlots and beef processing facilities

bull Culture and molecular characterization of antimicrobial‐resistant bacterial populations

Research Interestsbull Comparison of AMR bacterial populations in livestock

and non‐livestock environmentsbull Impact of antimicrobial selection vs nutrient

supplementation on increases in environmental AMR bacterial populations

bull Mitigation of AMR bacterial populations associated with animal agriculture

Bradley BearsonMicrobiologist

BradBearsonarsusdagov

515-294-0209

Selected Publicationsbull Bearson BL and BW Brunelle Fluoroquinolone

Induction of Phage‐mediated Gene Transfer in Multidrug‐resistant Salmonella Int J Antimicrob Agents 46(2)201‐204 2015

bull Bearson B L Allen H K Brunelle B W Lee I S Casjens S R and Stanton T B The agricultural antibiotic carbadox induces phage‐mediated gene transfer in Salmonella Front Microbiol 552 2014

bull Bearson B L Bearson S M D Kich J D and Lee I S An rfaHmutant of Salmonella enterica serovar Typhimurium is attenuated in swine and reduces intestinal colonization fecal shedding and disease severity due to virulent Salmonella Typhimurium Front Vet Sci 19 2014

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Boulevard NLAEAmes IA 50011

National Program101 ndash Animal Production (Pending)

CRIS Project (terminated)Animal and Manure Management for Sustainable Production and Reduced Environmental Impact

Production Systems StudiedSwine and Turkeys

Laboratory and Field Expertisebull Bacterial strain construction

using classical genetics and recombineering

bull Antibiotic induced phage‐mediated gene transfer in Salmonella

bull Salmonella challenge models for swine and turkeys to investigate pathogenesis colonization and vaccine efficacy

bull PCR Salmonella genetics bacterial transformation and transduction modification of media for selection and differentiation of Salmonella

Research Interestsbull Development of alternatives to antibiotics such as

vaccines and other targeted interventionsbull Investigation of antibiotic resistance gene transfer

among microorganisms in the host and in the environment including multidrug‐resistant Salmonella

Current Projectsbull Validation of a Salmonella vaccine in swine and turkeys

to protect animal health and enhance food safetybull Identification of multidrug‐resistant Salmonella serovars

containing prophage capable of antibiotic‐induced gene transfer

bull Transcriptional analysis of phage genes following Salmonella exposure to antibiotics

bull Identification of antibiotics that induce phage‐mediated gene transfer in Salmonella

Shawn BearsonResearch Microbiologist

Current Projectsbull Characterizing novel porcine‐microbiota‐Salmonella

interactions as potential targets to reduce Salmonellacolonization and persistence in the intestinal tract

bull Developing alternatives to antibioticsbull Cross‐protective vaccine development against Salmonella serovars in food animals

bull Biotherapeutic immunostimulants for treatment of swine colonized with Salmonella

Selected Publicationsbull Knetter SM et al 2015 Salmonella enterica serovar

Typhimurium‐infected pigs with different shedding levels exhibit distinct clinical peripheral cytokine and transcriptomic immune response phenotypes Innate Immun 21227‐241

bull Bearson SM et al 2013 Polynucleotide phosphorylase (PNPase) is required for Salmonella enterica serovar Typhimurium colonization in swine Microb Pathog 6563‐66

bull Bearson SM et al 2013 Profiling the gastrointestinal microbiota in response to Salmonella low versus high Salmonella shedding in the natural porcine host Infect Genet Evol 16330‐340

Food Safety and Enteric Pathogens Research Unit

Mailing AddressNational Animal Disease Center1920 Dayton Ave1403Ames IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Title here

Second Title here if applicable

Production Systems StudiedSwine and Turkey

Laboratory and Field Expertisebull Molecular microbiologybull Salmonella geneticsbull Host transcriptomicsbull Salmonella colonization and

persistence in food animals

ShawnBearsonarsusdagov

515-337-7455

Research InterestsMy current research efforts are characterizing the effects of antibiotics on MDR Salmonella and identifying antibiotic alternatives to decrease Salmonella on the farm reduce antibiotic dependence promote animal health and provide the public with a safe food supply My research investigations focus on three factors that influence Salmonella colonization and persistence in food animals virulence mechanisms of Salmonella the tactical response from the host and interactions with the host microbiota residing within the gastrointestinal tract

Ross C BeierResearch Chemist

RossBeierarsusdagov

979-260-9411

Current Projectsbull Conduct disinfectant susceptibility tests on 145

Salmonella strains from feed lot water‐sprinkled cattlebull Synthesize thymol‐‐D‐cellobioside for use in delivering

the antibacterial thymol to the lower swine gutbull Conduct disinfectant susceptibility tests on 134

Campylobacter coli and jejuni from swine cecal samples meat products and feces

Selected Publicationsbull Beier RC E Franz JL Bono RE Mandrell PM

Fratamico TR Callaway K Andrews TL Poole TL Crippen CL Sheffield RC Anderson and DJ Nisbet Disinfectant and antimicrobial susceptibility profiles of the big six non‐O157 Shiga toxin‐producing Escherichia coli from food animals and humans J Food Protect 2016 (In press)

bull Crippen TL CL Sheffield JA Byrd JF Esquivel RC Beier and K Yeater Poultry litter and the environment Physiochemical properties of litter and soil during successive flock rotations and after remote site deposition Sci Total Environ 553650661 2016

bull Beier RC SE Duke RL Ziprin RB Harvey ME Hume TL Poole HM Scott LD Highfield WQ Alali K Andrews RC Anderson and DJ Nisbet Antibiotic and disinfectant susceptibility profiles of vancomycin‐resistant Enterococcus faecium (VRE) isolated from community wastewater in Texas Bull Environ Contam Toxicol 80188194 2008

Food and Feed SafetyResearch Unit

Mailing AddressSouthern Plains AgriculturalResearch Center

Food and Feed SafetyResearch Unit

2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedFocus is on bacterial isolates in beef swine and poultry

Laboratory and Field Expertisebull Microbroth dilution

antimicrobial susceptibility testing

bull Microbroth dilution disinfectant susceptibility testing

bull PCRbull Gas Chromatographybull High‐Performance Liquid

Chromatographybull TLC HPTLCbull Chemical Synthesis

Research Interestsbull Establish a knowledge base for disinfectant susceptibility

in foodborne pathogensbull Identify disinfectant and antimicrobial co‐resistancebull Evaluate the impact of disinfectant resistance genes

Elaine BerryResearch Microbiologist

ElaineBerryarsusdagov

402-762-4204

Current Projectsbull Evaluate the influence of spatiotemporal environmental

and wildlife factors on pathogen and antibiotic resistance occurrence and transmission dynamics in cattle and waterways in a pasture‐based production system

bull Determine phenotypic and genotypic factors associated with persistence of E coli O157H7 in cattle production

bull Determine the effect of calcium hydroxide application to feedlot pens on E coli O157H7 total E coli and antibiotic resistance on feedlot pen surfaces and in cattle

Selected Publicationsbull Berry ED JE Wells JL Bono BL Woodbury N

Kalchayanand KN Norman TV Suslow G Lόpez‐Velasco and PD Millner Effect of proximity to a cattle feedlot on Escherichia coli O157H7 contamination of leafy greens and evaluation of the potential for airborne transmission Appl Environ Microbiol 811101‐1110 2015

bull Wells JE ED Berry N Kalchayanand LA Rempel M Kim and WT Oliver Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Assessment of Genotypic and Phenotypic Factors for Foodborne Pathogen Transmission and Development of Intervention Strategies

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Sampling and analyses for

bacterial pathogens in manures soils and other environmental and complex sample matrices

bull Treatment and intervention processes to reduce pathogens in cattle swine and their manure

Research Interestsbull Understanding and reducing the transmission and

persistence of zoonotic pathogens and antibiotic resistance in livestock and preharvest production environments

bull Reducing pathogen and antibiotic resistance transmission from animal production to produce water and the environment

Carl BolsterResearch Hydrologist

CarlBolsterarsusdagov

270-781-2632 ext 244

Current Projectsbull Evaluating effects of manure application rate and

timing on the leaching and runoff potential of antibiotic resistant bacteria and their associated genes as part of a National Pork Board funded project

bull Incorporating uncertainty estimates in model predictions of phosphorus loss from agricultural fields

bull Comparing predictions from annual and daily time‐step phosphorus transport models as part of a National Conservation Innovation Grant project

Selected Publicationsbull Abit SM Bolster CH Cantrell KB Flores JQ and SL

Walker 2014 Transport of Escherichia coli Salmonella typhimurium and microspheres in biochar‐amended soils with different textures J of Environ Qual 43371‐378

bull Bolster CH and Abit SM 2012 Biochar pyrolyzed at two temperatures impacts E coli transport through a sandy soil J of Environ Qual 41124‐133

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville RD ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Management

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental QualitySecond Title here if applicable

Production Systems StudiedPoultry and swine

Laboratory and Field Expertisebull Conducting laboratory‐scale

flow through experimentsbull Developing and using numerical

models for describing bacteria and solute fate and transport in the environment

bull Quantifying uncertainties in observed and modeled data

Research Interestsbull Understanding the factors controlling microbial

transport through biochar‐amended soilsbull Evaluating transport of antibiotic resistant bacteria

through soilsbull Improving modeling tools for describing fate and

transport of phosphorus in the environment

Brian BrunelleResearch Microbiologist

BrianBrunellearsusdagov

515-337-7612

Current Projectsbull Comparing transcriptional differences between

antibiotics that induce invasion in multidrug‐resistant Salmonella and those that have no effect

bull Genome sequencing of novel multidrug‐resistant Salmonella isolates

bull Assessing antibiotics that can enhance resistance in multidrug‐resistant Salmonella

Selected Publicationsbull Brunelle BW Bearson BL Bearson SMD 2015

Chloramphenicol and tetracycline decrease motility and increase invasion and attachment gene expression in specific isolates of multidrug‐resistant Salmonella entericaserovar Typhimurium Front Microbiol 5801

bull Brunelle BW Bearson SMD Bearson BL 2013 Tetracycline accelerates the temporally‐regulated invasion response in specific isolates of multidrug‐resistant Salmonella enterica serovar Typhimurium BMC Microbiology 13 202

Food Safety and Enteric Pathogen Research Unit

Mailing AddressNational Animal Disease Center1920 Dayton AvePO Box 70Ames IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Analysis of Virulence and Antibiotic Resistance Mechanisms of Salmonella and Development of Intervention Strategies

Production Systems StudiedSwine

Laboratory and Field Expertisebull Analysis of bacterial

transcription using real‐time PCR and RNA‐seq

bull Characterization of antibiotic resistance levels and associated genes

bull Conducting assays to measure different virulence phenotypes (cellular invasion motility etc)

Research Interestsbull Investigating the impact antibiotic usage has on

influencing multidrug‐resistant Salmonella virulence phenotypes

bull Identifying genes and regulation pathways associated with phenotypic differences in multidrug‐resistant Salmonella isolates exposed to antibiotics

John P BrooksResearch Microbiologist

JohnBrooksarsusdagov

662-320-7411

7

Current Projectsbull The effect of degraded antibiotic on soil microbial

ecology and antibacterial microbiomebull Aerosol carriage of antibiotic resistant genes and

bacteria from land application of poultry litterbull Antibiotic resistant bacteria and genes in naiumlve

broiler CAFOs

Selected Publicationsbull Brooks JP MR McLaughlin A Adeli DM Miles 2016

Cultivation and qPCR detection of pathogenic and antibiotic‐resistant bacterial establishment in naiumlve broiler houses J Environ Qual 45958‐966

bull Brooks JP Adeli A McLaughlin MR 2014 Microbial ecology bacterial pathogens and antibiotic resistant genes in swine manure as influenced by three swine management systems Water Res 5796‐103

bull Brooks JP McLaughlin MR Scheffler B and Miles DM 2010 Microbial and antibiotic resistant constituents associated with biological aerosols and poultry litter within a commercial poultry house Sci Tot Environ 4084770‐4777

Genetics and Sustainable Agriculture Research Unit

Mailing Address810 Highway 12 East PO Box 5367Mississippi State MS 39762

National Program(s)216 ndash Agricultural System Competitiveness and Sustainability

CRIS Project(s)Integration of Site‐Specific Crop Production Practices amp Industrial amp Animal Ag Byproducts to Improve Ag Competitiveness amp Sustainability

Production Systems StudiedSwine Poultry Forage amp Row Crop

Laboratory and Field Expertisebull Detection amp enumeration of

pathogens and antibacterial resistant genes and bacteria

bull Sampling soil water air amp CAFO environments

bull Quantitative microbial risk assessment of pathogens amp antibacterial resistant bacteria in the environment

Research Interestsbull Identify the movement and fate of pathogens and

antibacterial resistant genesbacteria through the environment and CAFO environments

bull Apply quantitative microbial risk assessment to anthropogenic impacted environments

bull Determine the impact of row crop agriculture on the soil microbial and antibacterial resistant biome

Tucker BurchResearch Agricultural

Engineer

TuckerBurcharsusdagov

715-387-3670

Current Projectsbull Occurrence and Distribution of Antibiotic Resistance

Genes (ARGs) in Groundwater of Kewaunee County Wisconsin

Selected Publicationsbull Burch TR Sadowsky MJ LaPara TM 2016 Modeling the

fate of antibiotic resistance genes and class 1 integronsduring thermophilic anaerobic digestion of municipal wastewater solids Appl Microbiol Biotechnol 100(3) 1437‐1444

bull Burch TR Sadowsky MJ LaPara TM 2014 Fate of antibiotic resistance genes and class 1 integrons in soil microcosms following the application of treated residual municipal wastewater solids Environ Sci Technol 48(10) 5620‐5627

bull Burch TR Sadowsky MJ LaPara TM 2013 Air‐drying beds reduce the quantities of antibiotic resistance genes and class 1 integrons in residual municipal wastewater solids Environ Sci Technol 47(17) 9965‐9971

bull Burch TR Sadowsky MJ LaPara TM 2013 Aerobic digestion reduces the quantity of antibiotic resistance genes in residual municipal wastewater solids Front Microbiol 4(Feb)

Dairy Forage Research CenterEnvironmentally Integrated Dairy Management Research Unit

Mailing Address2615 Yellowstone DriveMarshfield WI 54449

National Program(s)212 ndash Soil and Air

CRIS Project(s)Improving Nutrient Use Efficiency and Mitigating Nutrient and Pathogen Losses from Dairy Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull qPCRbull Bioaerosol samplingbull Quantitative microbial risk

assessment

Research Interestsbull Environmental distribution and transmission of

antibiotic resistance genes (ARGs)bull Quantitative microbial risk assessment

Todd CallawayResearch Microbiologist

ToddCallawayarsusdagov

979-260-9374 7

Current Projectsbull Effects of organic acids on the microbiome of food

animals and impact on foodborne pathogensbull Dietary impacts on foodborne pathogenic bacteria

and the microbial ecosystembull Phytochemicals and their ability to alter composition

of the gastrointestinal microbiome

Selected Publicationsbull Callaway T R T S Edrington and D J Nisbet 2014

Isolation of E coli O157H7 and Salmonella from migratory brown‐headed cowbirds (Molothrus ater) common grackles (Quiscalus quiscula) and cattle egrets (Bubulcus ibis) Foodborne Path Dis 11791‐794

bull Broadway P R J A Carroll J C Brooks J R Donaldson N C Burdick‐Sanchez T B Schmidt T R Brown and T R Callaway 2015 Salmonella transfer to the lymph nodes and synovial fluid of experimentally orally inoculated swine Agric Food Anal Bacteriol (In Press)

bull Grilli E F Foresti B Tugnoli M Fustini M G Zanoni P Pasquali T R Callaway A Piva and G L Alborali 2015 Microencapsulated sorbic acid and pure botanicals affect Salmonella Typhimurium shedding in pigs a close‐up look from weaning to slaughter in controlled and field conditions Foodborne Path Dis (In Press)

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedBeef Cattle Dairy Cattle Swine and Poultry

Laboratory and Field Expertisebull Microbial Physiologybull Microbial Ecologybull Continuous culturebull Mixed culture environmental

simulationsbull Environmental impacts on

survival of foodborne pathogenic bacteria

bull Animal model challengesbull Development of pre‐harvest

intervention strategiesbull Feedlot and dairy procedures

Research Interestsbull Understanding how the microbial ecosystem interacts

with foodborne pathogens at a functional nicheguild level

bull Developing non‐antibiotic methods of reducing foodborne pathogenic bacteria in the gut of food animals

Kimberly CookResearch Microbiologist

KimCookarsusdagov

270-781-2579 ext 232

Current Projectsbull Capture and identify mobile genetic elements

associated with bacteria in soils with applied poultry litter effect of application method

bull Evaluate persistence and concentration of antibiotics and bacteria with AR genes in waste treatment systems and soils with application manures

bull Transport and adhesion of bacteria with AR genesbull Evaluate AR properties of E coli and enterococci

isolates from agricultural ecosystems

Selected Publicationsbull Durso LM and KL Cook 2014 Impacts of antibiotic

use in agriculture what are the benefits and risks CurrOpinion Microbiol 1937‐44 2014

bull Cook KL AMP Netthisinghe and RA Gilfillen 2014 Detection of Pathogens Indicators and Antibiotic Resistance Genes after Land Application of Poultry Litter J Environ Qual 43 1546‐1558

bull Netthisinghe AMP KL Cook C Rice RA Gilfillen and KR Sistani 2013 Soil Nutrients Bacteria Populations and Veterinary Pharmaceuticals across a Backgrounding Beef Feedlot J Environ Qual 42 532‐544

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville Red ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Research

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental Quality

Production Systems StudiedPoultry Swine Beef

Laboratory and Field Expertisebull Soils manure and waste

treatment systemsbull PCR Quantitiative real‐time

PCRbull Culture and antimicrobial

susceptibilitybull Isolation and characterization of

mobile genetic elements carrying genes for antibiotic resistance

Research Interestsbull Characterizing persistence and transmission of

antibiotics antibiotic resistance (AR) genes and AR bacteria through agroecosystems

bull Capture and characterize mobile genetic elements carrying AR genes between microbial populations in soils with applied manures

bull Strain level differences in resistance transport and adhesion properties of bacteria with AR genes

Annie DonoghueResearch Leader (Physiologist)

AnnieDonoghuearsusdagov479-575-2413

7

Current Projectsbull Use of natural remedies to alleviate enteric

pathogens in organic and conventionally raised poultry

bull Alternatives to antibiotics for controlling Salmonella and Campylobacter in poultry and poultry products

Selected Publicationsbull Donoghue AM Venkitanarayanan K Arsi K Woo‐

Ming A Upadhyaya I Kollanoor‐Johny A Darre MJ Upadhyay A Fanatico A and Donoghue DJ 2015 Organic Poultry Developing Natural Solutions for Reducing Pathogens and Improving Production Organic Agriculture Research Symp in press

bull Arsi K Donoghue AM Woo‐Ming A Blore PJ and Donoghue DJ 2015 Intracloacal inoculation an effective screening method for determining the efficacy of probiotic bacterial isolates against Campylobactercolonization in broiler chickens J Food Prot 78 209‐213

bull Arsi K Donoghue AM Venkitanarayanan K Kollanoor‐Johny A Fanatico AC Blore PJ and Donoghue DJ2014 The efficacy of the natural plant extracts thymol and carvacrol against Campylobacter colonization in broiler chickens J Food Safety 34 321ndash325

Poultry Production and Products Safety Research Unit

Mailing AddressUniversity Of ArkansasPOSC O‐303Fayetteville AR 72701

National Program(s)108 ndash Food Safety103 ndash Animal Health

CRIS Project(s)Alternative Intervention and Control Strategies for Foodborne Pathogens in Poultry and Poultry Products

Novel Therapeutic Diagnostic and Management Strategies to Reduce Antibiotic Use in Poultry Production

Production Systems StudiedPoultry

Laboratory and Field ExpertiseLab uses traditional microbiological culture and molecular biological techniques to study food borne pathogens Organic and conventional practices for poultry production

Research Interestsbull developing alternatives to antibiotic use in poultry bull developing strategies to reduce or eliminate pathogen

contamination with a focus on Campylobacter and Salmonella

bull developing sustainable and organic farming practices for poultry producers

David DonavanResearch Molecular Biologist

DavidDonovanarsusdagov

Ce 443-690-4251 Office 301-504-9150

Current Projectsbull Mastitis a cow‐side diagnosticbull Mastitis treatment with triple‐acting antimicrobialsbull Clostridium perfringens novel endolysins that are heat‐resistantbull Yeast expressed endolysins as an alternative to antibiotics in animal feedbull CRISPRCas9 genomic engineering of cow and pig embryos

Selected Publicationsbull Rodriacuteguez‐Rubio L Martiacutenez B Rodriacuteguez A Donovan DM Goumltz F et al The

phage lytic proteins from the Staphylococcus aureus bacteriophage vB_SauS‐phiIPLA88 display multiple active catalytic domains and do not trigger staphylococcal resistance PloS one 2013 8(5)e64671

bull Singh PK Donovan DM Kumar A Intravitreal injection of the chimeric phage endolysin Ply187 protects mice from Staphylococcus aureus endophthalmitis Antimicrobial agents and chemotherapy 2014 58(8)4621‐9

bull Swift SM Seal BS Garrish JK Oakley BB Hiett K et al A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens‐Specific Cell Wall Binding Domain Creates an Anti‐Clostridium Antimicrobial with Improved Thermostability Viruses 2015 7(6)3019‐34

Link to all publications httpwwwncbinlmnihgovsitesmyncbi1jOJlsCcVSxQTbibliography41565643publicsort=dateampdirection=ascending

Animal Biosciences and Biotechnology Laboratory

Mailing AddressRoom 104 10300 Baltimore AveBLDG 230 BARC‐EastBeltsville MD 20705

National ProgramNP101 Food Animal Production

CRIS Project TitleDeveloping Genetic Biotechnologies for Increased Food Animal Production including Novel Antimicrobials for Improved Health and Product Safety

Production Systems StudiedDairy cattle Swine poultry Aquaculture

Laboratory and Field Expertisebull Molecular biologist with

transgenic and knockout mouse background

bull Heterologous gene expression in yeast bacteria mice and cell culture

bull Induced Pluripotent Stem cell production via lentiviral transduction

bull Mouse colony animal husbandry and embryo transfer

Research InterestsDavid M Donovan PhD Research Scientist (Molecular Biologist) at the US Department of Agriculture received his PhD in 1987 in molecular genetics of the yeast Saccharomyces cerevisiae and has 22 years experience in heterologous gene expression He spent 15 years at the NIH culminating in Section Chief Transgenic and Knockout Mouse lab NIA In 2002 he joined the USDA where he has been developing antimicrobials for the treatment of mastitis pathogens including Staphylococcus aureus His enzyme antimicrobials harbor three unique synergistic lytic domains and a protein transduction domain to target intracellular pathogens and have been shown to be highly refractory to resistance development His constructs eradicate both extracellular S aureus [in a rat nasal colonization model and murine systemic infections] and intracellular pathogens ex vivo in bovine mammary epithelial cells and in both a mouse model of mastitis and osteomyelitis He is working to identify protein feed additives as alternative to antibiotic growth promotants

Thomas F DuceyMicrobiologist

ThomasDuceyarsusdagov

843-669-5203 x112

Current Projectsbull Microbial responses to wetland restoration as a part

of the Mid‐Atlantic Region Conservation Effects Assessment Project

bull Response of the microbial rhizosphere and arbuscular mycorrhizae fungi to clover cover crop and conservation tillage in cotton production

bull Isolation of E coli and Enterococcus species from swine wastewater poultry litter and agriculturally‐impacted groundwater for the determination of baseline antibiotic resistance levels in agricultural production systems

Selected Publicationsbull Ducey et al Soil physicochemical conditions

denitrification rates and nosZ abundance in NC coastal plain restored wetlands 2015 J Environ Qual 44 1011‐1022

bull Ducey et al Microbial community analysis of swine wastewater anaerobic lagoons by next‐generation DNA sequencing 2013 Anaerobe 2150‐57

Coastal Plain Soil Water and Plant Research Center

Mailing Address2611 West Lucas StreetFlorence SC 29501

National Program(s)211 ndash Water Availability and Water Management212 ndash Climate Change Soils and Emissions214 ndash Agricultural and Industrial Byproducts

CRIS Project(s)Managing Water Availability and Quality (NP 211)Improving Chemical Physical and Biological Properties of Degraded Sandy Soils (NP 212)Innovative Bioresource Management Technologies (NP 214)

Production Systems StudiedCrops Poultry and Swine

Laboratory and Field Expertisebull Classical Microbiology

bull DetectionEnumerationIsolationbull New species identification

bull Molecular Biologybull T‐RFLPARISAbull qPCRReal Time PCRbull High‐throughput DNA Sequencing

(Ion Torrent)

Research Interestsbull Southeastern US coastal plain wetland restoration

and its effect on microbial community composition and function

bull Animal wastewater treatment systems with a particular focus on pathogen reduction and antibiotic resistance gene elimination

bull Microbial community analysis and response to crop conservation and cover cropping management practices

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Robin AndersonResearch Microbiologist

RobinAndersonarsusdagov

979-260-9317

Current Projectsbull Determine the role of gastrointestinal hydrogen ecology

on virulence gene expression in E coli Salmonella and Campylobacter

bull Develop prebiotic feed additives for pathogen control in swine and cattle

Selected Publicationsbull Petrujkić BT Sedej I Beier RC Anderson RC Harvey

RB Epps SVR Stipanovic RD Krueger NA and Nisbet DJ Ex vivo absorption of thymol and thymol‐β‐D‐glucopyranoside in piglet everted jejunal segments Journal of Agricultural and Food Chemistry 613757‐3762 2013

bull Anderson RC Harvey RB Wickersham TA MacDonald JC Ponce CH Brown M Pinchak WE Osterstock JB Krueger NA and Nisbet DJ Effect of distillers feedstuffs and lasalocid on Campylobactercarriage in feedlot cattle Journal of Food Protection 771968‐1975 2014

bull Epps SVR Petrujkić BT Sedej I Harvey RB Beier RC Stanton TB Phillips TD Hume ME Anderson RC and Nisbet DJ Comparison of anti‐Campylobacteractivity of free thymol and thymol‐β‐D‐glucopyranoside in absence or presence of β‐glycoside‐hydrolyzing gut bacteria Food Chemistry 17392‐98 2015

Food and Feed Safety Research Unit

Mailing AddressSouthern Plains Agricultural Research CtrFood amp Feed Safety Research Unit2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedBeef and dairy cattle swine and sheep

Laboratory and Field Expertisebull Rumen and gastrointestinal

microbiologybull Cultivation of anaerobesbull Bacterial physiology and

metabolismbull Preharvest food safety

Research Interestsbull Develop interventions to reduce the carriage of

foodborne pathogens in food animals and their production environments

bull Identify ecological factors impacting attachment and energy metabolism of enteropathogens within the gut

bull Identify selective factors impacting antimicrobial resistance acquisition dissemination and persistence

Terry ArthurResearch Microbiologist

TerranceArthurarsusdagov

402-762-4227

Current Projectsbull Effects of mass CTC treatment of calves entering feedlot

on animal health and AMR bacterial populationsbull Longitudinal study of antimicrobial‐resistant bacterial

populations in cattle feedlotbull Antimicrobial‐Resistant Fecal Bacteria from Ceftiofur‐

Treated and Non‐Antimicrobial‐Treated Co‐mingled Beef Cows at a Cow‐Calf Operation

Selected Publicationsbull Agga GE Arthur TM Brichta‐Harhay DM Durso

LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

bull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coli and Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Animal and environmental

sampling at cattle feedlots and beef processing facilities

bull Culture and molecular characterization of antimicrobial‐resistant bacterial populations

Research Interestsbull Comparison of AMR bacterial populations in livestock

and non‐livestock environmentsbull Impact of antimicrobial selection vs nutrient

supplementation on increases in environmental AMR bacterial populations

bull Mitigation of AMR bacterial populations associated with animal agriculture

Bradley BearsonMicrobiologist

BradBearsonarsusdagov

515-294-0209

Selected Publicationsbull Bearson BL and BW Brunelle Fluoroquinolone

Induction of Phage‐mediated Gene Transfer in Multidrug‐resistant Salmonella Int J Antimicrob Agents 46(2)201‐204 2015

bull Bearson B L Allen H K Brunelle B W Lee I S Casjens S R and Stanton T B The agricultural antibiotic carbadox induces phage‐mediated gene transfer in Salmonella Front Microbiol 552 2014

bull Bearson B L Bearson S M D Kich J D and Lee I S An rfaHmutant of Salmonella enterica serovar Typhimurium is attenuated in swine and reduces intestinal colonization fecal shedding and disease severity due to virulent Salmonella Typhimurium Front Vet Sci 19 2014

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Boulevard NLAEAmes IA 50011

National Program101 ndash Animal Production (Pending)

CRIS Project (terminated)Animal and Manure Management for Sustainable Production and Reduced Environmental Impact

Production Systems StudiedSwine and Turkeys

Laboratory and Field Expertisebull Bacterial strain construction

using classical genetics and recombineering

bull Antibiotic induced phage‐mediated gene transfer in Salmonella

bull Salmonella challenge models for swine and turkeys to investigate pathogenesis colonization and vaccine efficacy

bull PCR Salmonella genetics bacterial transformation and transduction modification of media for selection and differentiation of Salmonella

Research Interestsbull Development of alternatives to antibiotics such as

vaccines and other targeted interventionsbull Investigation of antibiotic resistance gene transfer

among microorganisms in the host and in the environment including multidrug‐resistant Salmonella

Current Projectsbull Validation of a Salmonella vaccine in swine and turkeys

to protect animal health and enhance food safetybull Identification of multidrug‐resistant Salmonella serovars

containing prophage capable of antibiotic‐induced gene transfer

bull Transcriptional analysis of phage genes following Salmonella exposure to antibiotics

bull Identification of antibiotics that induce phage‐mediated gene transfer in Salmonella

Shawn BearsonResearch Microbiologist

Current Projectsbull Characterizing novel porcine‐microbiota‐Salmonella

interactions as potential targets to reduce Salmonellacolonization and persistence in the intestinal tract

bull Developing alternatives to antibioticsbull Cross‐protective vaccine development against Salmonella serovars in food animals

bull Biotherapeutic immunostimulants for treatment of swine colonized with Salmonella

Selected Publicationsbull Knetter SM et al 2015 Salmonella enterica serovar

Typhimurium‐infected pigs with different shedding levels exhibit distinct clinical peripheral cytokine and transcriptomic immune response phenotypes Innate Immun 21227‐241

bull Bearson SM et al 2013 Polynucleotide phosphorylase (PNPase) is required for Salmonella enterica serovar Typhimurium colonization in swine Microb Pathog 6563‐66

bull Bearson SM et al 2013 Profiling the gastrointestinal microbiota in response to Salmonella low versus high Salmonella shedding in the natural porcine host Infect Genet Evol 16330‐340

Food Safety and Enteric Pathogens Research Unit

Mailing AddressNational Animal Disease Center1920 Dayton Ave1403Ames IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Title here

Second Title here if applicable

Production Systems StudiedSwine and Turkey

Laboratory and Field Expertisebull Molecular microbiologybull Salmonella geneticsbull Host transcriptomicsbull Salmonella colonization and

persistence in food animals

ShawnBearsonarsusdagov

515-337-7455

Research InterestsMy current research efforts are characterizing the effects of antibiotics on MDR Salmonella and identifying antibiotic alternatives to decrease Salmonella on the farm reduce antibiotic dependence promote animal health and provide the public with a safe food supply My research investigations focus on three factors that influence Salmonella colonization and persistence in food animals virulence mechanisms of Salmonella the tactical response from the host and interactions with the host microbiota residing within the gastrointestinal tract

Ross C BeierResearch Chemist

RossBeierarsusdagov

979-260-9411

Current Projectsbull Conduct disinfectant susceptibility tests on 145

Salmonella strains from feed lot water‐sprinkled cattlebull Synthesize thymol‐‐D‐cellobioside for use in delivering

the antibacterial thymol to the lower swine gutbull Conduct disinfectant susceptibility tests on 134

Campylobacter coli and jejuni from swine cecal samples meat products and feces

Selected Publicationsbull Beier RC E Franz JL Bono RE Mandrell PM

Fratamico TR Callaway K Andrews TL Poole TL Crippen CL Sheffield RC Anderson and DJ Nisbet Disinfectant and antimicrobial susceptibility profiles of the big six non‐O157 Shiga toxin‐producing Escherichia coli from food animals and humans J Food Protect 2016 (In press)

bull Crippen TL CL Sheffield JA Byrd JF Esquivel RC Beier and K Yeater Poultry litter and the environment Physiochemical properties of litter and soil during successive flock rotations and after remote site deposition Sci Total Environ 553650661 2016

bull Beier RC SE Duke RL Ziprin RB Harvey ME Hume TL Poole HM Scott LD Highfield WQ Alali K Andrews RC Anderson and DJ Nisbet Antibiotic and disinfectant susceptibility profiles of vancomycin‐resistant Enterococcus faecium (VRE) isolated from community wastewater in Texas Bull Environ Contam Toxicol 80188194 2008

Food and Feed SafetyResearch Unit

Mailing AddressSouthern Plains AgriculturalResearch Center

Food and Feed SafetyResearch Unit

2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedFocus is on bacterial isolates in beef swine and poultry

Laboratory and Field Expertisebull Microbroth dilution

antimicrobial susceptibility testing

bull Microbroth dilution disinfectant susceptibility testing

bull PCRbull Gas Chromatographybull High‐Performance Liquid

Chromatographybull TLC HPTLCbull Chemical Synthesis

Research Interestsbull Establish a knowledge base for disinfectant susceptibility

in foodborne pathogensbull Identify disinfectant and antimicrobial co‐resistancebull Evaluate the impact of disinfectant resistance genes

Elaine BerryResearch Microbiologist

ElaineBerryarsusdagov

402-762-4204

Current Projectsbull Evaluate the influence of spatiotemporal environmental

and wildlife factors on pathogen and antibiotic resistance occurrence and transmission dynamics in cattle and waterways in a pasture‐based production system

bull Determine phenotypic and genotypic factors associated with persistence of E coli O157H7 in cattle production

bull Determine the effect of calcium hydroxide application to feedlot pens on E coli O157H7 total E coli and antibiotic resistance on feedlot pen surfaces and in cattle

Selected Publicationsbull Berry ED JE Wells JL Bono BL Woodbury N

Kalchayanand KN Norman TV Suslow G Lόpez‐Velasco and PD Millner Effect of proximity to a cattle feedlot on Escherichia coli O157H7 contamination of leafy greens and evaluation of the potential for airborne transmission Appl Environ Microbiol 811101‐1110 2015

bull Wells JE ED Berry N Kalchayanand LA Rempel M Kim and WT Oliver Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Assessment of Genotypic and Phenotypic Factors for Foodborne Pathogen Transmission and Development of Intervention Strategies

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Sampling and analyses for

bacterial pathogens in manures soils and other environmental and complex sample matrices

bull Treatment and intervention processes to reduce pathogens in cattle swine and their manure

Research Interestsbull Understanding and reducing the transmission and

persistence of zoonotic pathogens and antibiotic resistance in livestock and preharvest production environments

bull Reducing pathogen and antibiotic resistance transmission from animal production to produce water and the environment

Carl BolsterResearch Hydrologist

CarlBolsterarsusdagov

270-781-2632 ext 244

Current Projectsbull Evaluating effects of manure application rate and

timing on the leaching and runoff potential of antibiotic resistant bacteria and their associated genes as part of a National Pork Board funded project

bull Incorporating uncertainty estimates in model predictions of phosphorus loss from agricultural fields

bull Comparing predictions from annual and daily time‐step phosphorus transport models as part of a National Conservation Innovation Grant project

Selected Publicationsbull Abit SM Bolster CH Cantrell KB Flores JQ and SL

Walker 2014 Transport of Escherichia coli Salmonella typhimurium and microspheres in biochar‐amended soils with different textures J of Environ Qual 43371‐378

bull Bolster CH and Abit SM 2012 Biochar pyrolyzed at two temperatures impacts E coli transport through a sandy soil J of Environ Qual 41124‐133

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville RD ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Management

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental QualitySecond Title here if applicable

Production Systems StudiedPoultry and swine

Laboratory and Field Expertisebull Conducting laboratory‐scale

flow through experimentsbull Developing and using numerical

models for describing bacteria and solute fate and transport in the environment

bull Quantifying uncertainties in observed and modeled data

Research Interestsbull Understanding the factors controlling microbial

transport through biochar‐amended soilsbull Evaluating transport of antibiotic resistant bacteria

through soilsbull Improving modeling tools for describing fate and

transport of phosphorus in the environment

Brian BrunelleResearch Microbiologist

BrianBrunellearsusdagov

515-337-7612

Current Projectsbull Comparing transcriptional differences between

antibiotics that induce invasion in multidrug‐resistant Salmonella and those that have no effect

bull Genome sequencing of novel multidrug‐resistant Salmonella isolates

bull Assessing antibiotics that can enhance resistance in multidrug‐resistant Salmonella

Selected Publicationsbull Brunelle BW Bearson BL Bearson SMD 2015

Chloramphenicol and tetracycline decrease motility and increase invasion and attachment gene expression in specific isolates of multidrug‐resistant Salmonella entericaserovar Typhimurium Front Microbiol 5801

bull Brunelle BW Bearson SMD Bearson BL 2013 Tetracycline accelerates the temporally‐regulated invasion response in specific isolates of multidrug‐resistant Salmonella enterica serovar Typhimurium BMC Microbiology 13 202

Food Safety and Enteric Pathogen Research Unit

Mailing AddressNational Animal Disease Center1920 Dayton AvePO Box 70Ames IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Analysis of Virulence and Antibiotic Resistance Mechanisms of Salmonella and Development of Intervention Strategies

Production Systems StudiedSwine

Laboratory and Field Expertisebull Analysis of bacterial

transcription using real‐time PCR and RNA‐seq

bull Characterization of antibiotic resistance levels and associated genes

bull Conducting assays to measure different virulence phenotypes (cellular invasion motility etc)

Research Interestsbull Investigating the impact antibiotic usage has on

influencing multidrug‐resistant Salmonella virulence phenotypes

bull Identifying genes and regulation pathways associated with phenotypic differences in multidrug‐resistant Salmonella isolates exposed to antibiotics

John P BrooksResearch Microbiologist

JohnBrooksarsusdagov

662-320-7411

7

Current Projectsbull The effect of degraded antibiotic on soil microbial

ecology and antibacterial microbiomebull Aerosol carriage of antibiotic resistant genes and

bacteria from land application of poultry litterbull Antibiotic resistant bacteria and genes in naiumlve

broiler CAFOs

Selected Publicationsbull Brooks JP MR McLaughlin A Adeli DM Miles 2016

Cultivation and qPCR detection of pathogenic and antibiotic‐resistant bacterial establishment in naiumlve broiler houses J Environ Qual 45958‐966

bull Brooks JP Adeli A McLaughlin MR 2014 Microbial ecology bacterial pathogens and antibiotic resistant genes in swine manure as influenced by three swine management systems Water Res 5796‐103

bull Brooks JP McLaughlin MR Scheffler B and Miles DM 2010 Microbial and antibiotic resistant constituents associated with biological aerosols and poultry litter within a commercial poultry house Sci Tot Environ 4084770‐4777

Genetics and Sustainable Agriculture Research Unit

Mailing Address810 Highway 12 East PO Box 5367Mississippi State MS 39762

National Program(s)216 ndash Agricultural System Competitiveness and Sustainability

CRIS Project(s)Integration of Site‐Specific Crop Production Practices amp Industrial amp Animal Ag Byproducts to Improve Ag Competitiveness amp Sustainability

Production Systems StudiedSwine Poultry Forage amp Row Crop

Laboratory and Field Expertisebull Detection amp enumeration of

pathogens and antibacterial resistant genes and bacteria

bull Sampling soil water air amp CAFO environments

bull Quantitative microbial risk assessment of pathogens amp antibacterial resistant bacteria in the environment

Research Interestsbull Identify the movement and fate of pathogens and

antibacterial resistant genesbacteria through the environment and CAFO environments

bull Apply quantitative microbial risk assessment to anthropogenic impacted environments

bull Determine the impact of row crop agriculture on the soil microbial and antibacterial resistant biome

Tucker BurchResearch Agricultural

Engineer

TuckerBurcharsusdagov

715-387-3670

Current Projectsbull Occurrence and Distribution of Antibiotic Resistance

Genes (ARGs) in Groundwater of Kewaunee County Wisconsin

Selected Publicationsbull Burch TR Sadowsky MJ LaPara TM 2016 Modeling the

fate of antibiotic resistance genes and class 1 integronsduring thermophilic anaerobic digestion of municipal wastewater solids Appl Microbiol Biotechnol 100(3) 1437‐1444

bull Burch TR Sadowsky MJ LaPara TM 2014 Fate of antibiotic resistance genes and class 1 integrons in soil microcosms following the application of treated residual municipal wastewater solids Environ Sci Technol 48(10) 5620‐5627

bull Burch TR Sadowsky MJ LaPara TM 2013 Air‐drying beds reduce the quantities of antibiotic resistance genes and class 1 integrons in residual municipal wastewater solids Environ Sci Technol 47(17) 9965‐9971

bull Burch TR Sadowsky MJ LaPara TM 2013 Aerobic digestion reduces the quantity of antibiotic resistance genes in residual municipal wastewater solids Front Microbiol 4(Feb)

Dairy Forage Research CenterEnvironmentally Integrated Dairy Management Research Unit

Mailing Address2615 Yellowstone DriveMarshfield WI 54449

National Program(s)212 ndash Soil and Air

CRIS Project(s)Improving Nutrient Use Efficiency and Mitigating Nutrient and Pathogen Losses from Dairy Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull qPCRbull Bioaerosol samplingbull Quantitative microbial risk

assessment

Research Interestsbull Environmental distribution and transmission of

antibiotic resistance genes (ARGs)bull Quantitative microbial risk assessment

Todd CallawayResearch Microbiologist

ToddCallawayarsusdagov

979-260-9374 7

Current Projectsbull Effects of organic acids on the microbiome of food

animals and impact on foodborne pathogensbull Dietary impacts on foodborne pathogenic bacteria

and the microbial ecosystembull Phytochemicals and their ability to alter composition

of the gastrointestinal microbiome

Selected Publicationsbull Callaway T R T S Edrington and D J Nisbet 2014

Isolation of E coli O157H7 and Salmonella from migratory brown‐headed cowbirds (Molothrus ater) common grackles (Quiscalus quiscula) and cattle egrets (Bubulcus ibis) Foodborne Path Dis 11791‐794

bull Broadway P R J A Carroll J C Brooks J R Donaldson N C Burdick‐Sanchez T B Schmidt T R Brown and T R Callaway 2015 Salmonella transfer to the lymph nodes and synovial fluid of experimentally orally inoculated swine Agric Food Anal Bacteriol (In Press)

bull Grilli E F Foresti B Tugnoli M Fustini M G Zanoni P Pasquali T R Callaway A Piva and G L Alborali 2015 Microencapsulated sorbic acid and pure botanicals affect Salmonella Typhimurium shedding in pigs a close‐up look from weaning to slaughter in controlled and field conditions Foodborne Path Dis (In Press)

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedBeef Cattle Dairy Cattle Swine and Poultry

Laboratory and Field Expertisebull Microbial Physiologybull Microbial Ecologybull Continuous culturebull Mixed culture environmental

simulationsbull Environmental impacts on

survival of foodborne pathogenic bacteria

bull Animal model challengesbull Development of pre‐harvest

intervention strategiesbull Feedlot and dairy procedures

Research Interestsbull Understanding how the microbial ecosystem interacts

with foodborne pathogens at a functional nicheguild level

bull Developing non‐antibiotic methods of reducing foodborne pathogenic bacteria in the gut of food animals

Kimberly CookResearch Microbiologist

KimCookarsusdagov

270-781-2579 ext 232

Current Projectsbull Capture and identify mobile genetic elements

associated with bacteria in soils with applied poultry litter effect of application method

bull Evaluate persistence and concentration of antibiotics and bacteria with AR genes in waste treatment systems and soils with application manures

bull Transport and adhesion of bacteria with AR genesbull Evaluate AR properties of E coli and enterococci

isolates from agricultural ecosystems

Selected Publicationsbull Durso LM and KL Cook 2014 Impacts of antibiotic

use in agriculture what are the benefits and risks CurrOpinion Microbiol 1937‐44 2014

bull Cook KL AMP Netthisinghe and RA Gilfillen 2014 Detection of Pathogens Indicators and Antibiotic Resistance Genes after Land Application of Poultry Litter J Environ Qual 43 1546‐1558

bull Netthisinghe AMP KL Cook C Rice RA Gilfillen and KR Sistani 2013 Soil Nutrients Bacteria Populations and Veterinary Pharmaceuticals across a Backgrounding Beef Feedlot J Environ Qual 42 532‐544

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville Red ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Research

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental Quality

Production Systems StudiedPoultry Swine Beef

Laboratory and Field Expertisebull Soils manure and waste

treatment systemsbull PCR Quantitiative real‐time

PCRbull Culture and antimicrobial

susceptibilitybull Isolation and characterization of

mobile genetic elements carrying genes for antibiotic resistance

Research Interestsbull Characterizing persistence and transmission of

antibiotics antibiotic resistance (AR) genes and AR bacteria through agroecosystems

bull Capture and characterize mobile genetic elements carrying AR genes between microbial populations in soils with applied manures

bull Strain level differences in resistance transport and adhesion properties of bacteria with AR genes

Annie DonoghueResearch Leader (Physiologist)

AnnieDonoghuearsusdagov479-575-2413

7

Current Projectsbull Use of natural remedies to alleviate enteric

pathogens in organic and conventionally raised poultry

bull Alternatives to antibiotics for controlling Salmonella and Campylobacter in poultry and poultry products

Selected Publicationsbull Donoghue AM Venkitanarayanan K Arsi K Woo‐

Ming A Upadhyaya I Kollanoor‐Johny A Darre MJ Upadhyay A Fanatico A and Donoghue DJ 2015 Organic Poultry Developing Natural Solutions for Reducing Pathogens and Improving Production Organic Agriculture Research Symp in press

bull Arsi K Donoghue AM Woo‐Ming A Blore PJ and Donoghue DJ 2015 Intracloacal inoculation an effective screening method for determining the efficacy of probiotic bacterial isolates against Campylobactercolonization in broiler chickens J Food Prot 78 209‐213

bull Arsi K Donoghue AM Venkitanarayanan K Kollanoor‐Johny A Fanatico AC Blore PJ and Donoghue DJ2014 The efficacy of the natural plant extracts thymol and carvacrol against Campylobacter colonization in broiler chickens J Food Safety 34 321ndash325

Poultry Production and Products Safety Research Unit

Mailing AddressUniversity Of ArkansasPOSC O‐303Fayetteville AR 72701

National Program(s)108 ndash Food Safety103 ndash Animal Health

CRIS Project(s)Alternative Intervention and Control Strategies for Foodborne Pathogens in Poultry and Poultry Products

Novel Therapeutic Diagnostic and Management Strategies to Reduce Antibiotic Use in Poultry Production

Production Systems StudiedPoultry

Laboratory and Field ExpertiseLab uses traditional microbiological culture and molecular biological techniques to study food borne pathogens Organic and conventional practices for poultry production

Research Interestsbull developing alternatives to antibiotic use in poultry bull developing strategies to reduce or eliminate pathogen

contamination with a focus on Campylobacter and Salmonella

bull developing sustainable and organic farming practices for poultry producers

David DonavanResearch Molecular Biologist

DavidDonovanarsusdagov

Ce 443-690-4251 Office 301-504-9150

Current Projectsbull Mastitis a cow‐side diagnosticbull Mastitis treatment with triple‐acting antimicrobialsbull Clostridium perfringens novel endolysins that are heat‐resistantbull Yeast expressed endolysins as an alternative to antibiotics in animal feedbull CRISPRCas9 genomic engineering of cow and pig embryos

Selected Publicationsbull Rodriacuteguez‐Rubio L Martiacutenez B Rodriacuteguez A Donovan DM Goumltz F et al The

phage lytic proteins from the Staphylococcus aureus bacteriophage vB_SauS‐phiIPLA88 display multiple active catalytic domains and do not trigger staphylococcal resistance PloS one 2013 8(5)e64671

bull Singh PK Donovan DM Kumar A Intravitreal injection of the chimeric phage endolysin Ply187 protects mice from Staphylococcus aureus endophthalmitis Antimicrobial agents and chemotherapy 2014 58(8)4621‐9

bull Swift SM Seal BS Garrish JK Oakley BB Hiett K et al A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens‐Specific Cell Wall Binding Domain Creates an Anti‐Clostridium Antimicrobial with Improved Thermostability Viruses 2015 7(6)3019‐34

Link to all publications httpwwwncbinlmnihgovsitesmyncbi1jOJlsCcVSxQTbibliography41565643publicsort=dateampdirection=ascending

Animal Biosciences and Biotechnology Laboratory

Mailing AddressRoom 104 10300 Baltimore AveBLDG 230 BARC‐EastBeltsville MD 20705

National ProgramNP101 Food Animal Production

CRIS Project TitleDeveloping Genetic Biotechnologies for Increased Food Animal Production including Novel Antimicrobials for Improved Health and Product Safety

Production Systems StudiedDairy cattle Swine poultry Aquaculture

Laboratory and Field Expertisebull Molecular biologist with

transgenic and knockout mouse background

bull Heterologous gene expression in yeast bacteria mice and cell culture

bull Induced Pluripotent Stem cell production via lentiviral transduction

bull Mouse colony animal husbandry and embryo transfer

Research InterestsDavid M Donovan PhD Research Scientist (Molecular Biologist) at the US Department of Agriculture received his PhD in 1987 in molecular genetics of the yeast Saccharomyces cerevisiae and has 22 years experience in heterologous gene expression He spent 15 years at the NIH culminating in Section Chief Transgenic and Knockout Mouse lab NIA In 2002 he joined the USDA where he has been developing antimicrobials for the treatment of mastitis pathogens including Staphylococcus aureus His enzyme antimicrobials harbor three unique synergistic lytic domains and a protein transduction domain to target intracellular pathogens and have been shown to be highly refractory to resistance development His constructs eradicate both extracellular S aureus [in a rat nasal colonization model and murine systemic infections] and intracellular pathogens ex vivo in bovine mammary epithelial cells and in both a mouse model of mastitis and osteomyelitis He is working to identify protein feed additives as alternative to antibiotic growth promotants

Thomas F DuceyMicrobiologist

ThomasDuceyarsusdagov

843-669-5203 x112

Current Projectsbull Microbial responses to wetland restoration as a part

of the Mid‐Atlantic Region Conservation Effects Assessment Project

bull Response of the microbial rhizosphere and arbuscular mycorrhizae fungi to clover cover crop and conservation tillage in cotton production

bull Isolation of E coli and Enterococcus species from swine wastewater poultry litter and agriculturally‐impacted groundwater for the determination of baseline antibiotic resistance levels in agricultural production systems

Selected Publicationsbull Ducey et al Soil physicochemical conditions

denitrification rates and nosZ abundance in NC coastal plain restored wetlands 2015 J Environ Qual 44 1011‐1022

bull Ducey et al Microbial community analysis of swine wastewater anaerobic lagoons by next‐generation DNA sequencing 2013 Anaerobe 2150‐57

Coastal Plain Soil Water and Plant Research Center

Mailing Address2611 West Lucas StreetFlorence SC 29501

National Program(s)211 ndash Water Availability and Water Management212 ndash Climate Change Soils and Emissions214 ndash Agricultural and Industrial Byproducts

CRIS Project(s)Managing Water Availability and Quality (NP 211)Improving Chemical Physical and Biological Properties of Degraded Sandy Soils (NP 212)Innovative Bioresource Management Technologies (NP 214)

Production Systems StudiedCrops Poultry and Swine

Laboratory and Field Expertisebull Classical Microbiology

bull DetectionEnumerationIsolationbull New species identification

bull Molecular Biologybull T‐RFLPARISAbull qPCRReal Time PCRbull High‐throughput DNA Sequencing

(Ion Torrent)

Research Interestsbull Southeastern US coastal plain wetland restoration

and its effect on microbial community composition and function

bull Animal wastewater treatment systems with a particular focus on pathogen reduction and antibiotic resistance gene elimination

bull Microbial community analysis and response to crop conservation and cover cropping management practices

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Terry ArthurResearch Microbiologist

TerranceArthurarsusdagov

402-762-4227

Current Projectsbull Effects of mass CTC treatment of calves entering feedlot

on animal health and AMR bacterial populationsbull Longitudinal study of antimicrobial‐resistant bacterial

populations in cattle feedlotbull Antimicrobial‐Resistant Fecal Bacteria from Ceftiofur‐

Treated and Non‐Antimicrobial‐Treated Co‐mingled Beef Cows at a Cow‐Calf Operation

Selected Publicationsbull Agga GE Arthur TM Brichta‐Harhay DM Durso

LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

bull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coli and Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Animal and environmental

sampling at cattle feedlots and beef processing facilities

bull Culture and molecular characterization of antimicrobial‐resistant bacterial populations

Research Interestsbull Comparison of AMR bacterial populations in livestock

and non‐livestock environmentsbull Impact of antimicrobial selection vs nutrient

supplementation on increases in environmental AMR bacterial populations

bull Mitigation of AMR bacterial populations associated with animal agriculture

Bradley BearsonMicrobiologist

BradBearsonarsusdagov

515-294-0209

Selected Publicationsbull Bearson BL and BW Brunelle Fluoroquinolone

Induction of Phage‐mediated Gene Transfer in Multidrug‐resistant Salmonella Int J Antimicrob Agents 46(2)201‐204 2015

bull Bearson B L Allen H K Brunelle B W Lee I S Casjens S R and Stanton T B The agricultural antibiotic carbadox induces phage‐mediated gene transfer in Salmonella Front Microbiol 552 2014

bull Bearson B L Bearson S M D Kich J D and Lee I S An rfaHmutant of Salmonella enterica serovar Typhimurium is attenuated in swine and reduces intestinal colonization fecal shedding and disease severity due to virulent Salmonella Typhimurium Front Vet Sci 19 2014

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Boulevard NLAEAmes IA 50011

National Program101 ndash Animal Production (Pending)

CRIS Project (terminated)Animal and Manure Management for Sustainable Production and Reduced Environmental Impact

Production Systems StudiedSwine and Turkeys

Laboratory and Field Expertisebull Bacterial strain construction

using classical genetics and recombineering

bull Antibiotic induced phage‐mediated gene transfer in Salmonella

bull Salmonella challenge models for swine and turkeys to investigate pathogenesis colonization and vaccine efficacy

bull PCR Salmonella genetics bacterial transformation and transduction modification of media for selection and differentiation of Salmonella

Research Interestsbull Development of alternatives to antibiotics such as

vaccines and other targeted interventionsbull Investigation of antibiotic resistance gene transfer

among microorganisms in the host and in the environment including multidrug‐resistant Salmonella

Current Projectsbull Validation of a Salmonella vaccine in swine and turkeys

to protect animal health and enhance food safetybull Identification of multidrug‐resistant Salmonella serovars

containing prophage capable of antibiotic‐induced gene transfer

bull Transcriptional analysis of phage genes following Salmonella exposure to antibiotics

bull Identification of antibiotics that induce phage‐mediated gene transfer in Salmonella

Shawn BearsonResearch Microbiologist

Current Projectsbull Characterizing novel porcine‐microbiota‐Salmonella

interactions as potential targets to reduce Salmonellacolonization and persistence in the intestinal tract

bull Developing alternatives to antibioticsbull Cross‐protective vaccine development against Salmonella serovars in food animals

bull Biotherapeutic immunostimulants for treatment of swine colonized with Salmonella

Selected Publicationsbull Knetter SM et al 2015 Salmonella enterica serovar

Typhimurium‐infected pigs with different shedding levels exhibit distinct clinical peripheral cytokine and transcriptomic immune response phenotypes Innate Immun 21227‐241

bull Bearson SM et al 2013 Polynucleotide phosphorylase (PNPase) is required for Salmonella enterica serovar Typhimurium colonization in swine Microb Pathog 6563‐66

bull Bearson SM et al 2013 Profiling the gastrointestinal microbiota in response to Salmonella low versus high Salmonella shedding in the natural porcine host Infect Genet Evol 16330‐340

Food Safety and Enteric Pathogens Research Unit

Mailing AddressNational Animal Disease Center1920 Dayton Ave1403Ames IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Title here

Second Title here if applicable

Production Systems StudiedSwine and Turkey

Laboratory and Field Expertisebull Molecular microbiologybull Salmonella geneticsbull Host transcriptomicsbull Salmonella colonization and

persistence in food animals

ShawnBearsonarsusdagov

515-337-7455

Research InterestsMy current research efforts are characterizing the effects of antibiotics on MDR Salmonella and identifying antibiotic alternatives to decrease Salmonella on the farm reduce antibiotic dependence promote animal health and provide the public with a safe food supply My research investigations focus on three factors that influence Salmonella colonization and persistence in food animals virulence mechanisms of Salmonella the tactical response from the host and interactions with the host microbiota residing within the gastrointestinal tract

Ross C BeierResearch Chemist

RossBeierarsusdagov

979-260-9411

Current Projectsbull Conduct disinfectant susceptibility tests on 145

Salmonella strains from feed lot water‐sprinkled cattlebull Synthesize thymol‐‐D‐cellobioside for use in delivering

the antibacterial thymol to the lower swine gutbull Conduct disinfectant susceptibility tests on 134

Campylobacter coli and jejuni from swine cecal samples meat products and feces

Selected Publicationsbull Beier RC E Franz JL Bono RE Mandrell PM

Fratamico TR Callaway K Andrews TL Poole TL Crippen CL Sheffield RC Anderson and DJ Nisbet Disinfectant and antimicrobial susceptibility profiles of the big six non‐O157 Shiga toxin‐producing Escherichia coli from food animals and humans J Food Protect 2016 (In press)

bull Crippen TL CL Sheffield JA Byrd JF Esquivel RC Beier and K Yeater Poultry litter and the environment Physiochemical properties of litter and soil during successive flock rotations and after remote site deposition Sci Total Environ 553650661 2016

bull Beier RC SE Duke RL Ziprin RB Harvey ME Hume TL Poole HM Scott LD Highfield WQ Alali K Andrews RC Anderson and DJ Nisbet Antibiotic and disinfectant susceptibility profiles of vancomycin‐resistant Enterococcus faecium (VRE) isolated from community wastewater in Texas Bull Environ Contam Toxicol 80188194 2008

Food and Feed SafetyResearch Unit

Mailing AddressSouthern Plains AgriculturalResearch Center

Food and Feed SafetyResearch Unit

2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedFocus is on bacterial isolates in beef swine and poultry

Laboratory and Field Expertisebull Microbroth dilution

antimicrobial susceptibility testing

bull Microbroth dilution disinfectant susceptibility testing

bull PCRbull Gas Chromatographybull High‐Performance Liquid

Chromatographybull TLC HPTLCbull Chemical Synthesis

Research Interestsbull Establish a knowledge base for disinfectant susceptibility

in foodborne pathogensbull Identify disinfectant and antimicrobial co‐resistancebull Evaluate the impact of disinfectant resistance genes

Elaine BerryResearch Microbiologist

ElaineBerryarsusdagov

402-762-4204

Current Projectsbull Evaluate the influence of spatiotemporal environmental

and wildlife factors on pathogen and antibiotic resistance occurrence and transmission dynamics in cattle and waterways in a pasture‐based production system

bull Determine phenotypic and genotypic factors associated with persistence of E coli O157H7 in cattle production

bull Determine the effect of calcium hydroxide application to feedlot pens on E coli O157H7 total E coli and antibiotic resistance on feedlot pen surfaces and in cattle

Selected Publicationsbull Berry ED JE Wells JL Bono BL Woodbury N

Kalchayanand KN Norman TV Suslow G Lόpez‐Velasco and PD Millner Effect of proximity to a cattle feedlot on Escherichia coli O157H7 contamination of leafy greens and evaluation of the potential for airborne transmission Appl Environ Microbiol 811101‐1110 2015

bull Wells JE ED Berry N Kalchayanand LA Rempel M Kim and WT Oliver Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Assessment of Genotypic and Phenotypic Factors for Foodborne Pathogen Transmission and Development of Intervention Strategies

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Sampling and analyses for

bacterial pathogens in manures soils and other environmental and complex sample matrices

bull Treatment and intervention processes to reduce pathogens in cattle swine and their manure

Research Interestsbull Understanding and reducing the transmission and

persistence of zoonotic pathogens and antibiotic resistance in livestock and preharvest production environments

bull Reducing pathogen and antibiotic resistance transmission from animal production to produce water and the environment

Carl BolsterResearch Hydrologist

CarlBolsterarsusdagov

270-781-2632 ext 244

Current Projectsbull Evaluating effects of manure application rate and

timing on the leaching and runoff potential of antibiotic resistant bacteria and their associated genes as part of a National Pork Board funded project

bull Incorporating uncertainty estimates in model predictions of phosphorus loss from agricultural fields

bull Comparing predictions from annual and daily time‐step phosphorus transport models as part of a National Conservation Innovation Grant project

Selected Publicationsbull Abit SM Bolster CH Cantrell KB Flores JQ and SL

Walker 2014 Transport of Escherichia coli Salmonella typhimurium and microspheres in biochar‐amended soils with different textures J of Environ Qual 43371‐378

bull Bolster CH and Abit SM 2012 Biochar pyrolyzed at two temperatures impacts E coli transport through a sandy soil J of Environ Qual 41124‐133

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville RD ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Management

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental QualitySecond Title here if applicable

Production Systems StudiedPoultry and swine

Laboratory and Field Expertisebull Conducting laboratory‐scale

flow through experimentsbull Developing and using numerical

models for describing bacteria and solute fate and transport in the environment

bull Quantifying uncertainties in observed and modeled data

Research Interestsbull Understanding the factors controlling microbial

transport through biochar‐amended soilsbull Evaluating transport of antibiotic resistant bacteria

through soilsbull Improving modeling tools for describing fate and

transport of phosphorus in the environment

Brian BrunelleResearch Microbiologist

BrianBrunellearsusdagov

515-337-7612

Current Projectsbull Comparing transcriptional differences between

antibiotics that induce invasion in multidrug‐resistant Salmonella and those that have no effect

bull Genome sequencing of novel multidrug‐resistant Salmonella isolates

bull Assessing antibiotics that can enhance resistance in multidrug‐resistant Salmonella

Selected Publicationsbull Brunelle BW Bearson BL Bearson SMD 2015

Chloramphenicol and tetracycline decrease motility and increase invasion and attachment gene expression in specific isolates of multidrug‐resistant Salmonella entericaserovar Typhimurium Front Microbiol 5801

bull Brunelle BW Bearson SMD Bearson BL 2013 Tetracycline accelerates the temporally‐regulated invasion response in specific isolates of multidrug‐resistant Salmonella enterica serovar Typhimurium BMC Microbiology 13 202

Food Safety and Enteric Pathogen Research Unit

Mailing AddressNational Animal Disease Center1920 Dayton AvePO Box 70Ames IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Analysis of Virulence and Antibiotic Resistance Mechanisms of Salmonella and Development of Intervention Strategies

Production Systems StudiedSwine

Laboratory and Field Expertisebull Analysis of bacterial

transcription using real‐time PCR and RNA‐seq

bull Characterization of antibiotic resistance levels and associated genes

bull Conducting assays to measure different virulence phenotypes (cellular invasion motility etc)

Research Interestsbull Investigating the impact antibiotic usage has on

influencing multidrug‐resistant Salmonella virulence phenotypes

bull Identifying genes and regulation pathways associated with phenotypic differences in multidrug‐resistant Salmonella isolates exposed to antibiotics

John P BrooksResearch Microbiologist

JohnBrooksarsusdagov

662-320-7411

7

Current Projectsbull The effect of degraded antibiotic on soil microbial

ecology and antibacterial microbiomebull Aerosol carriage of antibiotic resistant genes and

bacteria from land application of poultry litterbull Antibiotic resistant bacteria and genes in naiumlve

broiler CAFOs

Selected Publicationsbull Brooks JP MR McLaughlin A Adeli DM Miles 2016

Cultivation and qPCR detection of pathogenic and antibiotic‐resistant bacterial establishment in naiumlve broiler houses J Environ Qual 45958‐966

bull Brooks JP Adeli A McLaughlin MR 2014 Microbial ecology bacterial pathogens and antibiotic resistant genes in swine manure as influenced by three swine management systems Water Res 5796‐103

bull Brooks JP McLaughlin MR Scheffler B and Miles DM 2010 Microbial and antibiotic resistant constituents associated with biological aerosols and poultry litter within a commercial poultry house Sci Tot Environ 4084770‐4777

Genetics and Sustainable Agriculture Research Unit

Mailing Address810 Highway 12 East PO Box 5367Mississippi State MS 39762

National Program(s)216 ndash Agricultural System Competitiveness and Sustainability

CRIS Project(s)Integration of Site‐Specific Crop Production Practices amp Industrial amp Animal Ag Byproducts to Improve Ag Competitiveness amp Sustainability

Production Systems StudiedSwine Poultry Forage amp Row Crop

Laboratory and Field Expertisebull Detection amp enumeration of

pathogens and antibacterial resistant genes and bacteria

bull Sampling soil water air amp CAFO environments

bull Quantitative microbial risk assessment of pathogens amp antibacterial resistant bacteria in the environment

Research Interestsbull Identify the movement and fate of pathogens and

antibacterial resistant genesbacteria through the environment and CAFO environments

bull Apply quantitative microbial risk assessment to anthropogenic impacted environments

bull Determine the impact of row crop agriculture on the soil microbial and antibacterial resistant biome

Tucker BurchResearch Agricultural

Engineer

TuckerBurcharsusdagov

715-387-3670

Current Projectsbull Occurrence and Distribution of Antibiotic Resistance

Genes (ARGs) in Groundwater of Kewaunee County Wisconsin

Selected Publicationsbull Burch TR Sadowsky MJ LaPara TM 2016 Modeling the

fate of antibiotic resistance genes and class 1 integronsduring thermophilic anaerobic digestion of municipal wastewater solids Appl Microbiol Biotechnol 100(3) 1437‐1444

bull Burch TR Sadowsky MJ LaPara TM 2014 Fate of antibiotic resistance genes and class 1 integrons in soil microcosms following the application of treated residual municipal wastewater solids Environ Sci Technol 48(10) 5620‐5627

bull Burch TR Sadowsky MJ LaPara TM 2013 Air‐drying beds reduce the quantities of antibiotic resistance genes and class 1 integrons in residual municipal wastewater solids Environ Sci Technol 47(17) 9965‐9971

bull Burch TR Sadowsky MJ LaPara TM 2013 Aerobic digestion reduces the quantity of antibiotic resistance genes in residual municipal wastewater solids Front Microbiol 4(Feb)

Dairy Forage Research CenterEnvironmentally Integrated Dairy Management Research Unit

Mailing Address2615 Yellowstone DriveMarshfield WI 54449

National Program(s)212 ndash Soil and Air

CRIS Project(s)Improving Nutrient Use Efficiency and Mitigating Nutrient and Pathogen Losses from Dairy Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull qPCRbull Bioaerosol samplingbull Quantitative microbial risk

assessment

Research Interestsbull Environmental distribution and transmission of

antibiotic resistance genes (ARGs)bull Quantitative microbial risk assessment

Todd CallawayResearch Microbiologist

ToddCallawayarsusdagov

979-260-9374 7

Current Projectsbull Effects of organic acids on the microbiome of food

animals and impact on foodborne pathogensbull Dietary impacts on foodborne pathogenic bacteria

and the microbial ecosystembull Phytochemicals and their ability to alter composition

of the gastrointestinal microbiome

Selected Publicationsbull Callaway T R T S Edrington and D J Nisbet 2014

Isolation of E coli O157H7 and Salmonella from migratory brown‐headed cowbirds (Molothrus ater) common grackles (Quiscalus quiscula) and cattle egrets (Bubulcus ibis) Foodborne Path Dis 11791‐794

bull Broadway P R J A Carroll J C Brooks J R Donaldson N C Burdick‐Sanchez T B Schmidt T R Brown and T R Callaway 2015 Salmonella transfer to the lymph nodes and synovial fluid of experimentally orally inoculated swine Agric Food Anal Bacteriol (In Press)

bull Grilli E F Foresti B Tugnoli M Fustini M G Zanoni P Pasquali T R Callaway A Piva and G L Alborali 2015 Microencapsulated sorbic acid and pure botanicals affect Salmonella Typhimurium shedding in pigs a close‐up look from weaning to slaughter in controlled and field conditions Foodborne Path Dis (In Press)

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedBeef Cattle Dairy Cattle Swine and Poultry

Laboratory and Field Expertisebull Microbial Physiologybull Microbial Ecologybull Continuous culturebull Mixed culture environmental

simulationsbull Environmental impacts on

survival of foodborne pathogenic bacteria

bull Animal model challengesbull Development of pre‐harvest

intervention strategiesbull Feedlot and dairy procedures

Research Interestsbull Understanding how the microbial ecosystem interacts

with foodborne pathogens at a functional nicheguild level

bull Developing non‐antibiotic methods of reducing foodborne pathogenic bacteria in the gut of food animals

Kimberly CookResearch Microbiologist

KimCookarsusdagov

270-781-2579 ext 232

Current Projectsbull Capture and identify mobile genetic elements

associated with bacteria in soils with applied poultry litter effect of application method

bull Evaluate persistence and concentration of antibiotics and bacteria with AR genes in waste treatment systems and soils with application manures

bull Transport and adhesion of bacteria with AR genesbull Evaluate AR properties of E coli and enterococci

isolates from agricultural ecosystems

Selected Publicationsbull Durso LM and KL Cook 2014 Impacts of antibiotic

use in agriculture what are the benefits and risks CurrOpinion Microbiol 1937‐44 2014

bull Cook KL AMP Netthisinghe and RA Gilfillen 2014 Detection of Pathogens Indicators and Antibiotic Resistance Genes after Land Application of Poultry Litter J Environ Qual 43 1546‐1558

bull Netthisinghe AMP KL Cook C Rice RA Gilfillen and KR Sistani 2013 Soil Nutrients Bacteria Populations and Veterinary Pharmaceuticals across a Backgrounding Beef Feedlot J Environ Qual 42 532‐544

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville Red ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Research

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental Quality

Production Systems StudiedPoultry Swine Beef

Laboratory and Field Expertisebull Soils manure and waste

treatment systemsbull PCR Quantitiative real‐time

PCRbull Culture and antimicrobial

susceptibilitybull Isolation and characterization of

mobile genetic elements carrying genes for antibiotic resistance

Research Interestsbull Characterizing persistence and transmission of

antibiotics antibiotic resistance (AR) genes and AR bacteria through agroecosystems

bull Capture and characterize mobile genetic elements carrying AR genes between microbial populations in soils with applied manures

bull Strain level differences in resistance transport and adhesion properties of bacteria with AR genes

Annie DonoghueResearch Leader (Physiologist)

AnnieDonoghuearsusdagov479-575-2413

7

Current Projectsbull Use of natural remedies to alleviate enteric

pathogens in organic and conventionally raised poultry

bull Alternatives to antibiotics for controlling Salmonella and Campylobacter in poultry and poultry products

Selected Publicationsbull Donoghue AM Venkitanarayanan K Arsi K Woo‐

Ming A Upadhyaya I Kollanoor‐Johny A Darre MJ Upadhyay A Fanatico A and Donoghue DJ 2015 Organic Poultry Developing Natural Solutions for Reducing Pathogens and Improving Production Organic Agriculture Research Symp in press

bull Arsi K Donoghue AM Woo‐Ming A Blore PJ and Donoghue DJ 2015 Intracloacal inoculation an effective screening method for determining the efficacy of probiotic bacterial isolates against Campylobactercolonization in broiler chickens J Food Prot 78 209‐213

bull Arsi K Donoghue AM Venkitanarayanan K Kollanoor‐Johny A Fanatico AC Blore PJ and Donoghue DJ2014 The efficacy of the natural plant extracts thymol and carvacrol against Campylobacter colonization in broiler chickens J Food Safety 34 321ndash325

Poultry Production and Products Safety Research Unit

Mailing AddressUniversity Of ArkansasPOSC O‐303Fayetteville AR 72701

National Program(s)108 ndash Food Safety103 ndash Animal Health

CRIS Project(s)Alternative Intervention and Control Strategies for Foodborne Pathogens in Poultry and Poultry Products

Novel Therapeutic Diagnostic and Management Strategies to Reduce Antibiotic Use in Poultry Production

Production Systems StudiedPoultry

Laboratory and Field ExpertiseLab uses traditional microbiological culture and molecular biological techniques to study food borne pathogens Organic and conventional practices for poultry production

Research Interestsbull developing alternatives to antibiotic use in poultry bull developing strategies to reduce or eliminate pathogen

contamination with a focus on Campylobacter and Salmonella

bull developing sustainable and organic farming practices for poultry producers

David DonavanResearch Molecular Biologist

DavidDonovanarsusdagov

Ce 443-690-4251 Office 301-504-9150

Current Projectsbull Mastitis a cow‐side diagnosticbull Mastitis treatment with triple‐acting antimicrobialsbull Clostridium perfringens novel endolysins that are heat‐resistantbull Yeast expressed endolysins as an alternative to antibiotics in animal feedbull CRISPRCas9 genomic engineering of cow and pig embryos

Selected Publicationsbull Rodriacuteguez‐Rubio L Martiacutenez B Rodriacuteguez A Donovan DM Goumltz F et al The

phage lytic proteins from the Staphylococcus aureus bacteriophage vB_SauS‐phiIPLA88 display multiple active catalytic domains and do not trigger staphylococcal resistance PloS one 2013 8(5)e64671

bull Singh PK Donovan DM Kumar A Intravitreal injection of the chimeric phage endolysin Ply187 protects mice from Staphylococcus aureus endophthalmitis Antimicrobial agents and chemotherapy 2014 58(8)4621‐9

bull Swift SM Seal BS Garrish JK Oakley BB Hiett K et al A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens‐Specific Cell Wall Binding Domain Creates an Anti‐Clostridium Antimicrobial with Improved Thermostability Viruses 2015 7(6)3019‐34

Link to all publications httpwwwncbinlmnihgovsitesmyncbi1jOJlsCcVSxQTbibliography41565643publicsort=dateampdirection=ascending

Animal Biosciences and Biotechnology Laboratory

Mailing AddressRoom 104 10300 Baltimore AveBLDG 230 BARC‐EastBeltsville MD 20705

National ProgramNP101 Food Animal Production

CRIS Project TitleDeveloping Genetic Biotechnologies for Increased Food Animal Production including Novel Antimicrobials for Improved Health and Product Safety

Production Systems StudiedDairy cattle Swine poultry Aquaculture

Laboratory and Field Expertisebull Molecular biologist with

transgenic and knockout mouse background

bull Heterologous gene expression in yeast bacteria mice and cell culture

bull Induced Pluripotent Stem cell production via lentiviral transduction

bull Mouse colony animal husbandry and embryo transfer

Research InterestsDavid M Donovan PhD Research Scientist (Molecular Biologist) at the US Department of Agriculture received his PhD in 1987 in molecular genetics of the yeast Saccharomyces cerevisiae and has 22 years experience in heterologous gene expression He spent 15 years at the NIH culminating in Section Chief Transgenic and Knockout Mouse lab NIA In 2002 he joined the USDA where he has been developing antimicrobials for the treatment of mastitis pathogens including Staphylococcus aureus His enzyme antimicrobials harbor three unique synergistic lytic domains and a protein transduction domain to target intracellular pathogens and have been shown to be highly refractory to resistance development His constructs eradicate both extracellular S aureus [in a rat nasal colonization model and murine systemic infections] and intracellular pathogens ex vivo in bovine mammary epithelial cells and in both a mouse model of mastitis and osteomyelitis He is working to identify protein feed additives as alternative to antibiotic growth promotants

Thomas F DuceyMicrobiologist

ThomasDuceyarsusdagov

843-669-5203 x112

Current Projectsbull Microbial responses to wetland restoration as a part

of the Mid‐Atlantic Region Conservation Effects Assessment Project

bull Response of the microbial rhizosphere and arbuscular mycorrhizae fungi to clover cover crop and conservation tillage in cotton production

bull Isolation of E coli and Enterococcus species from swine wastewater poultry litter and agriculturally‐impacted groundwater for the determination of baseline antibiotic resistance levels in agricultural production systems

Selected Publicationsbull Ducey et al Soil physicochemical conditions

denitrification rates and nosZ abundance in NC coastal plain restored wetlands 2015 J Environ Qual 44 1011‐1022

bull Ducey et al Microbial community analysis of swine wastewater anaerobic lagoons by next‐generation DNA sequencing 2013 Anaerobe 2150‐57

Coastal Plain Soil Water and Plant Research Center

Mailing Address2611 West Lucas StreetFlorence SC 29501

National Program(s)211 ndash Water Availability and Water Management212 ndash Climate Change Soils and Emissions214 ndash Agricultural and Industrial Byproducts

CRIS Project(s)Managing Water Availability and Quality (NP 211)Improving Chemical Physical and Biological Properties of Degraded Sandy Soils (NP 212)Innovative Bioresource Management Technologies (NP 214)

Production Systems StudiedCrops Poultry and Swine

Laboratory and Field Expertisebull Classical Microbiology

bull DetectionEnumerationIsolationbull New species identification

bull Molecular Biologybull T‐RFLPARISAbull qPCRReal Time PCRbull High‐throughput DNA Sequencing

(Ion Torrent)

Research Interestsbull Southeastern US coastal plain wetland restoration

and its effect on microbial community composition and function

bull Animal wastewater treatment systems with a particular focus on pathogen reduction and antibiotic resistance gene elimination

bull Microbial community analysis and response to crop conservation and cover cropping management practices

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Bradley BearsonMicrobiologist

BradBearsonarsusdagov

515-294-0209

Selected Publicationsbull Bearson BL and BW Brunelle Fluoroquinolone

Induction of Phage‐mediated Gene Transfer in Multidrug‐resistant Salmonella Int J Antimicrob Agents 46(2)201‐204 2015

bull Bearson B L Allen H K Brunelle B W Lee I S Casjens S R and Stanton T B The agricultural antibiotic carbadox induces phage‐mediated gene transfer in Salmonella Front Microbiol 552 2014

bull Bearson B L Bearson S M D Kich J D and Lee I S An rfaHmutant of Salmonella enterica serovar Typhimurium is attenuated in swine and reduces intestinal colonization fecal shedding and disease severity due to virulent Salmonella Typhimurium Front Vet Sci 19 2014

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Boulevard NLAEAmes IA 50011

National Program101 ndash Animal Production (Pending)

CRIS Project (terminated)Animal and Manure Management for Sustainable Production and Reduced Environmental Impact

Production Systems StudiedSwine and Turkeys

Laboratory and Field Expertisebull Bacterial strain construction

using classical genetics and recombineering

bull Antibiotic induced phage‐mediated gene transfer in Salmonella

bull Salmonella challenge models for swine and turkeys to investigate pathogenesis colonization and vaccine efficacy

bull PCR Salmonella genetics bacterial transformation and transduction modification of media for selection and differentiation of Salmonella

Research Interestsbull Development of alternatives to antibiotics such as

vaccines and other targeted interventionsbull Investigation of antibiotic resistance gene transfer

among microorganisms in the host and in the environment including multidrug‐resistant Salmonella

Current Projectsbull Validation of a Salmonella vaccine in swine and turkeys

to protect animal health and enhance food safetybull Identification of multidrug‐resistant Salmonella serovars

containing prophage capable of antibiotic‐induced gene transfer

bull Transcriptional analysis of phage genes following Salmonella exposure to antibiotics

bull Identification of antibiotics that induce phage‐mediated gene transfer in Salmonella

Shawn BearsonResearch Microbiologist

Current Projectsbull Characterizing novel porcine‐microbiota‐Salmonella

interactions as potential targets to reduce Salmonellacolonization and persistence in the intestinal tract

bull Developing alternatives to antibioticsbull Cross‐protective vaccine development against Salmonella serovars in food animals

bull Biotherapeutic immunostimulants for treatment of swine colonized with Salmonella

Selected Publicationsbull Knetter SM et al 2015 Salmonella enterica serovar

Typhimurium‐infected pigs with different shedding levels exhibit distinct clinical peripheral cytokine and transcriptomic immune response phenotypes Innate Immun 21227‐241

bull Bearson SM et al 2013 Polynucleotide phosphorylase (PNPase) is required for Salmonella enterica serovar Typhimurium colonization in swine Microb Pathog 6563‐66

bull Bearson SM et al 2013 Profiling the gastrointestinal microbiota in response to Salmonella low versus high Salmonella shedding in the natural porcine host Infect Genet Evol 16330‐340

Food Safety and Enteric Pathogens Research Unit

Mailing AddressNational Animal Disease Center1920 Dayton Ave1403Ames IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Title here

Second Title here if applicable

Production Systems StudiedSwine and Turkey

Laboratory and Field Expertisebull Molecular microbiologybull Salmonella geneticsbull Host transcriptomicsbull Salmonella colonization and

persistence in food animals

ShawnBearsonarsusdagov

515-337-7455

Research InterestsMy current research efforts are characterizing the effects of antibiotics on MDR Salmonella and identifying antibiotic alternatives to decrease Salmonella on the farm reduce antibiotic dependence promote animal health and provide the public with a safe food supply My research investigations focus on three factors that influence Salmonella colonization and persistence in food animals virulence mechanisms of Salmonella the tactical response from the host and interactions with the host microbiota residing within the gastrointestinal tract

Ross C BeierResearch Chemist

RossBeierarsusdagov

979-260-9411

Current Projectsbull Conduct disinfectant susceptibility tests on 145

Salmonella strains from feed lot water‐sprinkled cattlebull Synthesize thymol‐‐D‐cellobioside for use in delivering

the antibacterial thymol to the lower swine gutbull Conduct disinfectant susceptibility tests on 134

Campylobacter coli and jejuni from swine cecal samples meat products and feces

Selected Publicationsbull Beier RC E Franz JL Bono RE Mandrell PM

Fratamico TR Callaway K Andrews TL Poole TL Crippen CL Sheffield RC Anderson and DJ Nisbet Disinfectant and antimicrobial susceptibility profiles of the big six non‐O157 Shiga toxin‐producing Escherichia coli from food animals and humans J Food Protect 2016 (In press)

bull Crippen TL CL Sheffield JA Byrd JF Esquivel RC Beier and K Yeater Poultry litter and the environment Physiochemical properties of litter and soil during successive flock rotations and after remote site deposition Sci Total Environ 553650661 2016

bull Beier RC SE Duke RL Ziprin RB Harvey ME Hume TL Poole HM Scott LD Highfield WQ Alali K Andrews RC Anderson and DJ Nisbet Antibiotic and disinfectant susceptibility profiles of vancomycin‐resistant Enterococcus faecium (VRE) isolated from community wastewater in Texas Bull Environ Contam Toxicol 80188194 2008

Food and Feed SafetyResearch Unit

Mailing AddressSouthern Plains AgriculturalResearch Center

Food and Feed SafetyResearch Unit

2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedFocus is on bacterial isolates in beef swine and poultry

Laboratory and Field Expertisebull Microbroth dilution

antimicrobial susceptibility testing

bull Microbroth dilution disinfectant susceptibility testing

bull PCRbull Gas Chromatographybull High‐Performance Liquid

Chromatographybull TLC HPTLCbull Chemical Synthesis

Research Interestsbull Establish a knowledge base for disinfectant susceptibility

in foodborne pathogensbull Identify disinfectant and antimicrobial co‐resistancebull Evaluate the impact of disinfectant resistance genes

Elaine BerryResearch Microbiologist

ElaineBerryarsusdagov

402-762-4204

Current Projectsbull Evaluate the influence of spatiotemporal environmental

and wildlife factors on pathogen and antibiotic resistance occurrence and transmission dynamics in cattle and waterways in a pasture‐based production system

bull Determine phenotypic and genotypic factors associated with persistence of E coli O157H7 in cattle production

bull Determine the effect of calcium hydroxide application to feedlot pens on E coli O157H7 total E coli and antibiotic resistance on feedlot pen surfaces and in cattle

Selected Publicationsbull Berry ED JE Wells JL Bono BL Woodbury N

Kalchayanand KN Norman TV Suslow G Lόpez‐Velasco and PD Millner Effect of proximity to a cattle feedlot on Escherichia coli O157H7 contamination of leafy greens and evaluation of the potential for airborne transmission Appl Environ Microbiol 811101‐1110 2015

bull Wells JE ED Berry N Kalchayanand LA Rempel M Kim and WT Oliver Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Assessment of Genotypic and Phenotypic Factors for Foodborne Pathogen Transmission and Development of Intervention Strategies

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Sampling and analyses for

bacterial pathogens in manures soils and other environmental and complex sample matrices

bull Treatment and intervention processes to reduce pathogens in cattle swine and their manure

Research Interestsbull Understanding and reducing the transmission and

persistence of zoonotic pathogens and antibiotic resistance in livestock and preharvest production environments

bull Reducing pathogen and antibiotic resistance transmission from animal production to produce water and the environment

Carl BolsterResearch Hydrologist

CarlBolsterarsusdagov

270-781-2632 ext 244

Current Projectsbull Evaluating effects of manure application rate and

timing on the leaching and runoff potential of antibiotic resistant bacteria and their associated genes as part of a National Pork Board funded project

bull Incorporating uncertainty estimates in model predictions of phosphorus loss from agricultural fields

bull Comparing predictions from annual and daily time‐step phosphorus transport models as part of a National Conservation Innovation Grant project

Selected Publicationsbull Abit SM Bolster CH Cantrell KB Flores JQ and SL

Walker 2014 Transport of Escherichia coli Salmonella typhimurium and microspheres in biochar‐amended soils with different textures J of Environ Qual 43371‐378

bull Bolster CH and Abit SM 2012 Biochar pyrolyzed at two temperatures impacts E coli transport through a sandy soil J of Environ Qual 41124‐133

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville RD ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Management

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental QualitySecond Title here if applicable

Production Systems StudiedPoultry and swine

Laboratory and Field Expertisebull Conducting laboratory‐scale

flow through experimentsbull Developing and using numerical

models for describing bacteria and solute fate and transport in the environment

bull Quantifying uncertainties in observed and modeled data

Research Interestsbull Understanding the factors controlling microbial

transport through biochar‐amended soilsbull Evaluating transport of antibiotic resistant bacteria

through soilsbull Improving modeling tools for describing fate and

transport of phosphorus in the environment

Brian BrunelleResearch Microbiologist

BrianBrunellearsusdagov

515-337-7612

Current Projectsbull Comparing transcriptional differences between

antibiotics that induce invasion in multidrug‐resistant Salmonella and those that have no effect

bull Genome sequencing of novel multidrug‐resistant Salmonella isolates

bull Assessing antibiotics that can enhance resistance in multidrug‐resistant Salmonella

Selected Publicationsbull Brunelle BW Bearson BL Bearson SMD 2015

Chloramphenicol and tetracycline decrease motility and increase invasion and attachment gene expression in specific isolates of multidrug‐resistant Salmonella entericaserovar Typhimurium Front Microbiol 5801

bull Brunelle BW Bearson SMD Bearson BL 2013 Tetracycline accelerates the temporally‐regulated invasion response in specific isolates of multidrug‐resistant Salmonella enterica serovar Typhimurium BMC Microbiology 13 202

Food Safety and Enteric Pathogen Research Unit

Mailing AddressNational Animal Disease Center1920 Dayton AvePO Box 70Ames IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Analysis of Virulence and Antibiotic Resistance Mechanisms of Salmonella and Development of Intervention Strategies

Production Systems StudiedSwine

Laboratory and Field Expertisebull Analysis of bacterial

transcription using real‐time PCR and RNA‐seq

bull Characterization of antibiotic resistance levels and associated genes

bull Conducting assays to measure different virulence phenotypes (cellular invasion motility etc)

Research Interestsbull Investigating the impact antibiotic usage has on

influencing multidrug‐resistant Salmonella virulence phenotypes

bull Identifying genes and regulation pathways associated with phenotypic differences in multidrug‐resistant Salmonella isolates exposed to antibiotics

John P BrooksResearch Microbiologist

JohnBrooksarsusdagov

662-320-7411

7

Current Projectsbull The effect of degraded antibiotic on soil microbial

ecology and antibacterial microbiomebull Aerosol carriage of antibiotic resistant genes and

bacteria from land application of poultry litterbull Antibiotic resistant bacteria and genes in naiumlve

broiler CAFOs

Selected Publicationsbull Brooks JP MR McLaughlin A Adeli DM Miles 2016

Cultivation and qPCR detection of pathogenic and antibiotic‐resistant bacterial establishment in naiumlve broiler houses J Environ Qual 45958‐966

bull Brooks JP Adeli A McLaughlin MR 2014 Microbial ecology bacterial pathogens and antibiotic resistant genes in swine manure as influenced by three swine management systems Water Res 5796‐103

bull Brooks JP McLaughlin MR Scheffler B and Miles DM 2010 Microbial and antibiotic resistant constituents associated with biological aerosols and poultry litter within a commercial poultry house Sci Tot Environ 4084770‐4777

Genetics and Sustainable Agriculture Research Unit

Mailing Address810 Highway 12 East PO Box 5367Mississippi State MS 39762

National Program(s)216 ndash Agricultural System Competitiveness and Sustainability

CRIS Project(s)Integration of Site‐Specific Crop Production Practices amp Industrial amp Animal Ag Byproducts to Improve Ag Competitiveness amp Sustainability

Production Systems StudiedSwine Poultry Forage amp Row Crop

Laboratory and Field Expertisebull Detection amp enumeration of

pathogens and antibacterial resistant genes and bacteria

bull Sampling soil water air amp CAFO environments

bull Quantitative microbial risk assessment of pathogens amp antibacterial resistant bacteria in the environment

Research Interestsbull Identify the movement and fate of pathogens and

antibacterial resistant genesbacteria through the environment and CAFO environments

bull Apply quantitative microbial risk assessment to anthropogenic impacted environments

bull Determine the impact of row crop agriculture on the soil microbial and antibacterial resistant biome

Tucker BurchResearch Agricultural

Engineer

TuckerBurcharsusdagov

715-387-3670

Current Projectsbull Occurrence and Distribution of Antibiotic Resistance

Genes (ARGs) in Groundwater of Kewaunee County Wisconsin

Selected Publicationsbull Burch TR Sadowsky MJ LaPara TM 2016 Modeling the

fate of antibiotic resistance genes and class 1 integronsduring thermophilic anaerobic digestion of municipal wastewater solids Appl Microbiol Biotechnol 100(3) 1437‐1444

bull Burch TR Sadowsky MJ LaPara TM 2014 Fate of antibiotic resistance genes and class 1 integrons in soil microcosms following the application of treated residual municipal wastewater solids Environ Sci Technol 48(10) 5620‐5627

bull Burch TR Sadowsky MJ LaPara TM 2013 Air‐drying beds reduce the quantities of antibiotic resistance genes and class 1 integrons in residual municipal wastewater solids Environ Sci Technol 47(17) 9965‐9971

bull Burch TR Sadowsky MJ LaPara TM 2013 Aerobic digestion reduces the quantity of antibiotic resistance genes in residual municipal wastewater solids Front Microbiol 4(Feb)

Dairy Forage Research CenterEnvironmentally Integrated Dairy Management Research Unit

Mailing Address2615 Yellowstone DriveMarshfield WI 54449

National Program(s)212 ndash Soil and Air

CRIS Project(s)Improving Nutrient Use Efficiency and Mitigating Nutrient and Pathogen Losses from Dairy Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull qPCRbull Bioaerosol samplingbull Quantitative microbial risk

assessment

Research Interestsbull Environmental distribution and transmission of

antibiotic resistance genes (ARGs)bull Quantitative microbial risk assessment

Todd CallawayResearch Microbiologist

ToddCallawayarsusdagov

979-260-9374 7

Current Projectsbull Effects of organic acids on the microbiome of food

animals and impact on foodborne pathogensbull Dietary impacts on foodborne pathogenic bacteria

and the microbial ecosystembull Phytochemicals and their ability to alter composition

of the gastrointestinal microbiome

Selected Publicationsbull Callaway T R T S Edrington and D J Nisbet 2014

Isolation of E coli O157H7 and Salmonella from migratory brown‐headed cowbirds (Molothrus ater) common grackles (Quiscalus quiscula) and cattle egrets (Bubulcus ibis) Foodborne Path Dis 11791‐794

bull Broadway P R J A Carroll J C Brooks J R Donaldson N C Burdick‐Sanchez T B Schmidt T R Brown and T R Callaway 2015 Salmonella transfer to the lymph nodes and synovial fluid of experimentally orally inoculated swine Agric Food Anal Bacteriol (In Press)

bull Grilli E F Foresti B Tugnoli M Fustini M G Zanoni P Pasquali T R Callaway A Piva and G L Alborali 2015 Microencapsulated sorbic acid and pure botanicals affect Salmonella Typhimurium shedding in pigs a close‐up look from weaning to slaughter in controlled and field conditions Foodborne Path Dis (In Press)

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedBeef Cattle Dairy Cattle Swine and Poultry

Laboratory and Field Expertisebull Microbial Physiologybull Microbial Ecologybull Continuous culturebull Mixed culture environmental

simulationsbull Environmental impacts on

survival of foodborne pathogenic bacteria

bull Animal model challengesbull Development of pre‐harvest

intervention strategiesbull Feedlot and dairy procedures

Research Interestsbull Understanding how the microbial ecosystem interacts

with foodborne pathogens at a functional nicheguild level

bull Developing non‐antibiotic methods of reducing foodborne pathogenic bacteria in the gut of food animals

Kimberly CookResearch Microbiologist

KimCookarsusdagov

270-781-2579 ext 232

Current Projectsbull Capture and identify mobile genetic elements

associated with bacteria in soils with applied poultry litter effect of application method

bull Evaluate persistence and concentration of antibiotics and bacteria with AR genes in waste treatment systems and soils with application manures

bull Transport and adhesion of bacteria with AR genesbull Evaluate AR properties of E coli and enterococci

isolates from agricultural ecosystems

Selected Publicationsbull Durso LM and KL Cook 2014 Impacts of antibiotic

use in agriculture what are the benefits and risks CurrOpinion Microbiol 1937‐44 2014

bull Cook KL AMP Netthisinghe and RA Gilfillen 2014 Detection of Pathogens Indicators and Antibiotic Resistance Genes after Land Application of Poultry Litter J Environ Qual 43 1546‐1558

bull Netthisinghe AMP KL Cook C Rice RA Gilfillen and KR Sistani 2013 Soil Nutrients Bacteria Populations and Veterinary Pharmaceuticals across a Backgrounding Beef Feedlot J Environ Qual 42 532‐544

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville Red ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Research

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental Quality

Production Systems StudiedPoultry Swine Beef

Laboratory and Field Expertisebull Soils manure and waste

treatment systemsbull PCR Quantitiative real‐time

PCRbull Culture and antimicrobial

susceptibilitybull Isolation and characterization of

mobile genetic elements carrying genes for antibiotic resistance

Research Interestsbull Characterizing persistence and transmission of

antibiotics antibiotic resistance (AR) genes and AR bacteria through agroecosystems

bull Capture and characterize mobile genetic elements carrying AR genes between microbial populations in soils with applied manures

bull Strain level differences in resistance transport and adhesion properties of bacteria with AR genes

Annie DonoghueResearch Leader (Physiologist)

AnnieDonoghuearsusdagov479-575-2413

7

Current Projectsbull Use of natural remedies to alleviate enteric

pathogens in organic and conventionally raised poultry

bull Alternatives to antibiotics for controlling Salmonella and Campylobacter in poultry and poultry products

Selected Publicationsbull Donoghue AM Venkitanarayanan K Arsi K Woo‐

Ming A Upadhyaya I Kollanoor‐Johny A Darre MJ Upadhyay A Fanatico A and Donoghue DJ 2015 Organic Poultry Developing Natural Solutions for Reducing Pathogens and Improving Production Organic Agriculture Research Symp in press

bull Arsi K Donoghue AM Woo‐Ming A Blore PJ and Donoghue DJ 2015 Intracloacal inoculation an effective screening method for determining the efficacy of probiotic bacterial isolates against Campylobactercolonization in broiler chickens J Food Prot 78 209‐213

bull Arsi K Donoghue AM Venkitanarayanan K Kollanoor‐Johny A Fanatico AC Blore PJ and Donoghue DJ2014 The efficacy of the natural plant extracts thymol and carvacrol against Campylobacter colonization in broiler chickens J Food Safety 34 321ndash325

Poultry Production and Products Safety Research Unit

Mailing AddressUniversity Of ArkansasPOSC O‐303Fayetteville AR 72701

National Program(s)108 ndash Food Safety103 ndash Animal Health

CRIS Project(s)Alternative Intervention and Control Strategies for Foodborne Pathogens in Poultry and Poultry Products

Novel Therapeutic Diagnostic and Management Strategies to Reduce Antibiotic Use in Poultry Production

Production Systems StudiedPoultry

Laboratory and Field ExpertiseLab uses traditional microbiological culture and molecular biological techniques to study food borne pathogens Organic and conventional practices for poultry production

Research Interestsbull developing alternatives to antibiotic use in poultry bull developing strategies to reduce or eliminate pathogen

contamination with a focus on Campylobacter and Salmonella

bull developing sustainable and organic farming practices for poultry producers

David DonavanResearch Molecular Biologist

DavidDonovanarsusdagov

Ce 443-690-4251 Office 301-504-9150

Current Projectsbull Mastitis a cow‐side diagnosticbull Mastitis treatment with triple‐acting antimicrobialsbull Clostridium perfringens novel endolysins that are heat‐resistantbull Yeast expressed endolysins as an alternative to antibiotics in animal feedbull CRISPRCas9 genomic engineering of cow and pig embryos

Selected Publicationsbull Rodriacuteguez‐Rubio L Martiacutenez B Rodriacuteguez A Donovan DM Goumltz F et al The

phage lytic proteins from the Staphylococcus aureus bacteriophage vB_SauS‐phiIPLA88 display multiple active catalytic domains and do not trigger staphylococcal resistance PloS one 2013 8(5)e64671

bull Singh PK Donovan DM Kumar A Intravitreal injection of the chimeric phage endolysin Ply187 protects mice from Staphylococcus aureus endophthalmitis Antimicrobial agents and chemotherapy 2014 58(8)4621‐9

bull Swift SM Seal BS Garrish JK Oakley BB Hiett K et al A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens‐Specific Cell Wall Binding Domain Creates an Anti‐Clostridium Antimicrobial with Improved Thermostability Viruses 2015 7(6)3019‐34

Link to all publications httpwwwncbinlmnihgovsitesmyncbi1jOJlsCcVSxQTbibliography41565643publicsort=dateampdirection=ascending

Animal Biosciences and Biotechnology Laboratory

Mailing AddressRoom 104 10300 Baltimore AveBLDG 230 BARC‐EastBeltsville MD 20705

National ProgramNP101 Food Animal Production

CRIS Project TitleDeveloping Genetic Biotechnologies for Increased Food Animal Production including Novel Antimicrobials for Improved Health and Product Safety

Production Systems StudiedDairy cattle Swine poultry Aquaculture

Laboratory and Field Expertisebull Molecular biologist with

transgenic and knockout mouse background

bull Heterologous gene expression in yeast bacteria mice and cell culture

bull Induced Pluripotent Stem cell production via lentiviral transduction

bull Mouse colony animal husbandry and embryo transfer

Research InterestsDavid M Donovan PhD Research Scientist (Molecular Biologist) at the US Department of Agriculture received his PhD in 1987 in molecular genetics of the yeast Saccharomyces cerevisiae and has 22 years experience in heterologous gene expression He spent 15 years at the NIH culminating in Section Chief Transgenic and Knockout Mouse lab NIA In 2002 he joined the USDA where he has been developing antimicrobials for the treatment of mastitis pathogens including Staphylococcus aureus His enzyme antimicrobials harbor three unique synergistic lytic domains and a protein transduction domain to target intracellular pathogens and have been shown to be highly refractory to resistance development His constructs eradicate both extracellular S aureus [in a rat nasal colonization model and murine systemic infections] and intracellular pathogens ex vivo in bovine mammary epithelial cells and in both a mouse model of mastitis and osteomyelitis He is working to identify protein feed additives as alternative to antibiotic growth promotants

Thomas F DuceyMicrobiologist

ThomasDuceyarsusdagov

843-669-5203 x112

Current Projectsbull Microbial responses to wetland restoration as a part

of the Mid‐Atlantic Region Conservation Effects Assessment Project

bull Response of the microbial rhizosphere and arbuscular mycorrhizae fungi to clover cover crop and conservation tillage in cotton production

bull Isolation of E coli and Enterococcus species from swine wastewater poultry litter and agriculturally‐impacted groundwater for the determination of baseline antibiotic resistance levels in agricultural production systems

Selected Publicationsbull Ducey et al Soil physicochemical conditions

denitrification rates and nosZ abundance in NC coastal plain restored wetlands 2015 J Environ Qual 44 1011‐1022

bull Ducey et al Microbial community analysis of swine wastewater anaerobic lagoons by next‐generation DNA sequencing 2013 Anaerobe 2150‐57

Coastal Plain Soil Water and Plant Research Center

Mailing Address2611 West Lucas StreetFlorence SC 29501

National Program(s)211 ndash Water Availability and Water Management212 ndash Climate Change Soils and Emissions214 ndash Agricultural and Industrial Byproducts

CRIS Project(s)Managing Water Availability and Quality (NP 211)Improving Chemical Physical and Biological Properties of Degraded Sandy Soils (NP 212)Innovative Bioresource Management Technologies (NP 214)

Production Systems StudiedCrops Poultry and Swine

Laboratory and Field Expertisebull Classical Microbiology

bull DetectionEnumerationIsolationbull New species identification

bull Molecular Biologybull T‐RFLPARISAbull qPCRReal Time PCRbull High‐throughput DNA Sequencing

(Ion Torrent)

Research Interestsbull Southeastern US coastal plain wetland restoration

and its effect on microbial community composition and function

bull Animal wastewater treatment systems with a particular focus on pathogen reduction and antibiotic resistance gene elimination

bull Microbial community analysis and response to crop conservation and cover cropping management practices

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Shawn BearsonResearch Microbiologist

Current Projectsbull Characterizing novel porcine‐microbiota‐Salmonella

interactions as potential targets to reduce Salmonellacolonization and persistence in the intestinal tract

bull Developing alternatives to antibioticsbull Cross‐protective vaccine development against Salmonella serovars in food animals

bull Biotherapeutic immunostimulants for treatment of swine colonized with Salmonella

Selected Publicationsbull Knetter SM et al 2015 Salmonella enterica serovar

Typhimurium‐infected pigs with different shedding levels exhibit distinct clinical peripheral cytokine and transcriptomic immune response phenotypes Innate Immun 21227‐241

bull Bearson SM et al 2013 Polynucleotide phosphorylase (PNPase) is required for Salmonella enterica serovar Typhimurium colonization in swine Microb Pathog 6563‐66

bull Bearson SM et al 2013 Profiling the gastrointestinal microbiota in response to Salmonella low versus high Salmonella shedding in the natural porcine host Infect Genet Evol 16330‐340

Food Safety and Enteric Pathogens Research Unit

Mailing AddressNational Animal Disease Center1920 Dayton Ave1403Ames IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Title here

Second Title here if applicable

Production Systems StudiedSwine and Turkey

Laboratory and Field Expertisebull Molecular microbiologybull Salmonella geneticsbull Host transcriptomicsbull Salmonella colonization and

persistence in food animals

ShawnBearsonarsusdagov

515-337-7455

Research InterestsMy current research efforts are characterizing the effects of antibiotics on MDR Salmonella and identifying antibiotic alternatives to decrease Salmonella on the farm reduce antibiotic dependence promote animal health and provide the public with a safe food supply My research investigations focus on three factors that influence Salmonella colonization and persistence in food animals virulence mechanisms of Salmonella the tactical response from the host and interactions with the host microbiota residing within the gastrointestinal tract

Ross C BeierResearch Chemist

RossBeierarsusdagov

979-260-9411

Current Projectsbull Conduct disinfectant susceptibility tests on 145

Salmonella strains from feed lot water‐sprinkled cattlebull Synthesize thymol‐‐D‐cellobioside for use in delivering

the antibacterial thymol to the lower swine gutbull Conduct disinfectant susceptibility tests on 134

Campylobacter coli and jejuni from swine cecal samples meat products and feces

Selected Publicationsbull Beier RC E Franz JL Bono RE Mandrell PM

Fratamico TR Callaway K Andrews TL Poole TL Crippen CL Sheffield RC Anderson and DJ Nisbet Disinfectant and antimicrobial susceptibility profiles of the big six non‐O157 Shiga toxin‐producing Escherichia coli from food animals and humans J Food Protect 2016 (In press)

bull Crippen TL CL Sheffield JA Byrd JF Esquivel RC Beier and K Yeater Poultry litter and the environment Physiochemical properties of litter and soil during successive flock rotations and after remote site deposition Sci Total Environ 553650661 2016

bull Beier RC SE Duke RL Ziprin RB Harvey ME Hume TL Poole HM Scott LD Highfield WQ Alali K Andrews RC Anderson and DJ Nisbet Antibiotic and disinfectant susceptibility profiles of vancomycin‐resistant Enterococcus faecium (VRE) isolated from community wastewater in Texas Bull Environ Contam Toxicol 80188194 2008

Food and Feed SafetyResearch Unit

Mailing AddressSouthern Plains AgriculturalResearch Center

Food and Feed SafetyResearch Unit

2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedFocus is on bacterial isolates in beef swine and poultry

Laboratory and Field Expertisebull Microbroth dilution

antimicrobial susceptibility testing

bull Microbroth dilution disinfectant susceptibility testing

bull PCRbull Gas Chromatographybull High‐Performance Liquid

Chromatographybull TLC HPTLCbull Chemical Synthesis

Research Interestsbull Establish a knowledge base for disinfectant susceptibility

in foodborne pathogensbull Identify disinfectant and antimicrobial co‐resistancebull Evaluate the impact of disinfectant resistance genes

Elaine BerryResearch Microbiologist

ElaineBerryarsusdagov

402-762-4204

Current Projectsbull Evaluate the influence of spatiotemporal environmental

and wildlife factors on pathogen and antibiotic resistance occurrence and transmission dynamics in cattle and waterways in a pasture‐based production system

bull Determine phenotypic and genotypic factors associated with persistence of E coli O157H7 in cattle production

bull Determine the effect of calcium hydroxide application to feedlot pens on E coli O157H7 total E coli and antibiotic resistance on feedlot pen surfaces and in cattle

Selected Publicationsbull Berry ED JE Wells JL Bono BL Woodbury N

Kalchayanand KN Norman TV Suslow G Lόpez‐Velasco and PD Millner Effect of proximity to a cattle feedlot on Escherichia coli O157H7 contamination of leafy greens and evaluation of the potential for airborne transmission Appl Environ Microbiol 811101‐1110 2015

bull Wells JE ED Berry N Kalchayanand LA Rempel M Kim and WT Oliver Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Assessment of Genotypic and Phenotypic Factors for Foodborne Pathogen Transmission and Development of Intervention Strategies

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Sampling and analyses for

bacterial pathogens in manures soils and other environmental and complex sample matrices

bull Treatment and intervention processes to reduce pathogens in cattle swine and their manure

Research Interestsbull Understanding and reducing the transmission and

persistence of zoonotic pathogens and antibiotic resistance in livestock and preharvest production environments

bull Reducing pathogen and antibiotic resistance transmission from animal production to produce water and the environment

Carl BolsterResearch Hydrologist

CarlBolsterarsusdagov

270-781-2632 ext 244

Current Projectsbull Evaluating effects of manure application rate and

timing on the leaching and runoff potential of antibiotic resistant bacteria and their associated genes as part of a National Pork Board funded project

bull Incorporating uncertainty estimates in model predictions of phosphorus loss from agricultural fields

bull Comparing predictions from annual and daily time‐step phosphorus transport models as part of a National Conservation Innovation Grant project

Selected Publicationsbull Abit SM Bolster CH Cantrell KB Flores JQ and SL

Walker 2014 Transport of Escherichia coli Salmonella typhimurium and microspheres in biochar‐amended soils with different textures J of Environ Qual 43371‐378

bull Bolster CH and Abit SM 2012 Biochar pyrolyzed at two temperatures impacts E coli transport through a sandy soil J of Environ Qual 41124‐133

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville RD ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Management

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental QualitySecond Title here if applicable

Production Systems StudiedPoultry and swine

Laboratory and Field Expertisebull Conducting laboratory‐scale

flow through experimentsbull Developing and using numerical

models for describing bacteria and solute fate and transport in the environment

bull Quantifying uncertainties in observed and modeled data

Research Interestsbull Understanding the factors controlling microbial

transport through biochar‐amended soilsbull Evaluating transport of antibiotic resistant bacteria

through soilsbull Improving modeling tools for describing fate and

transport of phosphorus in the environment

Brian BrunelleResearch Microbiologist

BrianBrunellearsusdagov

515-337-7612

Current Projectsbull Comparing transcriptional differences between

antibiotics that induce invasion in multidrug‐resistant Salmonella and those that have no effect

bull Genome sequencing of novel multidrug‐resistant Salmonella isolates

bull Assessing antibiotics that can enhance resistance in multidrug‐resistant Salmonella

Selected Publicationsbull Brunelle BW Bearson BL Bearson SMD 2015

Chloramphenicol and tetracycline decrease motility and increase invasion and attachment gene expression in specific isolates of multidrug‐resistant Salmonella entericaserovar Typhimurium Front Microbiol 5801

bull Brunelle BW Bearson SMD Bearson BL 2013 Tetracycline accelerates the temporally‐regulated invasion response in specific isolates of multidrug‐resistant Salmonella enterica serovar Typhimurium BMC Microbiology 13 202

Food Safety and Enteric Pathogen Research Unit

Mailing AddressNational Animal Disease Center1920 Dayton AvePO Box 70Ames IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Analysis of Virulence and Antibiotic Resistance Mechanisms of Salmonella and Development of Intervention Strategies

Production Systems StudiedSwine

Laboratory and Field Expertisebull Analysis of bacterial

transcription using real‐time PCR and RNA‐seq

bull Characterization of antibiotic resistance levels and associated genes

bull Conducting assays to measure different virulence phenotypes (cellular invasion motility etc)

Research Interestsbull Investigating the impact antibiotic usage has on

influencing multidrug‐resistant Salmonella virulence phenotypes

bull Identifying genes and regulation pathways associated with phenotypic differences in multidrug‐resistant Salmonella isolates exposed to antibiotics

John P BrooksResearch Microbiologist

JohnBrooksarsusdagov

662-320-7411

7

Current Projectsbull The effect of degraded antibiotic on soil microbial

ecology and antibacterial microbiomebull Aerosol carriage of antibiotic resistant genes and

bacteria from land application of poultry litterbull Antibiotic resistant bacteria and genes in naiumlve

broiler CAFOs

Selected Publicationsbull Brooks JP MR McLaughlin A Adeli DM Miles 2016

Cultivation and qPCR detection of pathogenic and antibiotic‐resistant bacterial establishment in naiumlve broiler houses J Environ Qual 45958‐966

bull Brooks JP Adeli A McLaughlin MR 2014 Microbial ecology bacterial pathogens and antibiotic resistant genes in swine manure as influenced by three swine management systems Water Res 5796‐103

bull Brooks JP McLaughlin MR Scheffler B and Miles DM 2010 Microbial and antibiotic resistant constituents associated with biological aerosols and poultry litter within a commercial poultry house Sci Tot Environ 4084770‐4777

Genetics and Sustainable Agriculture Research Unit

Mailing Address810 Highway 12 East PO Box 5367Mississippi State MS 39762

National Program(s)216 ndash Agricultural System Competitiveness and Sustainability

CRIS Project(s)Integration of Site‐Specific Crop Production Practices amp Industrial amp Animal Ag Byproducts to Improve Ag Competitiveness amp Sustainability

Production Systems StudiedSwine Poultry Forage amp Row Crop

Laboratory and Field Expertisebull Detection amp enumeration of

pathogens and antibacterial resistant genes and bacteria

bull Sampling soil water air amp CAFO environments

bull Quantitative microbial risk assessment of pathogens amp antibacterial resistant bacteria in the environment

Research Interestsbull Identify the movement and fate of pathogens and

antibacterial resistant genesbacteria through the environment and CAFO environments

bull Apply quantitative microbial risk assessment to anthropogenic impacted environments

bull Determine the impact of row crop agriculture on the soil microbial and antibacterial resistant biome

Tucker BurchResearch Agricultural

Engineer

TuckerBurcharsusdagov

715-387-3670

Current Projectsbull Occurrence and Distribution of Antibiotic Resistance

Genes (ARGs) in Groundwater of Kewaunee County Wisconsin

Selected Publicationsbull Burch TR Sadowsky MJ LaPara TM 2016 Modeling the

fate of antibiotic resistance genes and class 1 integronsduring thermophilic anaerobic digestion of municipal wastewater solids Appl Microbiol Biotechnol 100(3) 1437‐1444

bull Burch TR Sadowsky MJ LaPara TM 2014 Fate of antibiotic resistance genes and class 1 integrons in soil microcosms following the application of treated residual municipal wastewater solids Environ Sci Technol 48(10) 5620‐5627

bull Burch TR Sadowsky MJ LaPara TM 2013 Air‐drying beds reduce the quantities of antibiotic resistance genes and class 1 integrons in residual municipal wastewater solids Environ Sci Technol 47(17) 9965‐9971

bull Burch TR Sadowsky MJ LaPara TM 2013 Aerobic digestion reduces the quantity of antibiotic resistance genes in residual municipal wastewater solids Front Microbiol 4(Feb)

Dairy Forage Research CenterEnvironmentally Integrated Dairy Management Research Unit

Mailing Address2615 Yellowstone DriveMarshfield WI 54449

National Program(s)212 ndash Soil and Air

CRIS Project(s)Improving Nutrient Use Efficiency and Mitigating Nutrient and Pathogen Losses from Dairy Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull qPCRbull Bioaerosol samplingbull Quantitative microbial risk

assessment

Research Interestsbull Environmental distribution and transmission of

antibiotic resistance genes (ARGs)bull Quantitative microbial risk assessment

Todd CallawayResearch Microbiologist

ToddCallawayarsusdagov

979-260-9374 7

Current Projectsbull Effects of organic acids on the microbiome of food

animals and impact on foodborne pathogensbull Dietary impacts on foodborne pathogenic bacteria

and the microbial ecosystembull Phytochemicals and their ability to alter composition

of the gastrointestinal microbiome

Selected Publicationsbull Callaway T R T S Edrington and D J Nisbet 2014

Isolation of E coli O157H7 and Salmonella from migratory brown‐headed cowbirds (Molothrus ater) common grackles (Quiscalus quiscula) and cattle egrets (Bubulcus ibis) Foodborne Path Dis 11791‐794

bull Broadway P R J A Carroll J C Brooks J R Donaldson N C Burdick‐Sanchez T B Schmidt T R Brown and T R Callaway 2015 Salmonella transfer to the lymph nodes and synovial fluid of experimentally orally inoculated swine Agric Food Anal Bacteriol (In Press)

bull Grilli E F Foresti B Tugnoli M Fustini M G Zanoni P Pasquali T R Callaway A Piva and G L Alborali 2015 Microencapsulated sorbic acid and pure botanicals affect Salmonella Typhimurium shedding in pigs a close‐up look from weaning to slaughter in controlled and field conditions Foodborne Path Dis (In Press)

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedBeef Cattle Dairy Cattle Swine and Poultry

Laboratory and Field Expertisebull Microbial Physiologybull Microbial Ecologybull Continuous culturebull Mixed culture environmental

simulationsbull Environmental impacts on

survival of foodborne pathogenic bacteria

bull Animal model challengesbull Development of pre‐harvest

intervention strategiesbull Feedlot and dairy procedures

Research Interestsbull Understanding how the microbial ecosystem interacts

with foodborne pathogens at a functional nicheguild level

bull Developing non‐antibiotic methods of reducing foodborne pathogenic bacteria in the gut of food animals

Kimberly CookResearch Microbiologist

KimCookarsusdagov

270-781-2579 ext 232

Current Projectsbull Capture and identify mobile genetic elements

associated with bacteria in soils with applied poultry litter effect of application method

bull Evaluate persistence and concentration of antibiotics and bacteria with AR genes in waste treatment systems and soils with application manures

bull Transport and adhesion of bacteria with AR genesbull Evaluate AR properties of E coli and enterococci

isolates from agricultural ecosystems

Selected Publicationsbull Durso LM and KL Cook 2014 Impacts of antibiotic

use in agriculture what are the benefits and risks CurrOpinion Microbiol 1937‐44 2014

bull Cook KL AMP Netthisinghe and RA Gilfillen 2014 Detection of Pathogens Indicators and Antibiotic Resistance Genes after Land Application of Poultry Litter J Environ Qual 43 1546‐1558

bull Netthisinghe AMP KL Cook C Rice RA Gilfillen and KR Sistani 2013 Soil Nutrients Bacteria Populations and Veterinary Pharmaceuticals across a Backgrounding Beef Feedlot J Environ Qual 42 532‐544

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville Red ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Research

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental Quality

Production Systems StudiedPoultry Swine Beef

Laboratory and Field Expertisebull Soils manure and waste

treatment systemsbull PCR Quantitiative real‐time

PCRbull Culture and antimicrobial

susceptibilitybull Isolation and characterization of

mobile genetic elements carrying genes for antibiotic resistance

Research Interestsbull Characterizing persistence and transmission of

antibiotics antibiotic resistance (AR) genes and AR bacteria through agroecosystems

bull Capture and characterize mobile genetic elements carrying AR genes between microbial populations in soils with applied manures

bull Strain level differences in resistance transport and adhesion properties of bacteria with AR genes

Annie DonoghueResearch Leader (Physiologist)

AnnieDonoghuearsusdagov479-575-2413

7

Current Projectsbull Use of natural remedies to alleviate enteric

pathogens in organic and conventionally raised poultry

bull Alternatives to antibiotics for controlling Salmonella and Campylobacter in poultry and poultry products

Selected Publicationsbull Donoghue AM Venkitanarayanan K Arsi K Woo‐

Ming A Upadhyaya I Kollanoor‐Johny A Darre MJ Upadhyay A Fanatico A and Donoghue DJ 2015 Organic Poultry Developing Natural Solutions for Reducing Pathogens and Improving Production Organic Agriculture Research Symp in press

bull Arsi K Donoghue AM Woo‐Ming A Blore PJ and Donoghue DJ 2015 Intracloacal inoculation an effective screening method for determining the efficacy of probiotic bacterial isolates against Campylobactercolonization in broiler chickens J Food Prot 78 209‐213

bull Arsi K Donoghue AM Venkitanarayanan K Kollanoor‐Johny A Fanatico AC Blore PJ and Donoghue DJ2014 The efficacy of the natural plant extracts thymol and carvacrol against Campylobacter colonization in broiler chickens J Food Safety 34 321ndash325

Poultry Production and Products Safety Research Unit

Mailing AddressUniversity Of ArkansasPOSC O‐303Fayetteville AR 72701

National Program(s)108 ndash Food Safety103 ndash Animal Health

CRIS Project(s)Alternative Intervention and Control Strategies for Foodborne Pathogens in Poultry and Poultry Products

Novel Therapeutic Diagnostic and Management Strategies to Reduce Antibiotic Use in Poultry Production

Production Systems StudiedPoultry

Laboratory and Field ExpertiseLab uses traditional microbiological culture and molecular biological techniques to study food borne pathogens Organic and conventional practices for poultry production

Research Interestsbull developing alternatives to antibiotic use in poultry bull developing strategies to reduce or eliminate pathogen

contamination with a focus on Campylobacter and Salmonella

bull developing sustainable and organic farming practices for poultry producers

David DonavanResearch Molecular Biologist

DavidDonovanarsusdagov

Ce 443-690-4251 Office 301-504-9150

Current Projectsbull Mastitis a cow‐side diagnosticbull Mastitis treatment with triple‐acting antimicrobialsbull Clostridium perfringens novel endolysins that are heat‐resistantbull Yeast expressed endolysins as an alternative to antibiotics in animal feedbull CRISPRCas9 genomic engineering of cow and pig embryos

Selected Publicationsbull Rodriacuteguez‐Rubio L Martiacutenez B Rodriacuteguez A Donovan DM Goumltz F et al The

phage lytic proteins from the Staphylococcus aureus bacteriophage vB_SauS‐phiIPLA88 display multiple active catalytic domains and do not trigger staphylococcal resistance PloS one 2013 8(5)e64671

bull Singh PK Donovan DM Kumar A Intravitreal injection of the chimeric phage endolysin Ply187 protects mice from Staphylococcus aureus endophthalmitis Antimicrobial agents and chemotherapy 2014 58(8)4621‐9

bull Swift SM Seal BS Garrish JK Oakley BB Hiett K et al A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens‐Specific Cell Wall Binding Domain Creates an Anti‐Clostridium Antimicrobial with Improved Thermostability Viruses 2015 7(6)3019‐34

Link to all publications httpwwwncbinlmnihgovsitesmyncbi1jOJlsCcVSxQTbibliography41565643publicsort=dateampdirection=ascending

Animal Biosciences and Biotechnology Laboratory

Mailing AddressRoom 104 10300 Baltimore AveBLDG 230 BARC‐EastBeltsville MD 20705

National ProgramNP101 Food Animal Production

CRIS Project TitleDeveloping Genetic Biotechnologies for Increased Food Animal Production including Novel Antimicrobials for Improved Health and Product Safety

Production Systems StudiedDairy cattle Swine poultry Aquaculture

Laboratory and Field Expertisebull Molecular biologist with

transgenic and knockout mouse background

bull Heterologous gene expression in yeast bacteria mice and cell culture

bull Induced Pluripotent Stem cell production via lentiviral transduction

bull Mouse colony animal husbandry and embryo transfer

Research InterestsDavid M Donovan PhD Research Scientist (Molecular Biologist) at the US Department of Agriculture received his PhD in 1987 in molecular genetics of the yeast Saccharomyces cerevisiae and has 22 years experience in heterologous gene expression He spent 15 years at the NIH culminating in Section Chief Transgenic and Knockout Mouse lab NIA In 2002 he joined the USDA where he has been developing antimicrobials for the treatment of mastitis pathogens including Staphylococcus aureus His enzyme antimicrobials harbor three unique synergistic lytic domains and a protein transduction domain to target intracellular pathogens and have been shown to be highly refractory to resistance development His constructs eradicate both extracellular S aureus [in a rat nasal colonization model and murine systemic infections] and intracellular pathogens ex vivo in bovine mammary epithelial cells and in both a mouse model of mastitis and osteomyelitis He is working to identify protein feed additives as alternative to antibiotic growth promotants

Thomas F DuceyMicrobiologist

ThomasDuceyarsusdagov

843-669-5203 x112

Current Projectsbull Microbial responses to wetland restoration as a part

of the Mid‐Atlantic Region Conservation Effects Assessment Project

bull Response of the microbial rhizosphere and arbuscular mycorrhizae fungi to clover cover crop and conservation tillage in cotton production

bull Isolation of E coli and Enterococcus species from swine wastewater poultry litter and agriculturally‐impacted groundwater for the determination of baseline antibiotic resistance levels in agricultural production systems

Selected Publicationsbull Ducey et al Soil physicochemical conditions

denitrification rates and nosZ abundance in NC coastal plain restored wetlands 2015 J Environ Qual 44 1011‐1022

bull Ducey et al Microbial community analysis of swine wastewater anaerobic lagoons by next‐generation DNA sequencing 2013 Anaerobe 2150‐57

Coastal Plain Soil Water and Plant Research Center

Mailing Address2611 West Lucas StreetFlorence SC 29501

National Program(s)211 ndash Water Availability and Water Management212 ndash Climate Change Soils and Emissions214 ndash Agricultural and Industrial Byproducts

CRIS Project(s)Managing Water Availability and Quality (NP 211)Improving Chemical Physical and Biological Properties of Degraded Sandy Soils (NP 212)Innovative Bioresource Management Technologies (NP 214)

Production Systems StudiedCrops Poultry and Swine

Laboratory and Field Expertisebull Classical Microbiology

bull DetectionEnumerationIsolationbull New species identification

bull Molecular Biologybull T‐RFLPARISAbull qPCRReal Time PCRbull High‐throughput DNA Sequencing

(Ion Torrent)

Research Interestsbull Southeastern US coastal plain wetland restoration

and its effect on microbial community composition and function

bull Animal wastewater treatment systems with a particular focus on pathogen reduction and antibiotic resistance gene elimination

bull Microbial community analysis and response to crop conservation and cover cropping management practices

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Ross C BeierResearch Chemist

RossBeierarsusdagov

979-260-9411

Current Projectsbull Conduct disinfectant susceptibility tests on 145

Salmonella strains from feed lot water‐sprinkled cattlebull Synthesize thymol‐‐D‐cellobioside for use in delivering

the antibacterial thymol to the lower swine gutbull Conduct disinfectant susceptibility tests on 134

Campylobacter coli and jejuni from swine cecal samples meat products and feces

Selected Publicationsbull Beier RC E Franz JL Bono RE Mandrell PM

Fratamico TR Callaway K Andrews TL Poole TL Crippen CL Sheffield RC Anderson and DJ Nisbet Disinfectant and antimicrobial susceptibility profiles of the big six non‐O157 Shiga toxin‐producing Escherichia coli from food animals and humans J Food Protect 2016 (In press)

bull Crippen TL CL Sheffield JA Byrd JF Esquivel RC Beier and K Yeater Poultry litter and the environment Physiochemical properties of litter and soil during successive flock rotations and after remote site deposition Sci Total Environ 553650661 2016

bull Beier RC SE Duke RL Ziprin RB Harvey ME Hume TL Poole HM Scott LD Highfield WQ Alali K Andrews RC Anderson and DJ Nisbet Antibiotic and disinfectant susceptibility profiles of vancomycin‐resistant Enterococcus faecium (VRE) isolated from community wastewater in Texas Bull Environ Contam Toxicol 80188194 2008

Food and Feed SafetyResearch Unit

Mailing AddressSouthern Plains AgriculturalResearch Center

Food and Feed SafetyResearch Unit

2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedFocus is on bacterial isolates in beef swine and poultry

Laboratory and Field Expertisebull Microbroth dilution

antimicrobial susceptibility testing

bull Microbroth dilution disinfectant susceptibility testing

bull PCRbull Gas Chromatographybull High‐Performance Liquid

Chromatographybull TLC HPTLCbull Chemical Synthesis

Research Interestsbull Establish a knowledge base for disinfectant susceptibility

in foodborne pathogensbull Identify disinfectant and antimicrobial co‐resistancebull Evaluate the impact of disinfectant resistance genes

Elaine BerryResearch Microbiologist

ElaineBerryarsusdagov

402-762-4204

Current Projectsbull Evaluate the influence of spatiotemporal environmental

and wildlife factors on pathogen and antibiotic resistance occurrence and transmission dynamics in cattle and waterways in a pasture‐based production system

bull Determine phenotypic and genotypic factors associated with persistence of E coli O157H7 in cattle production

bull Determine the effect of calcium hydroxide application to feedlot pens on E coli O157H7 total E coli and antibiotic resistance on feedlot pen surfaces and in cattle

Selected Publicationsbull Berry ED JE Wells JL Bono BL Woodbury N

Kalchayanand KN Norman TV Suslow G Lόpez‐Velasco and PD Millner Effect of proximity to a cattle feedlot on Escherichia coli O157H7 contamination of leafy greens and evaluation of the potential for airborne transmission Appl Environ Microbiol 811101‐1110 2015

bull Wells JE ED Berry N Kalchayanand LA Rempel M Kim and WT Oliver Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Assessment of Genotypic and Phenotypic Factors for Foodborne Pathogen Transmission and Development of Intervention Strategies

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Sampling and analyses for

bacterial pathogens in manures soils and other environmental and complex sample matrices

bull Treatment and intervention processes to reduce pathogens in cattle swine and their manure

Research Interestsbull Understanding and reducing the transmission and

persistence of zoonotic pathogens and antibiotic resistance in livestock and preharvest production environments

bull Reducing pathogen and antibiotic resistance transmission from animal production to produce water and the environment

Carl BolsterResearch Hydrologist

CarlBolsterarsusdagov

270-781-2632 ext 244

Current Projectsbull Evaluating effects of manure application rate and

timing on the leaching and runoff potential of antibiotic resistant bacteria and their associated genes as part of a National Pork Board funded project

bull Incorporating uncertainty estimates in model predictions of phosphorus loss from agricultural fields

bull Comparing predictions from annual and daily time‐step phosphorus transport models as part of a National Conservation Innovation Grant project

Selected Publicationsbull Abit SM Bolster CH Cantrell KB Flores JQ and SL

Walker 2014 Transport of Escherichia coli Salmonella typhimurium and microspheres in biochar‐amended soils with different textures J of Environ Qual 43371‐378

bull Bolster CH and Abit SM 2012 Biochar pyrolyzed at two temperatures impacts E coli transport through a sandy soil J of Environ Qual 41124‐133

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville RD ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Management

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental QualitySecond Title here if applicable

Production Systems StudiedPoultry and swine

Laboratory and Field Expertisebull Conducting laboratory‐scale

flow through experimentsbull Developing and using numerical

models for describing bacteria and solute fate and transport in the environment

bull Quantifying uncertainties in observed and modeled data

Research Interestsbull Understanding the factors controlling microbial

transport through biochar‐amended soilsbull Evaluating transport of antibiotic resistant bacteria

through soilsbull Improving modeling tools for describing fate and

transport of phosphorus in the environment

Brian BrunelleResearch Microbiologist

BrianBrunellearsusdagov

515-337-7612

Current Projectsbull Comparing transcriptional differences between

antibiotics that induce invasion in multidrug‐resistant Salmonella and those that have no effect

bull Genome sequencing of novel multidrug‐resistant Salmonella isolates

bull Assessing antibiotics that can enhance resistance in multidrug‐resistant Salmonella

Selected Publicationsbull Brunelle BW Bearson BL Bearson SMD 2015

Chloramphenicol and tetracycline decrease motility and increase invasion and attachment gene expression in specific isolates of multidrug‐resistant Salmonella entericaserovar Typhimurium Front Microbiol 5801

bull Brunelle BW Bearson SMD Bearson BL 2013 Tetracycline accelerates the temporally‐regulated invasion response in specific isolates of multidrug‐resistant Salmonella enterica serovar Typhimurium BMC Microbiology 13 202

Food Safety and Enteric Pathogen Research Unit

Mailing AddressNational Animal Disease Center1920 Dayton AvePO Box 70Ames IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Analysis of Virulence and Antibiotic Resistance Mechanisms of Salmonella and Development of Intervention Strategies

Production Systems StudiedSwine

Laboratory and Field Expertisebull Analysis of bacterial

transcription using real‐time PCR and RNA‐seq

bull Characterization of antibiotic resistance levels and associated genes

bull Conducting assays to measure different virulence phenotypes (cellular invasion motility etc)

Research Interestsbull Investigating the impact antibiotic usage has on

influencing multidrug‐resistant Salmonella virulence phenotypes

bull Identifying genes and regulation pathways associated with phenotypic differences in multidrug‐resistant Salmonella isolates exposed to antibiotics

John P BrooksResearch Microbiologist

JohnBrooksarsusdagov

662-320-7411

7

Current Projectsbull The effect of degraded antibiotic on soil microbial

ecology and antibacterial microbiomebull Aerosol carriage of antibiotic resistant genes and

bacteria from land application of poultry litterbull Antibiotic resistant bacteria and genes in naiumlve

broiler CAFOs

Selected Publicationsbull Brooks JP MR McLaughlin A Adeli DM Miles 2016

Cultivation and qPCR detection of pathogenic and antibiotic‐resistant bacterial establishment in naiumlve broiler houses J Environ Qual 45958‐966

bull Brooks JP Adeli A McLaughlin MR 2014 Microbial ecology bacterial pathogens and antibiotic resistant genes in swine manure as influenced by three swine management systems Water Res 5796‐103

bull Brooks JP McLaughlin MR Scheffler B and Miles DM 2010 Microbial and antibiotic resistant constituents associated with biological aerosols and poultry litter within a commercial poultry house Sci Tot Environ 4084770‐4777

Genetics and Sustainable Agriculture Research Unit

Mailing Address810 Highway 12 East PO Box 5367Mississippi State MS 39762

National Program(s)216 ndash Agricultural System Competitiveness and Sustainability

CRIS Project(s)Integration of Site‐Specific Crop Production Practices amp Industrial amp Animal Ag Byproducts to Improve Ag Competitiveness amp Sustainability

Production Systems StudiedSwine Poultry Forage amp Row Crop

Laboratory and Field Expertisebull Detection amp enumeration of

pathogens and antibacterial resistant genes and bacteria

bull Sampling soil water air amp CAFO environments

bull Quantitative microbial risk assessment of pathogens amp antibacterial resistant bacteria in the environment

Research Interestsbull Identify the movement and fate of pathogens and

antibacterial resistant genesbacteria through the environment and CAFO environments

bull Apply quantitative microbial risk assessment to anthropogenic impacted environments

bull Determine the impact of row crop agriculture on the soil microbial and antibacterial resistant biome

Tucker BurchResearch Agricultural

Engineer

TuckerBurcharsusdagov

715-387-3670

Current Projectsbull Occurrence and Distribution of Antibiotic Resistance

Genes (ARGs) in Groundwater of Kewaunee County Wisconsin

Selected Publicationsbull Burch TR Sadowsky MJ LaPara TM 2016 Modeling the

fate of antibiotic resistance genes and class 1 integronsduring thermophilic anaerobic digestion of municipal wastewater solids Appl Microbiol Biotechnol 100(3) 1437‐1444

bull Burch TR Sadowsky MJ LaPara TM 2014 Fate of antibiotic resistance genes and class 1 integrons in soil microcosms following the application of treated residual municipal wastewater solids Environ Sci Technol 48(10) 5620‐5627

bull Burch TR Sadowsky MJ LaPara TM 2013 Air‐drying beds reduce the quantities of antibiotic resistance genes and class 1 integrons in residual municipal wastewater solids Environ Sci Technol 47(17) 9965‐9971

bull Burch TR Sadowsky MJ LaPara TM 2013 Aerobic digestion reduces the quantity of antibiotic resistance genes in residual municipal wastewater solids Front Microbiol 4(Feb)

Dairy Forage Research CenterEnvironmentally Integrated Dairy Management Research Unit

Mailing Address2615 Yellowstone DriveMarshfield WI 54449

National Program(s)212 ndash Soil and Air

CRIS Project(s)Improving Nutrient Use Efficiency and Mitigating Nutrient and Pathogen Losses from Dairy Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull qPCRbull Bioaerosol samplingbull Quantitative microbial risk

assessment

Research Interestsbull Environmental distribution and transmission of

antibiotic resistance genes (ARGs)bull Quantitative microbial risk assessment

Todd CallawayResearch Microbiologist

ToddCallawayarsusdagov

979-260-9374 7

Current Projectsbull Effects of organic acids on the microbiome of food

animals and impact on foodborne pathogensbull Dietary impacts on foodborne pathogenic bacteria

and the microbial ecosystembull Phytochemicals and their ability to alter composition

of the gastrointestinal microbiome

Selected Publicationsbull Callaway T R T S Edrington and D J Nisbet 2014

Isolation of E coli O157H7 and Salmonella from migratory brown‐headed cowbirds (Molothrus ater) common grackles (Quiscalus quiscula) and cattle egrets (Bubulcus ibis) Foodborne Path Dis 11791‐794

bull Broadway P R J A Carroll J C Brooks J R Donaldson N C Burdick‐Sanchez T B Schmidt T R Brown and T R Callaway 2015 Salmonella transfer to the lymph nodes and synovial fluid of experimentally orally inoculated swine Agric Food Anal Bacteriol (In Press)

bull Grilli E F Foresti B Tugnoli M Fustini M G Zanoni P Pasquali T R Callaway A Piva and G L Alborali 2015 Microencapsulated sorbic acid and pure botanicals affect Salmonella Typhimurium shedding in pigs a close‐up look from weaning to slaughter in controlled and field conditions Foodborne Path Dis (In Press)

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedBeef Cattle Dairy Cattle Swine and Poultry

Laboratory and Field Expertisebull Microbial Physiologybull Microbial Ecologybull Continuous culturebull Mixed culture environmental

simulationsbull Environmental impacts on

survival of foodborne pathogenic bacteria

bull Animal model challengesbull Development of pre‐harvest

intervention strategiesbull Feedlot and dairy procedures

Research Interestsbull Understanding how the microbial ecosystem interacts

with foodborne pathogens at a functional nicheguild level

bull Developing non‐antibiotic methods of reducing foodborne pathogenic bacteria in the gut of food animals

Kimberly CookResearch Microbiologist

KimCookarsusdagov

270-781-2579 ext 232

Current Projectsbull Capture and identify mobile genetic elements

associated with bacteria in soils with applied poultry litter effect of application method

bull Evaluate persistence and concentration of antibiotics and bacteria with AR genes in waste treatment systems and soils with application manures

bull Transport and adhesion of bacteria with AR genesbull Evaluate AR properties of E coli and enterococci

isolates from agricultural ecosystems

Selected Publicationsbull Durso LM and KL Cook 2014 Impacts of antibiotic

use in agriculture what are the benefits and risks CurrOpinion Microbiol 1937‐44 2014

bull Cook KL AMP Netthisinghe and RA Gilfillen 2014 Detection of Pathogens Indicators and Antibiotic Resistance Genes after Land Application of Poultry Litter J Environ Qual 43 1546‐1558

bull Netthisinghe AMP KL Cook C Rice RA Gilfillen and KR Sistani 2013 Soil Nutrients Bacteria Populations and Veterinary Pharmaceuticals across a Backgrounding Beef Feedlot J Environ Qual 42 532‐544

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville Red ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Research

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental Quality

Production Systems StudiedPoultry Swine Beef

Laboratory and Field Expertisebull Soils manure and waste

treatment systemsbull PCR Quantitiative real‐time

PCRbull Culture and antimicrobial

susceptibilitybull Isolation and characterization of

mobile genetic elements carrying genes for antibiotic resistance

Research Interestsbull Characterizing persistence and transmission of

antibiotics antibiotic resistance (AR) genes and AR bacteria through agroecosystems

bull Capture and characterize mobile genetic elements carrying AR genes between microbial populations in soils with applied manures

bull Strain level differences in resistance transport and adhesion properties of bacteria with AR genes

Annie DonoghueResearch Leader (Physiologist)

AnnieDonoghuearsusdagov479-575-2413

7

Current Projectsbull Use of natural remedies to alleviate enteric

pathogens in organic and conventionally raised poultry

bull Alternatives to antibiotics for controlling Salmonella and Campylobacter in poultry and poultry products

Selected Publicationsbull Donoghue AM Venkitanarayanan K Arsi K Woo‐

Ming A Upadhyaya I Kollanoor‐Johny A Darre MJ Upadhyay A Fanatico A and Donoghue DJ 2015 Organic Poultry Developing Natural Solutions for Reducing Pathogens and Improving Production Organic Agriculture Research Symp in press

bull Arsi K Donoghue AM Woo‐Ming A Blore PJ and Donoghue DJ 2015 Intracloacal inoculation an effective screening method for determining the efficacy of probiotic bacterial isolates against Campylobactercolonization in broiler chickens J Food Prot 78 209‐213

bull Arsi K Donoghue AM Venkitanarayanan K Kollanoor‐Johny A Fanatico AC Blore PJ and Donoghue DJ2014 The efficacy of the natural plant extracts thymol and carvacrol against Campylobacter colonization in broiler chickens J Food Safety 34 321ndash325

Poultry Production and Products Safety Research Unit

Mailing AddressUniversity Of ArkansasPOSC O‐303Fayetteville AR 72701

National Program(s)108 ndash Food Safety103 ndash Animal Health

CRIS Project(s)Alternative Intervention and Control Strategies for Foodborne Pathogens in Poultry and Poultry Products

Novel Therapeutic Diagnostic and Management Strategies to Reduce Antibiotic Use in Poultry Production

Production Systems StudiedPoultry

Laboratory and Field ExpertiseLab uses traditional microbiological culture and molecular biological techniques to study food borne pathogens Organic and conventional practices for poultry production

Research Interestsbull developing alternatives to antibiotic use in poultry bull developing strategies to reduce or eliminate pathogen

contamination with a focus on Campylobacter and Salmonella

bull developing sustainable and organic farming practices for poultry producers

David DonavanResearch Molecular Biologist

DavidDonovanarsusdagov

Ce 443-690-4251 Office 301-504-9150

Current Projectsbull Mastitis a cow‐side diagnosticbull Mastitis treatment with triple‐acting antimicrobialsbull Clostridium perfringens novel endolysins that are heat‐resistantbull Yeast expressed endolysins as an alternative to antibiotics in animal feedbull CRISPRCas9 genomic engineering of cow and pig embryos

Selected Publicationsbull Rodriacuteguez‐Rubio L Martiacutenez B Rodriacuteguez A Donovan DM Goumltz F et al The

phage lytic proteins from the Staphylococcus aureus bacteriophage vB_SauS‐phiIPLA88 display multiple active catalytic domains and do not trigger staphylococcal resistance PloS one 2013 8(5)e64671

bull Singh PK Donovan DM Kumar A Intravitreal injection of the chimeric phage endolysin Ply187 protects mice from Staphylococcus aureus endophthalmitis Antimicrobial agents and chemotherapy 2014 58(8)4621‐9

bull Swift SM Seal BS Garrish JK Oakley BB Hiett K et al A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens‐Specific Cell Wall Binding Domain Creates an Anti‐Clostridium Antimicrobial with Improved Thermostability Viruses 2015 7(6)3019‐34

Link to all publications httpwwwncbinlmnihgovsitesmyncbi1jOJlsCcVSxQTbibliography41565643publicsort=dateampdirection=ascending

Animal Biosciences and Biotechnology Laboratory

Mailing AddressRoom 104 10300 Baltimore AveBLDG 230 BARC‐EastBeltsville MD 20705

National ProgramNP101 Food Animal Production

CRIS Project TitleDeveloping Genetic Biotechnologies for Increased Food Animal Production including Novel Antimicrobials for Improved Health and Product Safety

Production Systems StudiedDairy cattle Swine poultry Aquaculture

Laboratory and Field Expertisebull Molecular biologist with

transgenic and knockout mouse background

bull Heterologous gene expression in yeast bacteria mice and cell culture

bull Induced Pluripotent Stem cell production via lentiviral transduction

bull Mouse colony animal husbandry and embryo transfer

Research InterestsDavid M Donovan PhD Research Scientist (Molecular Biologist) at the US Department of Agriculture received his PhD in 1987 in molecular genetics of the yeast Saccharomyces cerevisiae and has 22 years experience in heterologous gene expression He spent 15 years at the NIH culminating in Section Chief Transgenic and Knockout Mouse lab NIA In 2002 he joined the USDA where he has been developing antimicrobials for the treatment of mastitis pathogens including Staphylococcus aureus His enzyme antimicrobials harbor three unique synergistic lytic domains and a protein transduction domain to target intracellular pathogens and have been shown to be highly refractory to resistance development His constructs eradicate both extracellular S aureus [in a rat nasal colonization model and murine systemic infections] and intracellular pathogens ex vivo in bovine mammary epithelial cells and in both a mouse model of mastitis and osteomyelitis He is working to identify protein feed additives as alternative to antibiotic growth promotants

Thomas F DuceyMicrobiologist

ThomasDuceyarsusdagov

843-669-5203 x112

Current Projectsbull Microbial responses to wetland restoration as a part

of the Mid‐Atlantic Region Conservation Effects Assessment Project

bull Response of the microbial rhizosphere and arbuscular mycorrhizae fungi to clover cover crop and conservation tillage in cotton production

bull Isolation of E coli and Enterococcus species from swine wastewater poultry litter and agriculturally‐impacted groundwater for the determination of baseline antibiotic resistance levels in agricultural production systems

Selected Publicationsbull Ducey et al Soil physicochemical conditions

denitrification rates and nosZ abundance in NC coastal plain restored wetlands 2015 J Environ Qual 44 1011‐1022

bull Ducey et al Microbial community analysis of swine wastewater anaerobic lagoons by next‐generation DNA sequencing 2013 Anaerobe 2150‐57

Coastal Plain Soil Water and Plant Research Center

Mailing Address2611 West Lucas StreetFlorence SC 29501

National Program(s)211 ndash Water Availability and Water Management212 ndash Climate Change Soils and Emissions214 ndash Agricultural and Industrial Byproducts

CRIS Project(s)Managing Water Availability and Quality (NP 211)Improving Chemical Physical and Biological Properties of Degraded Sandy Soils (NP 212)Innovative Bioresource Management Technologies (NP 214)

Production Systems StudiedCrops Poultry and Swine

Laboratory and Field Expertisebull Classical Microbiology

bull DetectionEnumerationIsolationbull New species identification

bull Molecular Biologybull T‐RFLPARISAbull qPCRReal Time PCRbull High‐throughput DNA Sequencing

(Ion Torrent)

Research Interestsbull Southeastern US coastal plain wetland restoration

and its effect on microbial community composition and function

bull Animal wastewater treatment systems with a particular focus on pathogen reduction and antibiotic resistance gene elimination

bull Microbial community analysis and response to crop conservation and cover cropping management practices

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Elaine BerryResearch Microbiologist

ElaineBerryarsusdagov

402-762-4204

Current Projectsbull Evaluate the influence of spatiotemporal environmental

and wildlife factors on pathogen and antibiotic resistance occurrence and transmission dynamics in cattle and waterways in a pasture‐based production system

bull Determine phenotypic and genotypic factors associated with persistence of E coli O157H7 in cattle production

bull Determine the effect of calcium hydroxide application to feedlot pens on E coli O157H7 total E coli and antibiotic resistance on feedlot pen surfaces and in cattle

Selected Publicationsbull Berry ED JE Wells JL Bono BL Woodbury N

Kalchayanand KN Norman TV Suslow G Lόpez‐Velasco and PD Millner Effect of proximity to a cattle feedlot on Escherichia coli O157H7 contamination of leafy greens and evaluation of the potential for airborne transmission Appl Environ Microbiol 811101‐1110 2015

bull Wells JE ED Berry N Kalchayanand LA Rempel M Kim and WT Oliver Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Assessment of Genotypic and Phenotypic Factors for Foodborne Pathogen Transmission and Development of Intervention Strategies

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Sampling and analyses for

bacterial pathogens in manures soils and other environmental and complex sample matrices

bull Treatment and intervention processes to reduce pathogens in cattle swine and their manure

Research Interestsbull Understanding and reducing the transmission and

persistence of zoonotic pathogens and antibiotic resistance in livestock and preharvest production environments

bull Reducing pathogen and antibiotic resistance transmission from animal production to produce water and the environment

Carl BolsterResearch Hydrologist

CarlBolsterarsusdagov

270-781-2632 ext 244

Current Projectsbull Evaluating effects of manure application rate and

timing on the leaching and runoff potential of antibiotic resistant bacteria and their associated genes as part of a National Pork Board funded project

bull Incorporating uncertainty estimates in model predictions of phosphorus loss from agricultural fields

bull Comparing predictions from annual and daily time‐step phosphorus transport models as part of a National Conservation Innovation Grant project

Selected Publicationsbull Abit SM Bolster CH Cantrell KB Flores JQ and SL

Walker 2014 Transport of Escherichia coli Salmonella typhimurium and microspheres in biochar‐amended soils with different textures J of Environ Qual 43371‐378

bull Bolster CH and Abit SM 2012 Biochar pyrolyzed at two temperatures impacts E coli transport through a sandy soil J of Environ Qual 41124‐133

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville RD ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Management

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental QualitySecond Title here if applicable

Production Systems StudiedPoultry and swine

Laboratory and Field Expertisebull Conducting laboratory‐scale

flow through experimentsbull Developing and using numerical

models for describing bacteria and solute fate and transport in the environment

bull Quantifying uncertainties in observed and modeled data

Research Interestsbull Understanding the factors controlling microbial

transport through biochar‐amended soilsbull Evaluating transport of antibiotic resistant bacteria

through soilsbull Improving modeling tools for describing fate and

transport of phosphorus in the environment

Brian BrunelleResearch Microbiologist

BrianBrunellearsusdagov

515-337-7612

Current Projectsbull Comparing transcriptional differences between

antibiotics that induce invasion in multidrug‐resistant Salmonella and those that have no effect

bull Genome sequencing of novel multidrug‐resistant Salmonella isolates

bull Assessing antibiotics that can enhance resistance in multidrug‐resistant Salmonella

Selected Publicationsbull Brunelle BW Bearson BL Bearson SMD 2015

Chloramphenicol and tetracycline decrease motility and increase invasion and attachment gene expression in specific isolates of multidrug‐resistant Salmonella entericaserovar Typhimurium Front Microbiol 5801

bull Brunelle BW Bearson SMD Bearson BL 2013 Tetracycline accelerates the temporally‐regulated invasion response in specific isolates of multidrug‐resistant Salmonella enterica serovar Typhimurium BMC Microbiology 13 202

Food Safety and Enteric Pathogen Research Unit

Mailing AddressNational Animal Disease Center1920 Dayton AvePO Box 70Ames IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Analysis of Virulence and Antibiotic Resistance Mechanisms of Salmonella and Development of Intervention Strategies

Production Systems StudiedSwine

Laboratory and Field Expertisebull Analysis of bacterial

transcription using real‐time PCR and RNA‐seq

bull Characterization of antibiotic resistance levels and associated genes

bull Conducting assays to measure different virulence phenotypes (cellular invasion motility etc)

Research Interestsbull Investigating the impact antibiotic usage has on

influencing multidrug‐resistant Salmonella virulence phenotypes

bull Identifying genes and regulation pathways associated with phenotypic differences in multidrug‐resistant Salmonella isolates exposed to antibiotics

John P BrooksResearch Microbiologist

JohnBrooksarsusdagov

662-320-7411

7

Current Projectsbull The effect of degraded antibiotic on soil microbial

ecology and antibacterial microbiomebull Aerosol carriage of antibiotic resistant genes and

bacteria from land application of poultry litterbull Antibiotic resistant bacteria and genes in naiumlve

broiler CAFOs

Selected Publicationsbull Brooks JP MR McLaughlin A Adeli DM Miles 2016

Cultivation and qPCR detection of pathogenic and antibiotic‐resistant bacterial establishment in naiumlve broiler houses J Environ Qual 45958‐966

bull Brooks JP Adeli A McLaughlin MR 2014 Microbial ecology bacterial pathogens and antibiotic resistant genes in swine manure as influenced by three swine management systems Water Res 5796‐103

bull Brooks JP McLaughlin MR Scheffler B and Miles DM 2010 Microbial and antibiotic resistant constituents associated with biological aerosols and poultry litter within a commercial poultry house Sci Tot Environ 4084770‐4777

Genetics and Sustainable Agriculture Research Unit

Mailing Address810 Highway 12 East PO Box 5367Mississippi State MS 39762

National Program(s)216 ndash Agricultural System Competitiveness and Sustainability

CRIS Project(s)Integration of Site‐Specific Crop Production Practices amp Industrial amp Animal Ag Byproducts to Improve Ag Competitiveness amp Sustainability

Production Systems StudiedSwine Poultry Forage amp Row Crop

Laboratory and Field Expertisebull Detection amp enumeration of

pathogens and antibacterial resistant genes and bacteria

bull Sampling soil water air amp CAFO environments

bull Quantitative microbial risk assessment of pathogens amp antibacterial resistant bacteria in the environment

Research Interestsbull Identify the movement and fate of pathogens and

antibacterial resistant genesbacteria through the environment and CAFO environments

bull Apply quantitative microbial risk assessment to anthropogenic impacted environments

bull Determine the impact of row crop agriculture on the soil microbial and antibacterial resistant biome

Tucker BurchResearch Agricultural

Engineer

TuckerBurcharsusdagov

715-387-3670

Current Projectsbull Occurrence and Distribution of Antibiotic Resistance

Genes (ARGs) in Groundwater of Kewaunee County Wisconsin

Selected Publicationsbull Burch TR Sadowsky MJ LaPara TM 2016 Modeling the

fate of antibiotic resistance genes and class 1 integronsduring thermophilic anaerobic digestion of municipal wastewater solids Appl Microbiol Biotechnol 100(3) 1437‐1444

bull Burch TR Sadowsky MJ LaPara TM 2014 Fate of antibiotic resistance genes and class 1 integrons in soil microcosms following the application of treated residual municipal wastewater solids Environ Sci Technol 48(10) 5620‐5627

bull Burch TR Sadowsky MJ LaPara TM 2013 Air‐drying beds reduce the quantities of antibiotic resistance genes and class 1 integrons in residual municipal wastewater solids Environ Sci Technol 47(17) 9965‐9971

bull Burch TR Sadowsky MJ LaPara TM 2013 Aerobic digestion reduces the quantity of antibiotic resistance genes in residual municipal wastewater solids Front Microbiol 4(Feb)

Dairy Forage Research CenterEnvironmentally Integrated Dairy Management Research Unit

Mailing Address2615 Yellowstone DriveMarshfield WI 54449

National Program(s)212 ndash Soil and Air

CRIS Project(s)Improving Nutrient Use Efficiency and Mitigating Nutrient and Pathogen Losses from Dairy Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull qPCRbull Bioaerosol samplingbull Quantitative microbial risk

assessment

Research Interestsbull Environmental distribution and transmission of

antibiotic resistance genes (ARGs)bull Quantitative microbial risk assessment

Todd CallawayResearch Microbiologist

ToddCallawayarsusdagov

979-260-9374 7

Current Projectsbull Effects of organic acids on the microbiome of food

animals and impact on foodborne pathogensbull Dietary impacts on foodborne pathogenic bacteria

and the microbial ecosystembull Phytochemicals and their ability to alter composition

of the gastrointestinal microbiome

Selected Publicationsbull Callaway T R T S Edrington and D J Nisbet 2014

Isolation of E coli O157H7 and Salmonella from migratory brown‐headed cowbirds (Molothrus ater) common grackles (Quiscalus quiscula) and cattle egrets (Bubulcus ibis) Foodborne Path Dis 11791‐794

bull Broadway P R J A Carroll J C Brooks J R Donaldson N C Burdick‐Sanchez T B Schmidt T R Brown and T R Callaway 2015 Salmonella transfer to the lymph nodes and synovial fluid of experimentally orally inoculated swine Agric Food Anal Bacteriol (In Press)

bull Grilli E F Foresti B Tugnoli M Fustini M G Zanoni P Pasquali T R Callaway A Piva and G L Alborali 2015 Microencapsulated sorbic acid and pure botanicals affect Salmonella Typhimurium shedding in pigs a close‐up look from weaning to slaughter in controlled and field conditions Foodborne Path Dis (In Press)

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedBeef Cattle Dairy Cattle Swine and Poultry

Laboratory and Field Expertisebull Microbial Physiologybull Microbial Ecologybull Continuous culturebull Mixed culture environmental

simulationsbull Environmental impacts on

survival of foodborne pathogenic bacteria

bull Animal model challengesbull Development of pre‐harvest

intervention strategiesbull Feedlot and dairy procedures

Research Interestsbull Understanding how the microbial ecosystem interacts

with foodborne pathogens at a functional nicheguild level

bull Developing non‐antibiotic methods of reducing foodborne pathogenic bacteria in the gut of food animals

Kimberly CookResearch Microbiologist

KimCookarsusdagov

270-781-2579 ext 232

Current Projectsbull Capture and identify mobile genetic elements

associated with bacteria in soils with applied poultry litter effect of application method

bull Evaluate persistence and concentration of antibiotics and bacteria with AR genes in waste treatment systems and soils with application manures

bull Transport and adhesion of bacteria with AR genesbull Evaluate AR properties of E coli and enterococci

isolates from agricultural ecosystems

Selected Publicationsbull Durso LM and KL Cook 2014 Impacts of antibiotic

use in agriculture what are the benefits and risks CurrOpinion Microbiol 1937‐44 2014

bull Cook KL AMP Netthisinghe and RA Gilfillen 2014 Detection of Pathogens Indicators and Antibiotic Resistance Genes after Land Application of Poultry Litter J Environ Qual 43 1546‐1558

bull Netthisinghe AMP KL Cook C Rice RA Gilfillen and KR Sistani 2013 Soil Nutrients Bacteria Populations and Veterinary Pharmaceuticals across a Backgrounding Beef Feedlot J Environ Qual 42 532‐544

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville Red ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Research

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental Quality

Production Systems StudiedPoultry Swine Beef

Laboratory and Field Expertisebull Soils manure and waste

treatment systemsbull PCR Quantitiative real‐time

PCRbull Culture and antimicrobial

susceptibilitybull Isolation and characterization of

mobile genetic elements carrying genes for antibiotic resistance

Research Interestsbull Characterizing persistence and transmission of

antibiotics antibiotic resistance (AR) genes and AR bacteria through agroecosystems

bull Capture and characterize mobile genetic elements carrying AR genes between microbial populations in soils with applied manures

bull Strain level differences in resistance transport and adhesion properties of bacteria with AR genes

Annie DonoghueResearch Leader (Physiologist)

AnnieDonoghuearsusdagov479-575-2413

7

Current Projectsbull Use of natural remedies to alleviate enteric

pathogens in organic and conventionally raised poultry

bull Alternatives to antibiotics for controlling Salmonella and Campylobacter in poultry and poultry products

Selected Publicationsbull Donoghue AM Venkitanarayanan K Arsi K Woo‐

Ming A Upadhyaya I Kollanoor‐Johny A Darre MJ Upadhyay A Fanatico A and Donoghue DJ 2015 Organic Poultry Developing Natural Solutions for Reducing Pathogens and Improving Production Organic Agriculture Research Symp in press

bull Arsi K Donoghue AM Woo‐Ming A Blore PJ and Donoghue DJ 2015 Intracloacal inoculation an effective screening method for determining the efficacy of probiotic bacterial isolates against Campylobactercolonization in broiler chickens J Food Prot 78 209‐213

bull Arsi K Donoghue AM Venkitanarayanan K Kollanoor‐Johny A Fanatico AC Blore PJ and Donoghue DJ2014 The efficacy of the natural plant extracts thymol and carvacrol against Campylobacter colonization in broiler chickens J Food Safety 34 321ndash325

Poultry Production and Products Safety Research Unit

Mailing AddressUniversity Of ArkansasPOSC O‐303Fayetteville AR 72701

National Program(s)108 ndash Food Safety103 ndash Animal Health

CRIS Project(s)Alternative Intervention and Control Strategies for Foodborne Pathogens in Poultry and Poultry Products

Novel Therapeutic Diagnostic and Management Strategies to Reduce Antibiotic Use in Poultry Production

Production Systems StudiedPoultry

Laboratory and Field ExpertiseLab uses traditional microbiological culture and molecular biological techniques to study food borne pathogens Organic and conventional practices for poultry production

Research Interestsbull developing alternatives to antibiotic use in poultry bull developing strategies to reduce or eliminate pathogen

contamination with a focus on Campylobacter and Salmonella

bull developing sustainable and organic farming practices for poultry producers

David DonavanResearch Molecular Biologist

DavidDonovanarsusdagov

Ce 443-690-4251 Office 301-504-9150

Current Projectsbull Mastitis a cow‐side diagnosticbull Mastitis treatment with triple‐acting antimicrobialsbull Clostridium perfringens novel endolysins that are heat‐resistantbull Yeast expressed endolysins as an alternative to antibiotics in animal feedbull CRISPRCas9 genomic engineering of cow and pig embryos

Selected Publicationsbull Rodriacuteguez‐Rubio L Martiacutenez B Rodriacuteguez A Donovan DM Goumltz F et al The

phage lytic proteins from the Staphylococcus aureus bacteriophage vB_SauS‐phiIPLA88 display multiple active catalytic domains and do not trigger staphylococcal resistance PloS one 2013 8(5)e64671

bull Singh PK Donovan DM Kumar A Intravitreal injection of the chimeric phage endolysin Ply187 protects mice from Staphylococcus aureus endophthalmitis Antimicrobial agents and chemotherapy 2014 58(8)4621‐9

bull Swift SM Seal BS Garrish JK Oakley BB Hiett K et al A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens‐Specific Cell Wall Binding Domain Creates an Anti‐Clostridium Antimicrobial with Improved Thermostability Viruses 2015 7(6)3019‐34

Link to all publications httpwwwncbinlmnihgovsitesmyncbi1jOJlsCcVSxQTbibliography41565643publicsort=dateampdirection=ascending

Animal Biosciences and Biotechnology Laboratory

Mailing AddressRoom 104 10300 Baltimore AveBLDG 230 BARC‐EastBeltsville MD 20705

National ProgramNP101 Food Animal Production

CRIS Project TitleDeveloping Genetic Biotechnologies for Increased Food Animal Production including Novel Antimicrobials for Improved Health and Product Safety

Production Systems StudiedDairy cattle Swine poultry Aquaculture

Laboratory and Field Expertisebull Molecular biologist with

transgenic and knockout mouse background

bull Heterologous gene expression in yeast bacteria mice and cell culture

bull Induced Pluripotent Stem cell production via lentiviral transduction

bull Mouse colony animal husbandry and embryo transfer

Research InterestsDavid M Donovan PhD Research Scientist (Molecular Biologist) at the US Department of Agriculture received his PhD in 1987 in molecular genetics of the yeast Saccharomyces cerevisiae and has 22 years experience in heterologous gene expression He spent 15 years at the NIH culminating in Section Chief Transgenic and Knockout Mouse lab NIA In 2002 he joined the USDA where he has been developing antimicrobials for the treatment of mastitis pathogens including Staphylococcus aureus His enzyme antimicrobials harbor three unique synergistic lytic domains and a protein transduction domain to target intracellular pathogens and have been shown to be highly refractory to resistance development His constructs eradicate both extracellular S aureus [in a rat nasal colonization model and murine systemic infections] and intracellular pathogens ex vivo in bovine mammary epithelial cells and in both a mouse model of mastitis and osteomyelitis He is working to identify protein feed additives as alternative to antibiotic growth promotants

Thomas F DuceyMicrobiologist

ThomasDuceyarsusdagov

843-669-5203 x112

Current Projectsbull Microbial responses to wetland restoration as a part

of the Mid‐Atlantic Region Conservation Effects Assessment Project

bull Response of the microbial rhizosphere and arbuscular mycorrhizae fungi to clover cover crop and conservation tillage in cotton production

bull Isolation of E coli and Enterococcus species from swine wastewater poultry litter and agriculturally‐impacted groundwater for the determination of baseline antibiotic resistance levels in agricultural production systems

Selected Publicationsbull Ducey et al Soil physicochemical conditions

denitrification rates and nosZ abundance in NC coastal plain restored wetlands 2015 J Environ Qual 44 1011‐1022

bull Ducey et al Microbial community analysis of swine wastewater anaerobic lagoons by next‐generation DNA sequencing 2013 Anaerobe 2150‐57

Coastal Plain Soil Water and Plant Research Center

Mailing Address2611 West Lucas StreetFlorence SC 29501

National Program(s)211 ndash Water Availability and Water Management212 ndash Climate Change Soils and Emissions214 ndash Agricultural and Industrial Byproducts

CRIS Project(s)Managing Water Availability and Quality (NP 211)Improving Chemical Physical and Biological Properties of Degraded Sandy Soils (NP 212)Innovative Bioresource Management Technologies (NP 214)

Production Systems StudiedCrops Poultry and Swine

Laboratory and Field Expertisebull Classical Microbiology

bull DetectionEnumerationIsolationbull New species identification

bull Molecular Biologybull T‐RFLPARISAbull qPCRReal Time PCRbull High‐throughput DNA Sequencing

(Ion Torrent)

Research Interestsbull Southeastern US coastal plain wetland restoration

and its effect on microbial community composition and function

bull Animal wastewater treatment systems with a particular focus on pathogen reduction and antibiotic resistance gene elimination

bull Microbial community analysis and response to crop conservation and cover cropping management practices

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Carl BolsterResearch Hydrologist

CarlBolsterarsusdagov

270-781-2632 ext 244

Current Projectsbull Evaluating effects of manure application rate and

timing on the leaching and runoff potential of antibiotic resistant bacteria and their associated genes as part of a National Pork Board funded project

bull Incorporating uncertainty estimates in model predictions of phosphorus loss from agricultural fields

bull Comparing predictions from annual and daily time‐step phosphorus transport models as part of a National Conservation Innovation Grant project

Selected Publicationsbull Abit SM Bolster CH Cantrell KB Flores JQ and SL

Walker 2014 Transport of Escherichia coli Salmonella typhimurium and microspheres in biochar‐amended soils with different textures J of Environ Qual 43371‐378

bull Bolster CH and Abit SM 2012 Biochar pyrolyzed at two temperatures impacts E coli transport through a sandy soil J of Environ Qual 41124‐133

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville RD ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Management

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental QualitySecond Title here if applicable

Production Systems StudiedPoultry and swine

Laboratory and Field Expertisebull Conducting laboratory‐scale

flow through experimentsbull Developing and using numerical

models for describing bacteria and solute fate and transport in the environment

bull Quantifying uncertainties in observed and modeled data

Research Interestsbull Understanding the factors controlling microbial

transport through biochar‐amended soilsbull Evaluating transport of antibiotic resistant bacteria

through soilsbull Improving modeling tools for describing fate and

transport of phosphorus in the environment

Brian BrunelleResearch Microbiologist

BrianBrunellearsusdagov

515-337-7612

Current Projectsbull Comparing transcriptional differences between

antibiotics that induce invasion in multidrug‐resistant Salmonella and those that have no effect

bull Genome sequencing of novel multidrug‐resistant Salmonella isolates

bull Assessing antibiotics that can enhance resistance in multidrug‐resistant Salmonella

Selected Publicationsbull Brunelle BW Bearson BL Bearson SMD 2015

Chloramphenicol and tetracycline decrease motility and increase invasion and attachment gene expression in specific isolates of multidrug‐resistant Salmonella entericaserovar Typhimurium Front Microbiol 5801

bull Brunelle BW Bearson SMD Bearson BL 2013 Tetracycline accelerates the temporally‐regulated invasion response in specific isolates of multidrug‐resistant Salmonella enterica serovar Typhimurium BMC Microbiology 13 202

Food Safety and Enteric Pathogen Research Unit

Mailing AddressNational Animal Disease Center1920 Dayton AvePO Box 70Ames IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Analysis of Virulence and Antibiotic Resistance Mechanisms of Salmonella and Development of Intervention Strategies

Production Systems StudiedSwine

Laboratory and Field Expertisebull Analysis of bacterial

transcription using real‐time PCR and RNA‐seq

bull Characterization of antibiotic resistance levels and associated genes

bull Conducting assays to measure different virulence phenotypes (cellular invasion motility etc)

Research Interestsbull Investigating the impact antibiotic usage has on

influencing multidrug‐resistant Salmonella virulence phenotypes

bull Identifying genes and regulation pathways associated with phenotypic differences in multidrug‐resistant Salmonella isolates exposed to antibiotics

John P BrooksResearch Microbiologist

JohnBrooksarsusdagov

662-320-7411

7

Current Projectsbull The effect of degraded antibiotic on soil microbial

ecology and antibacterial microbiomebull Aerosol carriage of antibiotic resistant genes and

bacteria from land application of poultry litterbull Antibiotic resistant bacteria and genes in naiumlve

broiler CAFOs

Selected Publicationsbull Brooks JP MR McLaughlin A Adeli DM Miles 2016

Cultivation and qPCR detection of pathogenic and antibiotic‐resistant bacterial establishment in naiumlve broiler houses J Environ Qual 45958‐966

bull Brooks JP Adeli A McLaughlin MR 2014 Microbial ecology bacterial pathogens and antibiotic resistant genes in swine manure as influenced by three swine management systems Water Res 5796‐103

bull Brooks JP McLaughlin MR Scheffler B and Miles DM 2010 Microbial and antibiotic resistant constituents associated with biological aerosols and poultry litter within a commercial poultry house Sci Tot Environ 4084770‐4777

Genetics and Sustainable Agriculture Research Unit

Mailing Address810 Highway 12 East PO Box 5367Mississippi State MS 39762

National Program(s)216 ndash Agricultural System Competitiveness and Sustainability

CRIS Project(s)Integration of Site‐Specific Crop Production Practices amp Industrial amp Animal Ag Byproducts to Improve Ag Competitiveness amp Sustainability

Production Systems StudiedSwine Poultry Forage amp Row Crop

Laboratory and Field Expertisebull Detection amp enumeration of

pathogens and antibacterial resistant genes and bacteria

bull Sampling soil water air amp CAFO environments

bull Quantitative microbial risk assessment of pathogens amp antibacterial resistant bacteria in the environment

Research Interestsbull Identify the movement and fate of pathogens and

antibacterial resistant genesbacteria through the environment and CAFO environments

bull Apply quantitative microbial risk assessment to anthropogenic impacted environments

bull Determine the impact of row crop agriculture on the soil microbial and antibacterial resistant biome

Tucker BurchResearch Agricultural

Engineer

TuckerBurcharsusdagov

715-387-3670

Current Projectsbull Occurrence and Distribution of Antibiotic Resistance

Genes (ARGs) in Groundwater of Kewaunee County Wisconsin

Selected Publicationsbull Burch TR Sadowsky MJ LaPara TM 2016 Modeling the

fate of antibiotic resistance genes and class 1 integronsduring thermophilic anaerobic digestion of municipal wastewater solids Appl Microbiol Biotechnol 100(3) 1437‐1444

bull Burch TR Sadowsky MJ LaPara TM 2014 Fate of antibiotic resistance genes and class 1 integrons in soil microcosms following the application of treated residual municipal wastewater solids Environ Sci Technol 48(10) 5620‐5627

bull Burch TR Sadowsky MJ LaPara TM 2013 Air‐drying beds reduce the quantities of antibiotic resistance genes and class 1 integrons in residual municipal wastewater solids Environ Sci Technol 47(17) 9965‐9971

bull Burch TR Sadowsky MJ LaPara TM 2013 Aerobic digestion reduces the quantity of antibiotic resistance genes in residual municipal wastewater solids Front Microbiol 4(Feb)

Dairy Forage Research CenterEnvironmentally Integrated Dairy Management Research Unit

Mailing Address2615 Yellowstone DriveMarshfield WI 54449

National Program(s)212 ndash Soil and Air

CRIS Project(s)Improving Nutrient Use Efficiency and Mitigating Nutrient and Pathogen Losses from Dairy Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull qPCRbull Bioaerosol samplingbull Quantitative microbial risk

assessment

Research Interestsbull Environmental distribution and transmission of

antibiotic resistance genes (ARGs)bull Quantitative microbial risk assessment

Todd CallawayResearch Microbiologist

ToddCallawayarsusdagov

979-260-9374 7

Current Projectsbull Effects of organic acids on the microbiome of food

animals and impact on foodborne pathogensbull Dietary impacts on foodborne pathogenic bacteria

and the microbial ecosystembull Phytochemicals and their ability to alter composition

of the gastrointestinal microbiome

Selected Publicationsbull Callaway T R T S Edrington and D J Nisbet 2014

Isolation of E coli O157H7 and Salmonella from migratory brown‐headed cowbirds (Molothrus ater) common grackles (Quiscalus quiscula) and cattle egrets (Bubulcus ibis) Foodborne Path Dis 11791‐794

bull Broadway P R J A Carroll J C Brooks J R Donaldson N C Burdick‐Sanchez T B Schmidt T R Brown and T R Callaway 2015 Salmonella transfer to the lymph nodes and synovial fluid of experimentally orally inoculated swine Agric Food Anal Bacteriol (In Press)

bull Grilli E F Foresti B Tugnoli M Fustini M G Zanoni P Pasquali T R Callaway A Piva and G L Alborali 2015 Microencapsulated sorbic acid and pure botanicals affect Salmonella Typhimurium shedding in pigs a close‐up look from weaning to slaughter in controlled and field conditions Foodborne Path Dis (In Press)

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedBeef Cattle Dairy Cattle Swine and Poultry

Laboratory and Field Expertisebull Microbial Physiologybull Microbial Ecologybull Continuous culturebull Mixed culture environmental

simulationsbull Environmental impacts on

survival of foodborne pathogenic bacteria

bull Animal model challengesbull Development of pre‐harvest

intervention strategiesbull Feedlot and dairy procedures

Research Interestsbull Understanding how the microbial ecosystem interacts

with foodborne pathogens at a functional nicheguild level

bull Developing non‐antibiotic methods of reducing foodborne pathogenic bacteria in the gut of food animals

Kimberly CookResearch Microbiologist

KimCookarsusdagov

270-781-2579 ext 232

Current Projectsbull Capture and identify mobile genetic elements

associated with bacteria in soils with applied poultry litter effect of application method

bull Evaluate persistence and concentration of antibiotics and bacteria with AR genes in waste treatment systems and soils with application manures

bull Transport and adhesion of bacteria with AR genesbull Evaluate AR properties of E coli and enterococci

isolates from agricultural ecosystems

Selected Publicationsbull Durso LM and KL Cook 2014 Impacts of antibiotic

use in agriculture what are the benefits and risks CurrOpinion Microbiol 1937‐44 2014

bull Cook KL AMP Netthisinghe and RA Gilfillen 2014 Detection of Pathogens Indicators and Antibiotic Resistance Genes after Land Application of Poultry Litter J Environ Qual 43 1546‐1558

bull Netthisinghe AMP KL Cook C Rice RA Gilfillen and KR Sistani 2013 Soil Nutrients Bacteria Populations and Veterinary Pharmaceuticals across a Backgrounding Beef Feedlot J Environ Qual 42 532‐544

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville Red ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Research

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental Quality

Production Systems StudiedPoultry Swine Beef

Laboratory and Field Expertisebull Soils manure and waste

treatment systemsbull PCR Quantitiative real‐time

PCRbull Culture and antimicrobial

susceptibilitybull Isolation and characterization of

mobile genetic elements carrying genes for antibiotic resistance

Research Interestsbull Characterizing persistence and transmission of

antibiotics antibiotic resistance (AR) genes and AR bacteria through agroecosystems

bull Capture and characterize mobile genetic elements carrying AR genes between microbial populations in soils with applied manures

bull Strain level differences in resistance transport and adhesion properties of bacteria with AR genes

Annie DonoghueResearch Leader (Physiologist)

AnnieDonoghuearsusdagov479-575-2413

7

Current Projectsbull Use of natural remedies to alleviate enteric

pathogens in organic and conventionally raised poultry

bull Alternatives to antibiotics for controlling Salmonella and Campylobacter in poultry and poultry products

Selected Publicationsbull Donoghue AM Venkitanarayanan K Arsi K Woo‐

Ming A Upadhyaya I Kollanoor‐Johny A Darre MJ Upadhyay A Fanatico A and Donoghue DJ 2015 Organic Poultry Developing Natural Solutions for Reducing Pathogens and Improving Production Organic Agriculture Research Symp in press

bull Arsi K Donoghue AM Woo‐Ming A Blore PJ and Donoghue DJ 2015 Intracloacal inoculation an effective screening method for determining the efficacy of probiotic bacterial isolates against Campylobactercolonization in broiler chickens J Food Prot 78 209‐213

bull Arsi K Donoghue AM Venkitanarayanan K Kollanoor‐Johny A Fanatico AC Blore PJ and Donoghue DJ2014 The efficacy of the natural plant extracts thymol and carvacrol against Campylobacter colonization in broiler chickens J Food Safety 34 321ndash325

Poultry Production and Products Safety Research Unit

Mailing AddressUniversity Of ArkansasPOSC O‐303Fayetteville AR 72701

National Program(s)108 ndash Food Safety103 ndash Animal Health

CRIS Project(s)Alternative Intervention and Control Strategies for Foodborne Pathogens in Poultry and Poultry Products

Novel Therapeutic Diagnostic and Management Strategies to Reduce Antibiotic Use in Poultry Production

Production Systems StudiedPoultry

Laboratory and Field ExpertiseLab uses traditional microbiological culture and molecular biological techniques to study food borne pathogens Organic and conventional practices for poultry production

Research Interestsbull developing alternatives to antibiotic use in poultry bull developing strategies to reduce or eliminate pathogen

contamination with a focus on Campylobacter and Salmonella

bull developing sustainable and organic farming practices for poultry producers

David DonavanResearch Molecular Biologist

DavidDonovanarsusdagov

Ce 443-690-4251 Office 301-504-9150

Current Projectsbull Mastitis a cow‐side diagnosticbull Mastitis treatment with triple‐acting antimicrobialsbull Clostridium perfringens novel endolysins that are heat‐resistantbull Yeast expressed endolysins as an alternative to antibiotics in animal feedbull CRISPRCas9 genomic engineering of cow and pig embryos

Selected Publicationsbull Rodriacuteguez‐Rubio L Martiacutenez B Rodriacuteguez A Donovan DM Goumltz F et al The

phage lytic proteins from the Staphylococcus aureus bacteriophage vB_SauS‐phiIPLA88 display multiple active catalytic domains and do not trigger staphylococcal resistance PloS one 2013 8(5)e64671

bull Singh PK Donovan DM Kumar A Intravitreal injection of the chimeric phage endolysin Ply187 protects mice from Staphylococcus aureus endophthalmitis Antimicrobial agents and chemotherapy 2014 58(8)4621‐9

bull Swift SM Seal BS Garrish JK Oakley BB Hiett K et al A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens‐Specific Cell Wall Binding Domain Creates an Anti‐Clostridium Antimicrobial with Improved Thermostability Viruses 2015 7(6)3019‐34

Link to all publications httpwwwncbinlmnihgovsitesmyncbi1jOJlsCcVSxQTbibliography41565643publicsort=dateampdirection=ascending

Animal Biosciences and Biotechnology Laboratory

Mailing AddressRoom 104 10300 Baltimore AveBLDG 230 BARC‐EastBeltsville MD 20705

National ProgramNP101 Food Animal Production

CRIS Project TitleDeveloping Genetic Biotechnologies for Increased Food Animal Production including Novel Antimicrobials for Improved Health and Product Safety

Production Systems StudiedDairy cattle Swine poultry Aquaculture

Laboratory and Field Expertisebull Molecular biologist with

transgenic and knockout mouse background

bull Heterologous gene expression in yeast bacteria mice and cell culture

bull Induced Pluripotent Stem cell production via lentiviral transduction

bull Mouse colony animal husbandry and embryo transfer

Research InterestsDavid M Donovan PhD Research Scientist (Molecular Biologist) at the US Department of Agriculture received his PhD in 1987 in molecular genetics of the yeast Saccharomyces cerevisiae and has 22 years experience in heterologous gene expression He spent 15 years at the NIH culminating in Section Chief Transgenic and Knockout Mouse lab NIA In 2002 he joined the USDA where he has been developing antimicrobials for the treatment of mastitis pathogens including Staphylococcus aureus His enzyme antimicrobials harbor three unique synergistic lytic domains and a protein transduction domain to target intracellular pathogens and have been shown to be highly refractory to resistance development His constructs eradicate both extracellular S aureus [in a rat nasal colonization model and murine systemic infections] and intracellular pathogens ex vivo in bovine mammary epithelial cells and in both a mouse model of mastitis and osteomyelitis He is working to identify protein feed additives as alternative to antibiotic growth promotants

Thomas F DuceyMicrobiologist

ThomasDuceyarsusdagov

843-669-5203 x112

Current Projectsbull Microbial responses to wetland restoration as a part

of the Mid‐Atlantic Region Conservation Effects Assessment Project

bull Response of the microbial rhizosphere and arbuscular mycorrhizae fungi to clover cover crop and conservation tillage in cotton production

bull Isolation of E coli and Enterococcus species from swine wastewater poultry litter and agriculturally‐impacted groundwater for the determination of baseline antibiotic resistance levels in agricultural production systems

Selected Publicationsbull Ducey et al Soil physicochemical conditions

denitrification rates and nosZ abundance in NC coastal plain restored wetlands 2015 J Environ Qual 44 1011‐1022

bull Ducey et al Microbial community analysis of swine wastewater anaerobic lagoons by next‐generation DNA sequencing 2013 Anaerobe 2150‐57

Coastal Plain Soil Water and Plant Research Center

Mailing Address2611 West Lucas StreetFlorence SC 29501

National Program(s)211 ndash Water Availability and Water Management212 ndash Climate Change Soils and Emissions214 ndash Agricultural and Industrial Byproducts

CRIS Project(s)Managing Water Availability and Quality (NP 211)Improving Chemical Physical and Biological Properties of Degraded Sandy Soils (NP 212)Innovative Bioresource Management Technologies (NP 214)

Production Systems StudiedCrops Poultry and Swine

Laboratory and Field Expertisebull Classical Microbiology

bull DetectionEnumerationIsolationbull New species identification

bull Molecular Biologybull T‐RFLPARISAbull qPCRReal Time PCRbull High‐throughput DNA Sequencing

(Ion Torrent)

Research Interestsbull Southeastern US coastal plain wetland restoration

and its effect on microbial community composition and function

bull Animal wastewater treatment systems with a particular focus on pathogen reduction and antibiotic resistance gene elimination

bull Microbial community analysis and response to crop conservation and cover cropping management practices

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Brian BrunelleResearch Microbiologist

BrianBrunellearsusdagov

515-337-7612

Current Projectsbull Comparing transcriptional differences between

antibiotics that induce invasion in multidrug‐resistant Salmonella and those that have no effect

bull Genome sequencing of novel multidrug‐resistant Salmonella isolates

bull Assessing antibiotics that can enhance resistance in multidrug‐resistant Salmonella

Selected Publicationsbull Brunelle BW Bearson BL Bearson SMD 2015

Chloramphenicol and tetracycline decrease motility and increase invasion and attachment gene expression in specific isolates of multidrug‐resistant Salmonella entericaserovar Typhimurium Front Microbiol 5801

bull Brunelle BW Bearson SMD Bearson BL 2013 Tetracycline accelerates the temporally‐regulated invasion response in specific isolates of multidrug‐resistant Salmonella enterica serovar Typhimurium BMC Microbiology 13 202

Food Safety and Enteric Pathogen Research Unit

Mailing AddressNational Animal Disease Center1920 Dayton AvePO Box 70Ames IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Analysis of Virulence and Antibiotic Resistance Mechanisms of Salmonella and Development of Intervention Strategies

Production Systems StudiedSwine

Laboratory and Field Expertisebull Analysis of bacterial

transcription using real‐time PCR and RNA‐seq

bull Characterization of antibiotic resistance levels and associated genes

bull Conducting assays to measure different virulence phenotypes (cellular invasion motility etc)

Research Interestsbull Investigating the impact antibiotic usage has on

influencing multidrug‐resistant Salmonella virulence phenotypes

bull Identifying genes and regulation pathways associated with phenotypic differences in multidrug‐resistant Salmonella isolates exposed to antibiotics

John P BrooksResearch Microbiologist

JohnBrooksarsusdagov

662-320-7411

7

Current Projectsbull The effect of degraded antibiotic on soil microbial

ecology and antibacterial microbiomebull Aerosol carriage of antibiotic resistant genes and

bacteria from land application of poultry litterbull Antibiotic resistant bacteria and genes in naiumlve

broiler CAFOs

Selected Publicationsbull Brooks JP MR McLaughlin A Adeli DM Miles 2016

Cultivation and qPCR detection of pathogenic and antibiotic‐resistant bacterial establishment in naiumlve broiler houses J Environ Qual 45958‐966

bull Brooks JP Adeli A McLaughlin MR 2014 Microbial ecology bacterial pathogens and antibiotic resistant genes in swine manure as influenced by three swine management systems Water Res 5796‐103

bull Brooks JP McLaughlin MR Scheffler B and Miles DM 2010 Microbial and antibiotic resistant constituents associated with biological aerosols and poultry litter within a commercial poultry house Sci Tot Environ 4084770‐4777

Genetics and Sustainable Agriculture Research Unit

Mailing Address810 Highway 12 East PO Box 5367Mississippi State MS 39762

National Program(s)216 ndash Agricultural System Competitiveness and Sustainability

CRIS Project(s)Integration of Site‐Specific Crop Production Practices amp Industrial amp Animal Ag Byproducts to Improve Ag Competitiveness amp Sustainability

Production Systems StudiedSwine Poultry Forage amp Row Crop

Laboratory and Field Expertisebull Detection amp enumeration of

pathogens and antibacterial resistant genes and bacteria

bull Sampling soil water air amp CAFO environments

bull Quantitative microbial risk assessment of pathogens amp antibacterial resistant bacteria in the environment

Research Interestsbull Identify the movement and fate of pathogens and

antibacterial resistant genesbacteria through the environment and CAFO environments

bull Apply quantitative microbial risk assessment to anthropogenic impacted environments

bull Determine the impact of row crop agriculture on the soil microbial and antibacterial resistant biome

Tucker BurchResearch Agricultural

Engineer

TuckerBurcharsusdagov

715-387-3670

Current Projectsbull Occurrence and Distribution of Antibiotic Resistance

Genes (ARGs) in Groundwater of Kewaunee County Wisconsin

Selected Publicationsbull Burch TR Sadowsky MJ LaPara TM 2016 Modeling the

fate of antibiotic resistance genes and class 1 integronsduring thermophilic anaerobic digestion of municipal wastewater solids Appl Microbiol Biotechnol 100(3) 1437‐1444

bull Burch TR Sadowsky MJ LaPara TM 2014 Fate of antibiotic resistance genes and class 1 integrons in soil microcosms following the application of treated residual municipal wastewater solids Environ Sci Technol 48(10) 5620‐5627

bull Burch TR Sadowsky MJ LaPara TM 2013 Air‐drying beds reduce the quantities of antibiotic resistance genes and class 1 integrons in residual municipal wastewater solids Environ Sci Technol 47(17) 9965‐9971

bull Burch TR Sadowsky MJ LaPara TM 2013 Aerobic digestion reduces the quantity of antibiotic resistance genes in residual municipal wastewater solids Front Microbiol 4(Feb)

Dairy Forage Research CenterEnvironmentally Integrated Dairy Management Research Unit

Mailing Address2615 Yellowstone DriveMarshfield WI 54449

National Program(s)212 ndash Soil and Air

CRIS Project(s)Improving Nutrient Use Efficiency and Mitigating Nutrient and Pathogen Losses from Dairy Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull qPCRbull Bioaerosol samplingbull Quantitative microbial risk

assessment

Research Interestsbull Environmental distribution and transmission of

antibiotic resistance genes (ARGs)bull Quantitative microbial risk assessment

Todd CallawayResearch Microbiologist

ToddCallawayarsusdagov

979-260-9374 7

Current Projectsbull Effects of organic acids on the microbiome of food

animals and impact on foodborne pathogensbull Dietary impacts on foodborne pathogenic bacteria

and the microbial ecosystembull Phytochemicals and their ability to alter composition

of the gastrointestinal microbiome

Selected Publicationsbull Callaway T R T S Edrington and D J Nisbet 2014

Isolation of E coli O157H7 and Salmonella from migratory brown‐headed cowbirds (Molothrus ater) common grackles (Quiscalus quiscula) and cattle egrets (Bubulcus ibis) Foodborne Path Dis 11791‐794

bull Broadway P R J A Carroll J C Brooks J R Donaldson N C Burdick‐Sanchez T B Schmidt T R Brown and T R Callaway 2015 Salmonella transfer to the lymph nodes and synovial fluid of experimentally orally inoculated swine Agric Food Anal Bacteriol (In Press)

bull Grilli E F Foresti B Tugnoli M Fustini M G Zanoni P Pasquali T R Callaway A Piva and G L Alborali 2015 Microencapsulated sorbic acid and pure botanicals affect Salmonella Typhimurium shedding in pigs a close‐up look from weaning to slaughter in controlled and field conditions Foodborne Path Dis (In Press)

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedBeef Cattle Dairy Cattle Swine and Poultry

Laboratory and Field Expertisebull Microbial Physiologybull Microbial Ecologybull Continuous culturebull Mixed culture environmental

simulationsbull Environmental impacts on

survival of foodborne pathogenic bacteria

bull Animal model challengesbull Development of pre‐harvest

intervention strategiesbull Feedlot and dairy procedures

Research Interestsbull Understanding how the microbial ecosystem interacts

with foodborne pathogens at a functional nicheguild level

bull Developing non‐antibiotic methods of reducing foodborne pathogenic bacteria in the gut of food animals

Kimberly CookResearch Microbiologist

KimCookarsusdagov

270-781-2579 ext 232

Current Projectsbull Capture and identify mobile genetic elements

associated with bacteria in soils with applied poultry litter effect of application method

bull Evaluate persistence and concentration of antibiotics and bacteria with AR genes in waste treatment systems and soils with application manures

bull Transport and adhesion of bacteria with AR genesbull Evaluate AR properties of E coli and enterococci

isolates from agricultural ecosystems

Selected Publicationsbull Durso LM and KL Cook 2014 Impacts of antibiotic

use in agriculture what are the benefits and risks CurrOpinion Microbiol 1937‐44 2014

bull Cook KL AMP Netthisinghe and RA Gilfillen 2014 Detection of Pathogens Indicators and Antibiotic Resistance Genes after Land Application of Poultry Litter J Environ Qual 43 1546‐1558

bull Netthisinghe AMP KL Cook C Rice RA Gilfillen and KR Sistani 2013 Soil Nutrients Bacteria Populations and Veterinary Pharmaceuticals across a Backgrounding Beef Feedlot J Environ Qual 42 532‐544

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville Red ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Research

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental Quality

Production Systems StudiedPoultry Swine Beef

Laboratory and Field Expertisebull Soils manure and waste

treatment systemsbull PCR Quantitiative real‐time

PCRbull Culture and antimicrobial

susceptibilitybull Isolation and characterization of

mobile genetic elements carrying genes for antibiotic resistance

Research Interestsbull Characterizing persistence and transmission of

antibiotics antibiotic resistance (AR) genes and AR bacteria through agroecosystems

bull Capture and characterize mobile genetic elements carrying AR genes between microbial populations in soils with applied manures

bull Strain level differences in resistance transport and adhesion properties of bacteria with AR genes

Annie DonoghueResearch Leader (Physiologist)

AnnieDonoghuearsusdagov479-575-2413

7

Current Projectsbull Use of natural remedies to alleviate enteric

pathogens in organic and conventionally raised poultry

bull Alternatives to antibiotics for controlling Salmonella and Campylobacter in poultry and poultry products

Selected Publicationsbull Donoghue AM Venkitanarayanan K Arsi K Woo‐

Ming A Upadhyaya I Kollanoor‐Johny A Darre MJ Upadhyay A Fanatico A and Donoghue DJ 2015 Organic Poultry Developing Natural Solutions for Reducing Pathogens and Improving Production Organic Agriculture Research Symp in press

bull Arsi K Donoghue AM Woo‐Ming A Blore PJ and Donoghue DJ 2015 Intracloacal inoculation an effective screening method for determining the efficacy of probiotic bacterial isolates against Campylobactercolonization in broiler chickens J Food Prot 78 209‐213

bull Arsi K Donoghue AM Venkitanarayanan K Kollanoor‐Johny A Fanatico AC Blore PJ and Donoghue DJ2014 The efficacy of the natural plant extracts thymol and carvacrol against Campylobacter colonization in broiler chickens J Food Safety 34 321ndash325

Poultry Production and Products Safety Research Unit

Mailing AddressUniversity Of ArkansasPOSC O‐303Fayetteville AR 72701

National Program(s)108 ndash Food Safety103 ndash Animal Health

CRIS Project(s)Alternative Intervention and Control Strategies for Foodborne Pathogens in Poultry and Poultry Products

Novel Therapeutic Diagnostic and Management Strategies to Reduce Antibiotic Use in Poultry Production

Production Systems StudiedPoultry

Laboratory and Field ExpertiseLab uses traditional microbiological culture and molecular biological techniques to study food borne pathogens Organic and conventional practices for poultry production

Research Interestsbull developing alternatives to antibiotic use in poultry bull developing strategies to reduce or eliminate pathogen

contamination with a focus on Campylobacter and Salmonella

bull developing sustainable and organic farming practices for poultry producers

David DonavanResearch Molecular Biologist

DavidDonovanarsusdagov

Ce 443-690-4251 Office 301-504-9150

Current Projectsbull Mastitis a cow‐side diagnosticbull Mastitis treatment with triple‐acting antimicrobialsbull Clostridium perfringens novel endolysins that are heat‐resistantbull Yeast expressed endolysins as an alternative to antibiotics in animal feedbull CRISPRCas9 genomic engineering of cow and pig embryos

Selected Publicationsbull Rodriacuteguez‐Rubio L Martiacutenez B Rodriacuteguez A Donovan DM Goumltz F et al The

phage lytic proteins from the Staphylococcus aureus bacteriophage vB_SauS‐phiIPLA88 display multiple active catalytic domains and do not trigger staphylococcal resistance PloS one 2013 8(5)e64671

bull Singh PK Donovan DM Kumar A Intravitreal injection of the chimeric phage endolysin Ply187 protects mice from Staphylococcus aureus endophthalmitis Antimicrobial agents and chemotherapy 2014 58(8)4621‐9

bull Swift SM Seal BS Garrish JK Oakley BB Hiett K et al A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens‐Specific Cell Wall Binding Domain Creates an Anti‐Clostridium Antimicrobial with Improved Thermostability Viruses 2015 7(6)3019‐34

Link to all publications httpwwwncbinlmnihgovsitesmyncbi1jOJlsCcVSxQTbibliography41565643publicsort=dateampdirection=ascending

Animal Biosciences and Biotechnology Laboratory

Mailing AddressRoom 104 10300 Baltimore AveBLDG 230 BARC‐EastBeltsville MD 20705

National ProgramNP101 Food Animal Production

CRIS Project TitleDeveloping Genetic Biotechnologies for Increased Food Animal Production including Novel Antimicrobials for Improved Health and Product Safety

Production Systems StudiedDairy cattle Swine poultry Aquaculture

Laboratory and Field Expertisebull Molecular biologist with

transgenic and knockout mouse background

bull Heterologous gene expression in yeast bacteria mice and cell culture

bull Induced Pluripotent Stem cell production via lentiviral transduction

bull Mouse colony animal husbandry and embryo transfer

Research InterestsDavid M Donovan PhD Research Scientist (Molecular Biologist) at the US Department of Agriculture received his PhD in 1987 in molecular genetics of the yeast Saccharomyces cerevisiae and has 22 years experience in heterologous gene expression He spent 15 years at the NIH culminating in Section Chief Transgenic and Knockout Mouse lab NIA In 2002 he joined the USDA where he has been developing antimicrobials for the treatment of mastitis pathogens including Staphylococcus aureus His enzyme antimicrobials harbor three unique synergistic lytic domains and a protein transduction domain to target intracellular pathogens and have been shown to be highly refractory to resistance development His constructs eradicate both extracellular S aureus [in a rat nasal colonization model and murine systemic infections] and intracellular pathogens ex vivo in bovine mammary epithelial cells and in both a mouse model of mastitis and osteomyelitis He is working to identify protein feed additives as alternative to antibiotic growth promotants

Thomas F DuceyMicrobiologist

ThomasDuceyarsusdagov

843-669-5203 x112

Current Projectsbull Microbial responses to wetland restoration as a part

of the Mid‐Atlantic Region Conservation Effects Assessment Project

bull Response of the microbial rhizosphere and arbuscular mycorrhizae fungi to clover cover crop and conservation tillage in cotton production

bull Isolation of E coli and Enterococcus species from swine wastewater poultry litter and agriculturally‐impacted groundwater for the determination of baseline antibiotic resistance levels in agricultural production systems

Selected Publicationsbull Ducey et al Soil physicochemical conditions

denitrification rates and nosZ abundance in NC coastal plain restored wetlands 2015 J Environ Qual 44 1011‐1022

bull Ducey et al Microbial community analysis of swine wastewater anaerobic lagoons by next‐generation DNA sequencing 2013 Anaerobe 2150‐57

Coastal Plain Soil Water and Plant Research Center

Mailing Address2611 West Lucas StreetFlorence SC 29501

National Program(s)211 ndash Water Availability and Water Management212 ndash Climate Change Soils and Emissions214 ndash Agricultural and Industrial Byproducts

CRIS Project(s)Managing Water Availability and Quality (NP 211)Improving Chemical Physical and Biological Properties of Degraded Sandy Soils (NP 212)Innovative Bioresource Management Technologies (NP 214)

Production Systems StudiedCrops Poultry and Swine

Laboratory and Field Expertisebull Classical Microbiology

bull DetectionEnumerationIsolationbull New species identification

bull Molecular Biologybull T‐RFLPARISAbull qPCRReal Time PCRbull High‐throughput DNA Sequencing

(Ion Torrent)

Research Interestsbull Southeastern US coastal plain wetland restoration

and its effect on microbial community composition and function

bull Animal wastewater treatment systems with a particular focus on pathogen reduction and antibiotic resistance gene elimination

bull Microbial community analysis and response to crop conservation and cover cropping management practices

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

John P BrooksResearch Microbiologist

JohnBrooksarsusdagov

662-320-7411

7

Current Projectsbull The effect of degraded antibiotic on soil microbial

ecology and antibacterial microbiomebull Aerosol carriage of antibiotic resistant genes and

bacteria from land application of poultry litterbull Antibiotic resistant bacteria and genes in naiumlve

broiler CAFOs

Selected Publicationsbull Brooks JP MR McLaughlin A Adeli DM Miles 2016

Cultivation and qPCR detection of pathogenic and antibiotic‐resistant bacterial establishment in naiumlve broiler houses J Environ Qual 45958‐966

bull Brooks JP Adeli A McLaughlin MR 2014 Microbial ecology bacterial pathogens and antibiotic resistant genes in swine manure as influenced by three swine management systems Water Res 5796‐103

bull Brooks JP McLaughlin MR Scheffler B and Miles DM 2010 Microbial and antibiotic resistant constituents associated with biological aerosols and poultry litter within a commercial poultry house Sci Tot Environ 4084770‐4777

Genetics and Sustainable Agriculture Research Unit

Mailing Address810 Highway 12 East PO Box 5367Mississippi State MS 39762

National Program(s)216 ndash Agricultural System Competitiveness and Sustainability

CRIS Project(s)Integration of Site‐Specific Crop Production Practices amp Industrial amp Animal Ag Byproducts to Improve Ag Competitiveness amp Sustainability

Production Systems StudiedSwine Poultry Forage amp Row Crop

Laboratory and Field Expertisebull Detection amp enumeration of

pathogens and antibacterial resistant genes and bacteria

bull Sampling soil water air amp CAFO environments

bull Quantitative microbial risk assessment of pathogens amp antibacterial resistant bacteria in the environment

Research Interestsbull Identify the movement and fate of pathogens and

antibacterial resistant genesbacteria through the environment and CAFO environments

bull Apply quantitative microbial risk assessment to anthropogenic impacted environments

bull Determine the impact of row crop agriculture on the soil microbial and antibacterial resistant biome

Tucker BurchResearch Agricultural

Engineer

TuckerBurcharsusdagov

715-387-3670

Current Projectsbull Occurrence and Distribution of Antibiotic Resistance

Genes (ARGs) in Groundwater of Kewaunee County Wisconsin

Selected Publicationsbull Burch TR Sadowsky MJ LaPara TM 2016 Modeling the

fate of antibiotic resistance genes and class 1 integronsduring thermophilic anaerobic digestion of municipal wastewater solids Appl Microbiol Biotechnol 100(3) 1437‐1444

bull Burch TR Sadowsky MJ LaPara TM 2014 Fate of antibiotic resistance genes and class 1 integrons in soil microcosms following the application of treated residual municipal wastewater solids Environ Sci Technol 48(10) 5620‐5627

bull Burch TR Sadowsky MJ LaPara TM 2013 Air‐drying beds reduce the quantities of antibiotic resistance genes and class 1 integrons in residual municipal wastewater solids Environ Sci Technol 47(17) 9965‐9971

bull Burch TR Sadowsky MJ LaPara TM 2013 Aerobic digestion reduces the quantity of antibiotic resistance genes in residual municipal wastewater solids Front Microbiol 4(Feb)

Dairy Forage Research CenterEnvironmentally Integrated Dairy Management Research Unit

Mailing Address2615 Yellowstone DriveMarshfield WI 54449

National Program(s)212 ndash Soil and Air

CRIS Project(s)Improving Nutrient Use Efficiency and Mitigating Nutrient and Pathogen Losses from Dairy Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull qPCRbull Bioaerosol samplingbull Quantitative microbial risk

assessment

Research Interestsbull Environmental distribution and transmission of

antibiotic resistance genes (ARGs)bull Quantitative microbial risk assessment

Todd CallawayResearch Microbiologist

ToddCallawayarsusdagov

979-260-9374 7

Current Projectsbull Effects of organic acids on the microbiome of food

animals and impact on foodborne pathogensbull Dietary impacts on foodborne pathogenic bacteria

and the microbial ecosystembull Phytochemicals and their ability to alter composition

of the gastrointestinal microbiome

Selected Publicationsbull Callaway T R T S Edrington and D J Nisbet 2014

Isolation of E coli O157H7 and Salmonella from migratory brown‐headed cowbirds (Molothrus ater) common grackles (Quiscalus quiscula) and cattle egrets (Bubulcus ibis) Foodborne Path Dis 11791‐794

bull Broadway P R J A Carroll J C Brooks J R Donaldson N C Burdick‐Sanchez T B Schmidt T R Brown and T R Callaway 2015 Salmonella transfer to the lymph nodes and synovial fluid of experimentally orally inoculated swine Agric Food Anal Bacteriol (In Press)

bull Grilli E F Foresti B Tugnoli M Fustini M G Zanoni P Pasquali T R Callaway A Piva and G L Alborali 2015 Microencapsulated sorbic acid and pure botanicals affect Salmonella Typhimurium shedding in pigs a close‐up look from weaning to slaughter in controlled and field conditions Foodborne Path Dis (In Press)

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedBeef Cattle Dairy Cattle Swine and Poultry

Laboratory and Field Expertisebull Microbial Physiologybull Microbial Ecologybull Continuous culturebull Mixed culture environmental

simulationsbull Environmental impacts on

survival of foodborne pathogenic bacteria

bull Animal model challengesbull Development of pre‐harvest

intervention strategiesbull Feedlot and dairy procedures

Research Interestsbull Understanding how the microbial ecosystem interacts

with foodborne pathogens at a functional nicheguild level

bull Developing non‐antibiotic methods of reducing foodborne pathogenic bacteria in the gut of food animals

Kimberly CookResearch Microbiologist

KimCookarsusdagov

270-781-2579 ext 232

Current Projectsbull Capture and identify mobile genetic elements

associated with bacteria in soils with applied poultry litter effect of application method

bull Evaluate persistence and concentration of antibiotics and bacteria with AR genes in waste treatment systems and soils with application manures

bull Transport and adhesion of bacteria with AR genesbull Evaluate AR properties of E coli and enterococci

isolates from agricultural ecosystems

Selected Publicationsbull Durso LM and KL Cook 2014 Impacts of antibiotic

use in agriculture what are the benefits and risks CurrOpinion Microbiol 1937‐44 2014

bull Cook KL AMP Netthisinghe and RA Gilfillen 2014 Detection of Pathogens Indicators and Antibiotic Resistance Genes after Land Application of Poultry Litter J Environ Qual 43 1546‐1558

bull Netthisinghe AMP KL Cook C Rice RA Gilfillen and KR Sistani 2013 Soil Nutrients Bacteria Populations and Veterinary Pharmaceuticals across a Backgrounding Beef Feedlot J Environ Qual 42 532‐544

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville Red ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Research

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental Quality

Production Systems StudiedPoultry Swine Beef

Laboratory and Field Expertisebull Soils manure and waste

treatment systemsbull PCR Quantitiative real‐time

PCRbull Culture and antimicrobial

susceptibilitybull Isolation and characterization of

mobile genetic elements carrying genes for antibiotic resistance

Research Interestsbull Characterizing persistence and transmission of

antibiotics antibiotic resistance (AR) genes and AR bacteria through agroecosystems

bull Capture and characterize mobile genetic elements carrying AR genes between microbial populations in soils with applied manures

bull Strain level differences in resistance transport and adhesion properties of bacteria with AR genes

Annie DonoghueResearch Leader (Physiologist)

AnnieDonoghuearsusdagov479-575-2413

7

Current Projectsbull Use of natural remedies to alleviate enteric

pathogens in organic and conventionally raised poultry

bull Alternatives to antibiotics for controlling Salmonella and Campylobacter in poultry and poultry products

Selected Publicationsbull Donoghue AM Venkitanarayanan K Arsi K Woo‐

Ming A Upadhyaya I Kollanoor‐Johny A Darre MJ Upadhyay A Fanatico A and Donoghue DJ 2015 Organic Poultry Developing Natural Solutions for Reducing Pathogens and Improving Production Organic Agriculture Research Symp in press

bull Arsi K Donoghue AM Woo‐Ming A Blore PJ and Donoghue DJ 2015 Intracloacal inoculation an effective screening method for determining the efficacy of probiotic bacterial isolates against Campylobactercolonization in broiler chickens J Food Prot 78 209‐213

bull Arsi K Donoghue AM Venkitanarayanan K Kollanoor‐Johny A Fanatico AC Blore PJ and Donoghue DJ2014 The efficacy of the natural plant extracts thymol and carvacrol against Campylobacter colonization in broiler chickens J Food Safety 34 321ndash325

Poultry Production and Products Safety Research Unit

Mailing AddressUniversity Of ArkansasPOSC O‐303Fayetteville AR 72701

National Program(s)108 ndash Food Safety103 ndash Animal Health

CRIS Project(s)Alternative Intervention and Control Strategies for Foodborne Pathogens in Poultry and Poultry Products

Novel Therapeutic Diagnostic and Management Strategies to Reduce Antibiotic Use in Poultry Production

Production Systems StudiedPoultry

Laboratory and Field ExpertiseLab uses traditional microbiological culture and molecular biological techniques to study food borne pathogens Organic and conventional practices for poultry production

Research Interestsbull developing alternatives to antibiotic use in poultry bull developing strategies to reduce or eliminate pathogen

contamination with a focus on Campylobacter and Salmonella

bull developing sustainable and organic farming practices for poultry producers

David DonavanResearch Molecular Biologist

DavidDonovanarsusdagov

Ce 443-690-4251 Office 301-504-9150

Current Projectsbull Mastitis a cow‐side diagnosticbull Mastitis treatment with triple‐acting antimicrobialsbull Clostridium perfringens novel endolysins that are heat‐resistantbull Yeast expressed endolysins as an alternative to antibiotics in animal feedbull CRISPRCas9 genomic engineering of cow and pig embryos

Selected Publicationsbull Rodriacuteguez‐Rubio L Martiacutenez B Rodriacuteguez A Donovan DM Goumltz F et al The

phage lytic proteins from the Staphylococcus aureus bacteriophage vB_SauS‐phiIPLA88 display multiple active catalytic domains and do not trigger staphylococcal resistance PloS one 2013 8(5)e64671

bull Singh PK Donovan DM Kumar A Intravitreal injection of the chimeric phage endolysin Ply187 protects mice from Staphylococcus aureus endophthalmitis Antimicrobial agents and chemotherapy 2014 58(8)4621‐9

bull Swift SM Seal BS Garrish JK Oakley BB Hiett K et al A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens‐Specific Cell Wall Binding Domain Creates an Anti‐Clostridium Antimicrobial with Improved Thermostability Viruses 2015 7(6)3019‐34

Link to all publications httpwwwncbinlmnihgovsitesmyncbi1jOJlsCcVSxQTbibliography41565643publicsort=dateampdirection=ascending

Animal Biosciences and Biotechnology Laboratory

Mailing AddressRoom 104 10300 Baltimore AveBLDG 230 BARC‐EastBeltsville MD 20705

National ProgramNP101 Food Animal Production

CRIS Project TitleDeveloping Genetic Biotechnologies for Increased Food Animal Production including Novel Antimicrobials for Improved Health and Product Safety

Production Systems StudiedDairy cattle Swine poultry Aquaculture

Laboratory and Field Expertisebull Molecular biologist with

transgenic and knockout mouse background

bull Heterologous gene expression in yeast bacteria mice and cell culture

bull Induced Pluripotent Stem cell production via lentiviral transduction

bull Mouse colony animal husbandry and embryo transfer

Research InterestsDavid M Donovan PhD Research Scientist (Molecular Biologist) at the US Department of Agriculture received his PhD in 1987 in molecular genetics of the yeast Saccharomyces cerevisiae and has 22 years experience in heterologous gene expression He spent 15 years at the NIH culminating in Section Chief Transgenic and Knockout Mouse lab NIA In 2002 he joined the USDA where he has been developing antimicrobials for the treatment of mastitis pathogens including Staphylococcus aureus His enzyme antimicrobials harbor three unique synergistic lytic domains and a protein transduction domain to target intracellular pathogens and have been shown to be highly refractory to resistance development His constructs eradicate both extracellular S aureus [in a rat nasal colonization model and murine systemic infections] and intracellular pathogens ex vivo in bovine mammary epithelial cells and in both a mouse model of mastitis and osteomyelitis He is working to identify protein feed additives as alternative to antibiotic growth promotants

Thomas F DuceyMicrobiologist

ThomasDuceyarsusdagov

843-669-5203 x112

Current Projectsbull Microbial responses to wetland restoration as a part

of the Mid‐Atlantic Region Conservation Effects Assessment Project

bull Response of the microbial rhizosphere and arbuscular mycorrhizae fungi to clover cover crop and conservation tillage in cotton production

bull Isolation of E coli and Enterococcus species from swine wastewater poultry litter and agriculturally‐impacted groundwater for the determination of baseline antibiotic resistance levels in agricultural production systems

Selected Publicationsbull Ducey et al Soil physicochemical conditions

denitrification rates and nosZ abundance in NC coastal plain restored wetlands 2015 J Environ Qual 44 1011‐1022

bull Ducey et al Microbial community analysis of swine wastewater anaerobic lagoons by next‐generation DNA sequencing 2013 Anaerobe 2150‐57

Coastal Plain Soil Water and Plant Research Center

Mailing Address2611 West Lucas StreetFlorence SC 29501

National Program(s)211 ndash Water Availability and Water Management212 ndash Climate Change Soils and Emissions214 ndash Agricultural and Industrial Byproducts

CRIS Project(s)Managing Water Availability and Quality (NP 211)Improving Chemical Physical and Biological Properties of Degraded Sandy Soils (NP 212)Innovative Bioresource Management Technologies (NP 214)

Production Systems StudiedCrops Poultry and Swine

Laboratory and Field Expertisebull Classical Microbiology

bull DetectionEnumerationIsolationbull New species identification

bull Molecular Biologybull T‐RFLPARISAbull qPCRReal Time PCRbull High‐throughput DNA Sequencing

(Ion Torrent)

Research Interestsbull Southeastern US coastal plain wetland restoration

and its effect on microbial community composition and function

bull Animal wastewater treatment systems with a particular focus on pathogen reduction and antibiotic resistance gene elimination

bull Microbial community analysis and response to crop conservation and cover cropping management practices

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Tucker BurchResearch Agricultural

Engineer

TuckerBurcharsusdagov

715-387-3670

Current Projectsbull Occurrence and Distribution of Antibiotic Resistance

Genes (ARGs) in Groundwater of Kewaunee County Wisconsin

Selected Publicationsbull Burch TR Sadowsky MJ LaPara TM 2016 Modeling the

fate of antibiotic resistance genes and class 1 integronsduring thermophilic anaerobic digestion of municipal wastewater solids Appl Microbiol Biotechnol 100(3) 1437‐1444

bull Burch TR Sadowsky MJ LaPara TM 2014 Fate of antibiotic resistance genes and class 1 integrons in soil microcosms following the application of treated residual municipal wastewater solids Environ Sci Technol 48(10) 5620‐5627

bull Burch TR Sadowsky MJ LaPara TM 2013 Air‐drying beds reduce the quantities of antibiotic resistance genes and class 1 integrons in residual municipal wastewater solids Environ Sci Technol 47(17) 9965‐9971

bull Burch TR Sadowsky MJ LaPara TM 2013 Aerobic digestion reduces the quantity of antibiotic resistance genes in residual municipal wastewater solids Front Microbiol 4(Feb)

Dairy Forage Research CenterEnvironmentally Integrated Dairy Management Research Unit

Mailing Address2615 Yellowstone DriveMarshfield WI 54449

National Program(s)212 ndash Soil and Air

CRIS Project(s)Improving Nutrient Use Efficiency and Mitigating Nutrient and Pathogen Losses from Dairy Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull qPCRbull Bioaerosol samplingbull Quantitative microbial risk

assessment

Research Interestsbull Environmental distribution and transmission of

antibiotic resistance genes (ARGs)bull Quantitative microbial risk assessment

Todd CallawayResearch Microbiologist

ToddCallawayarsusdagov

979-260-9374 7

Current Projectsbull Effects of organic acids on the microbiome of food

animals and impact on foodborne pathogensbull Dietary impacts on foodborne pathogenic bacteria

and the microbial ecosystembull Phytochemicals and their ability to alter composition

of the gastrointestinal microbiome

Selected Publicationsbull Callaway T R T S Edrington and D J Nisbet 2014

Isolation of E coli O157H7 and Salmonella from migratory brown‐headed cowbirds (Molothrus ater) common grackles (Quiscalus quiscula) and cattle egrets (Bubulcus ibis) Foodborne Path Dis 11791‐794

bull Broadway P R J A Carroll J C Brooks J R Donaldson N C Burdick‐Sanchez T B Schmidt T R Brown and T R Callaway 2015 Salmonella transfer to the lymph nodes and synovial fluid of experimentally orally inoculated swine Agric Food Anal Bacteriol (In Press)

bull Grilli E F Foresti B Tugnoli M Fustini M G Zanoni P Pasquali T R Callaway A Piva and G L Alborali 2015 Microencapsulated sorbic acid and pure botanicals affect Salmonella Typhimurium shedding in pigs a close‐up look from weaning to slaughter in controlled and field conditions Foodborne Path Dis (In Press)

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedBeef Cattle Dairy Cattle Swine and Poultry

Laboratory and Field Expertisebull Microbial Physiologybull Microbial Ecologybull Continuous culturebull Mixed culture environmental

simulationsbull Environmental impacts on

survival of foodborne pathogenic bacteria

bull Animal model challengesbull Development of pre‐harvest

intervention strategiesbull Feedlot and dairy procedures

Research Interestsbull Understanding how the microbial ecosystem interacts

with foodborne pathogens at a functional nicheguild level

bull Developing non‐antibiotic methods of reducing foodborne pathogenic bacteria in the gut of food animals

Kimberly CookResearch Microbiologist

KimCookarsusdagov

270-781-2579 ext 232

Current Projectsbull Capture and identify mobile genetic elements

associated with bacteria in soils with applied poultry litter effect of application method

bull Evaluate persistence and concentration of antibiotics and bacteria with AR genes in waste treatment systems and soils with application manures

bull Transport and adhesion of bacteria with AR genesbull Evaluate AR properties of E coli and enterococci

isolates from agricultural ecosystems

Selected Publicationsbull Durso LM and KL Cook 2014 Impacts of antibiotic

use in agriculture what are the benefits and risks CurrOpinion Microbiol 1937‐44 2014

bull Cook KL AMP Netthisinghe and RA Gilfillen 2014 Detection of Pathogens Indicators and Antibiotic Resistance Genes after Land Application of Poultry Litter J Environ Qual 43 1546‐1558

bull Netthisinghe AMP KL Cook C Rice RA Gilfillen and KR Sistani 2013 Soil Nutrients Bacteria Populations and Veterinary Pharmaceuticals across a Backgrounding Beef Feedlot J Environ Qual 42 532‐544

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville Red ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Research

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental Quality

Production Systems StudiedPoultry Swine Beef

Laboratory and Field Expertisebull Soils manure and waste

treatment systemsbull PCR Quantitiative real‐time

PCRbull Culture and antimicrobial

susceptibilitybull Isolation and characterization of

mobile genetic elements carrying genes for antibiotic resistance

Research Interestsbull Characterizing persistence and transmission of

antibiotics antibiotic resistance (AR) genes and AR bacteria through agroecosystems

bull Capture and characterize mobile genetic elements carrying AR genes between microbial populations in soils with applied manures

bull Strain level differences in resistance transport and adhesion properties of bacteria with AR genes

Annie DonoghueResearch Leader (Physiologist)

AnnieDonoghuearsusdagov479-575-2413

7

Current Projectsbull Use of natural remedies to alleviate enteric

pathogens in organic and conventionally raised poultry

bull Alternatives to antibiotics for controlling Salmonella and Campylobacter in poultry and poultry products

Selected Publicationsbull Donoghue AM Venkitanarayanan K Arsi K Woo‐

Ming A Upadhyaya I Kollanoor‐Johny A Darre MJ Upadhyay A Fanatico A and Donoghue DJ 2015 Organic Poultry Developing Natural Solutions for Reducing Pathogens and Improving Production Organic Agriculture Research Symp in press

bull Arsi K Donoghue AM Woo‐Ming A Blore PJ and Donoghue DJ 2015 Intracloacal inoculation an effective screening method for determining the efficacy of probiotic bacterial isolates against Campylobactercolonization in broiler chickens J Food Prot 78 209‐213

bull Arsi K Donoghue AM Venkitanarayanan K Kollanoor‐Johny A Fanatico AC Blore PJ and Donoghue DJ2014 The efficacy of the natural plant extracts thymol and carvacrol against Campylobacter colonization in broiler chickens J Food Safety 34 321ndash325

Poultry Production and Products Safety Research Unit

Mailing AddressUniversity Of ArkansasPOSC O‐303Fayetteville AR 72701

National Program(s)108 ndash Food Safety103 ndash Animal Health

CRIS Project(s)Alternative Intervention and Control Strategies for Foodborne Pathogens in Poultry and Poultry Products

Novel Therapeutic Diagnostic and Management Strategies to Reduce Antibiotic Use in Poultry Production

Production Systems StudiedPoultry

Laboratory and Field ExpertiseLab uses traditional microbiological culture and molecular biological techniques to study food borne pathogens Organic and conventional practices for poultry production

Research Interestsbull developing alternatives to antibiotic use in poultry bull developing strategies to reduce or eliminate pathogen

contamination with a focus on Campylobacter and Salmonella

bull developing sustainable and organic farming practices for poultry producers

David DonavanResearch Molecular Biologist

DavidDonovanarsusdagov

Ce 443-690-4251 Office 301-504-9150

Current Projectsbull Mastitis a cow‐side diagnosticbull Mastitis treatment with triple‐acting antimicrobialsbull Clostridium perfringens novel endolysins that are heat‐resistantbull Yeast expressed endolysins as an alternative to antibiotics in animal feedbull CRISPRCas9 genomic engineering of cow and pig embryos

Selected Publicationsbull Rodriacuteguez‐Rubio L Martiacutenez B Rodriacuteguez A Donovan DM Goumltz F et al The

phage lytic proteins from the Staphylococcus aureus bacteriophage vB_SauS‐phiIPLA88 display multiple active catalytic domains and do not trigger staphylococcal resistance PloS one 2013 8(5)e64671

bull Singh PK Donovan DM Kumar A Intravitreal injection of the chimeric phage endolysin Ply187 protects mice from Staphylococcus aureus endophthalmitis Antimicrobial agents and chemotherapy 2014 58(8)4621‐9

bull Swift SM Seal BS Garrish JK Oakley BB Hiett K et al A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens‐Specific Cell Wall Binding Domain Creates an Anti‐Clostridium Antimicrobial with Improved Thermostability Viruses 2015 7(6)3019‐34

Link to all publications httpwwwncbinlmnihgovsitesmyncbi1jOJlsCcVSxQTbibliography41565643publicsort=dateampdirection=ascending

Animal Biosciences and Biotechnology Laboratory

Mailing AddressRoom 104 10300 Baltimore AveBLDG 230 BARC‐EastBeltsville MD 20705

National ProgramNP101 Food Animal Production

CRIS Project TitleDeveloping Genetic Biotechnologies for Increased Food Animal Production including Novel Antimicrobials for Improved Health and Product Safety

Production Systems StudiedDairy cattle Swine poultry Aquaculture

Laboratory and Field Expertisebull Molecular biologist with

transgenic and knockout mouse background

bull Heterologous gene expression in yeast bacteria mice and cell culture

bull Induced Pluripotent Stem cell production via lentiviral transduction

bull Mouse colony animal husbandry and embryo transfer

Research InterestsDavid M Donovan PhD Research Scientist (Molecular Biologist) at the US Department of Agriculture received his PhD in 1987 in molecular genetics of the yeast Saccharomyces cerevisiae and has 22 years experience in heterologous gene expression He spent 15 years at the NIH culminating in Section Chief Transgenic and Knockout Mouse lab NIA In 2002 he joined the USDA where he has been developing antimicrobials for the treatment of mastitis pathogens including Staphylococcus aureus His enzyme antimicrobials harbor three unique synergistic lytic domains and a protein transduction domain to target intracellular pathogens and have been shown to be highly refractory to resistance development His constructs eradicate both extracellular S aureus [in a rat nasal colonization model and murine systemic infections] and intracellular pathogens ex vivo in bovine mammary epithelial cells and in both a mouse model of mastitis and osteomyelitis He is working to identify protein feed additives as alternative to antibiotic growth promotants

Thomas F DuceyMicrobiologist

ThomasDuceyarsusdagov

843-669-5203 x112

Current Projectsbull Microbial responses to wetland restoration as a part

of the Mid‐Atlantic Region Conservation Effects Assessment Project

bull Response of the microbial rhizosphere and arbuscular mycorrhizae fungi to clover cover crop and conservation tillage in cotton production

bull Isolation of E coli and Enterococcus species from swine wastewater poultry litter and agriculturally‐impacted groundwater for the determination of baseline antibiotic resistance levels in agricultural production systems

Selected Publicationsbull Ducey et al Soil physicochemical conditions

denitrification rates and nosZ abundance in NC coastal plain restored wetlands 2015 J Environ Qual 44 1011‐1022

bull Ducey et al Microbial community analysis of swine wastewater anaerobic lagoons by next‐generation DNA sequencing 2013 Anaerobe 2150‐57

Coastal Plain Soil Water and Plant Research Center

Mailing Address2611 West Lucas StreetFlorence SC 29501

National Program(s)211 ndash Water Availability and Water Management212 ndash Climate Change Soils and Emissions214 ndash Agricultural and Industrial Byproducts

CRIS Project(s)Managing Water Availability and Quality (NP 211)Improving Chemical Physical and Biological Properties of Degraded Sandy Soils (NP 212)Innovative Bioresource Management Technologies (NP 214)

Production Systems StudiedCrops Poultry and Swine

Laboratory and Field Expertisebull Classical Microbiology

bull DetectionEnumerationIsolationbull New species identification

bull Molecular Biologybull T‐RFLPARISAbull qPCRReal Time PCRbull High‐throughput DNA Sequencing

(Ion Torrent)

Research Interestsbull Southeastern US coastal plain wetland restoration

and its effect on microbial community composition and function

bull Animal wastewater treatment systems with a particular focus on pathogen reduction and antibiotic resistance gene elimination

bull Microbial community analysis and response to crop conservation and cover cropping management practices

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Todd CallawayResearch Microbiologist

ToddCallawayarsusdagov

979-260-9374 7

Current Projectsbull Effects of organic acids on the microbiome of food

animals and impact on foodborne pathogensbull Dietary impacts on foodborne pathogenic bacteria

and the microbial ecosystembull Phytochemicals and their ability to alter composition

of the gastrointestinal microbiome

Selected Publicationsbull Callaway T R T S Edrington and D J Nisbet 2014

Isolation of E coli O157H7 and Salmonella from migratory brown‐headed cowbirds (Molothrus ater) common grackles (Quiscalus quiscula) and cattle egrets (Bubulcus ibis) Foodborne Path Dis 11791‐794

bull Broadway P R J A Carroll J C Brooks J R Donaldson N C Burdick‐Sanchez T B Schmidt T R Brown and T R Callaway 2015 Salmonella transfer to the lymph nodes and synovial fluid of experimentally orally inoculated swine Agric Food Anal Bacteriol (In Press)

bull Grilli E F Foresti B Tugnoli M Fustini M G Zanoni P Pasquali T R Callaway A Piva and G L Alborali 2015 Microencapsulated sorbic acid and pure botanicals affect Salmonella Typhimurium shedding in pigs a close‐up look from weaning to slaughter in controlled and field conditions Foodborne Path Dis (In Press)

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Interventions to Reduce Foodborne Pathogens in Swine and Cattle

Production Systems StudiedBeef Cattle Dairy Cattle Swine and Poultry

Laboratory and Field Expertisebull Microbial Physiologybull Microbial Ecologybull Continuous culturebull Mixed culture environmental

simulationsbull Environmental impacts on

survival of foodborne pathogenic bacteria

bull Animal model challengesbull Development of pre‐harvest

intervention strategiesbull Feedlot and dairy procedures

Research Interestsbull Understanding how the microbial ecosystem interacts

with foodborne pathogens at a functional nicheguild level

bull Developing non‐antibiotic methods of reducing foodborne pathogenic bacteria in the gut of food animals

Kimberly CookResearch Microbiologist

KimCookarsusdagov

270-781-2579 ext 232

Current Projectsbull Capture and identify mobile genetic elements

associated with bacteria in soils with applied poultry litter effect of application method

bull Evaluate persistence and concentration of antibiotics and bacteria with AR genes in waste treatment systems and soils with application manures

bull Transport and adhesion of bacteria with AR genesbull Evaluate AR properties of E coli and enterococci

isolates from agricultural ecosystems

Selected Publicationsbull Durso LM and KL Cook 2014 Impacts of antibiotic

use in agriculture what are the benefits and risks CurrOpinion Microbiol 1937‐44 2014

bull Cook KL AMP Netthisinghe and RA Gilfillen 2014 Detection of Pathogens Indicators and Antibiotic Resistance Genes after Land Application of Poultry Litter J Environ Qual 43 1546‐1558

bull Netthisinghe AMP KL Cook C Rice RA Gilfillen and KR Sistani 2013 Soil Nutrients Bacteria Populations and Veterinary Pharmaceuticals across a Backgrounding Beef Feedlot J Environ Qual 42 532‐544

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville Red ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Research

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental Quality

Production Systems StudiedPoultry Swine Beef

Laboratory and Field Expertisebull Soils manure and waste

treatment systemsbull PCR Quantitiative real‐time

PCRbull Culture and antimicrobial

susceptibilitybull Isolation and characterization of

mobile genetic elements carrying genes for antibiotic resistance

Research Interestsbull Characterizing persistence and transmission of

antibiotics antibiotic resistance (AR) genes and AR bacteria through agroecosystems

bull Capture and characterize mobile genetic elements carrying AR genes between microbial populations in soils with applied manures

bull Strain level differences in resistance transport and adhesion properties of bacteria with AR genes

Annie DonoghueResearch Leader (Physiologist)

AnnieDonoghuearsusdagov479-575-2413

7

Current Projectsbull Use of natural remedies to alleviate enteric

pathogens in organic and conventionally raised poultry

bull Alternatives to antibiotics for controlling Salmonella and Campylobacter in poultry and poultry products

Selected Publicationsbull Donoghue AM Venkitanarayanan K Arsi K Woo‐

Ming A Upadhyaya I Kollanoor‐Johny A Darre MJ Upadhyay A Fanatico A and Donoghue DJ 2015 Organic Poultry Developing Natural Solutions for Reducing Pathogens and Improving Production Organic Agriculture Research Symp in press

bull Arsi K Donoghue AM Woo‐Ming A Blore PJ and Donoghue DJ 2015 Intracloacal inoculation an effective screening method for determining the efficacy of probiotic bacterial isolates against Campylobactercolonization in broiler chickens J Food Prot 78 209‐213

bull Arsi K Donoghue AM Venkitanarayanan K Kollanoor‐Johny A Fanatico AC Blore PJ and Donoghue DJ2014 The efficacy of the natural plant extracts thymol and carvacrol against Campylobacter colonization in broiler chickens J Food Safety 34 321ndash325

Poultry Production and Products Safety Research Unit

Mailing AddressUniversity Of ArkansasPOSC O‐303Fayetteville AR 72701

National Program(s)108 ndash Food Safety103 ndash Animal Health

CRIS Project(s)Alternative Intervention and Control Strategies for Foodborne Pathogens in Poultry and Poultry Products

Novel Therapeutic Diagnostic and Management Strategies to Reduce Antibiotic Use in Poultry Production

Production Systems StudiedPoultry

Laboratory and Field ExpertiseLab uses traditional microbiological culture and molecular biological techniques to study food borne pathogens Organic and conventional practices for poultry production

Research Interestsbull developing alternatives to antibiotic use in poultry bull developing strategies to reduce or eliminate pathogen

contamination with a focus on Campylobacter and Salmonella

bull developing sustainable and organic farming practices for poultry producers

David DonavanResearch Molecular Biologist

DavidDonovanarsusdagov

Ce 443-690-4251 Office 301-504-9150

Current Projectsbull Mastitis a cow‐side diagnosticbull Mastitis treatment with triple‐acting antimicrobialsbull Clostridium perfringens novel endolysins that are heat‐resistantbull Yeast expressed endolysins as an alternative to antibiotics in animal feedbull CRISPRCas9 genomic engineering of cow and pig embryos

Selected Publicationsbull Rodriacuteguez‐Rubio L Martiacutenez B Rodriacuteguez A Donovan DM Goumltz F et al The

phage lytic proteins from the Staphylococcus aureus bacteriophage vB_SauS‐phiIPLA88 display multiple active catalytic domains and do not trigger staphylococcal resistance PloS one 2013 8(5)e64671

bull Singh PK Donovan DM Kumar A Intravitreal injection of the chimeric phage endolysin Ply187 protects mice from Staphylococcus aureus endophthalmitis Antimicrobial agents and chemotherapy 2014 58(8)4621‐9

bull Swift SM Seal BS Garrish JK Oakley BB Hiett K et al A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens‐Specific Cell Wall Binding Domain Creates an Anti‐Clostridium Antimicrobial with Improved Thermostability Viruses 2015 7(6)3019‐34

Link to all publications httpwwwncbinlmnihgovsitesmyncbi1jOJlsCcVSxQTbibliography41565643publicsort=dateampdirection=ascending

Animal Biosciences and Biotechnology Laboratory

Mailing AddressRoom 104 10300 Baltimore AveBLDG 230 BARC‐EastBeltsville MD 20705

National ProgramNP101 Food Animal Production

CRIS Project TitleDeveloping Genetic Biotechnologies for Increased Food Animal Production including Novel Antimicrobials for Improved Health and Product Safety

Production Systems StudiedDairy cattle Swine poultry Aquaculture

Laboratory and Field Expertisebull Molecular biologist with

transgenic and knockout mouse background

bull Heterologous gene expression in yeast bacteria mice and cell culture

bull Induced Pluripotent Stem cell production via lentiviral transduction

bull Mouse colony animal husbandry and embryo transfer

Research InterestsDavid M Donovan PhD Research Scientist (Molecular Biologist) at the US Department of Agriculture received his PhD in 1987 in molecular genetics of the yeast Saccharomyces cerevisiae and has 22 years experience in heterologous gene expression He spent 15 years at the NIH culminating in Section Chief Transgenic and Knockout Mouse lab NIA In 2002 he joined the USDA where he has been developing antimicrobials for the treatment of mastitis pathogens including Staphylococcus aureus His enzyme antimicrobials harbor three unique synergistic lytic domains and a protein transduction domain to target intracellular pathogens and have been shown to be highly refractory to resistance development His constructs eradicate both extracellular S aureus [in a rat nasal colonization model and murine systemic infections] and intracellular pathogens ex vivo in bovine mammary epithelial cells and in both a mouse model of mastitis and osteomyelitis He is working to identify protein feed additives as alternative to antibiotic growth promotants

Thomas F DuceyMicrobiologist

ThomasDuceyarsusdagov

843-669-5203 x112

Current Projectsbull Microbial responses to wetland restoration as a part

of the Mid‐Atlantic Region Conservation Effects Assessment Project

bull Response of the microbial rhizosphere and arbuscular mycorrhizae fungi to clover cover crop and conservation tillage in cotton production

bull Isolation of E coli and Enterococcus species from swine wastewater poultry litter and agriculturally‐impacted groundwater for the determination of baseline antibiotic resistance levels in agricultural production systems

Selected Publicationsbull Ducey et al Soil physicochemical conditions

denitrification rates and nosZ abundance in NC coastal plain restored wetlands 2015 J Environ Qual 44 1011‐1022

bull Ducey et al Microbial community analysis of swine wastewater anaerobic lagoons by next‐generation DNA sequencing 2013 Anaerobe 2150‐57

Coastal Plain Soil Water and Plant Research Center

Mailing Address2611 West Lucas StreetFlorence SC 29501

National Program(s)211 ndash Water Availability and Water Management212 ndash Climate Change Soils and Emissions214 ndash Agricultural and Industrial Byproducts

CRIS Project(s)Managing Water Availability and Quality (NP 211)Improving Chemical Physical and Biological Properties of Degraded Sandy Soils (NP 212)Innovative Bioresource Management Technologies (NP 214)

Production Systems StudiedCrops Poultry and Swine

Laboratory and Field Expertisebull Classical Microbiology

bull DetectionEnumerationIsolationbull New species identification

bull Molecular Biologybull T‐RFLPARISAbull qPCRReal Time PCRbull High‐throughput DNA Sequencing

(Ion Torrent)

Research Interestsbull Southeastern US coastal plain wetland restoration

and its effect on microbial community composition and function

bull Animal wastewater treatment systems with a particular focus on pathogen reduction and antibiotic resistance gene elimination

bull Microbial community analysis and response to crop conservation and cover cropping management practices

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Kimberly CookResearch Microbiologist

KimCookarsusdagov

270-781-2579 ext 232

Current Projectsbull Capture and identify mobile genetic elements

associated with bacteria in soils with applied poultry litter effect of application method

bull Evaluate persistence and concentration of antibiotics and bacteria with AR genes in waste treatment systems and soils with application manures

bull Transport and adhesion of bacteria with AR genesbull Evaluate AR properties of E coli and enterococci

isolates from agricultural ecosystems

Selected Publicationsbull Durso LM and KL Cook 2014 Impacts of antibiotic

use in agriculture what are the benefits and risks CurrOpinion Microbiol 1937‐44 2014

bull Cook KL AMP Netthisinghe and RA Gilfillen 2014 Detection of Pathogens Indicators and Antibiotic Resistance Genes after Land Application of Poultry Litter J Environ Qual 43 1546‐1558

bull Netthisinghe AMP KL Cook C Rice RA Gilfillen and KR Sistani 2013 Soil Nutrients Bacteria Populations and Veterinary Pharmaceuticals across a Backgrounding Beef Feedlot J Environ Qual 42 532‐544

Food Animal Environmental Systems Research Unit

Mailing Address2413 Nashville Red ndash B5Bowling Green KY 42101

National Program(s)212 ndash Soil and Air Research

CRIS Project(s)Efficient Management and Use of Animal Manure to Protect Human Health and Environmental Quality

Production Systems StudiedPoultry Swine Beef

Laboratory and Field Expertisebull Soils manure and waste

treatment systemsbull PCR Quantitiative real‐time

PCRbull Culture and antimicrobial

susceptibilitybull Isolation and characterization of

mobile genetic elements carrying genes for antibiotic resistance

Research Interestsbull Characterizing persistence and transmission of

antibiotics antibiotic resistance (AR) genes and AR bacteria through agroecosystems

bull Capture and characterize mobile genetic elements carrying AR genes between microbial populations in soils with applied manures

bull Strain level differences in resistance transport and adhesion properties of bacteria with AR genes

Annie DonoghueResearch Leader (Physiologist)

AnnieDonoghuearsusdagov479-575-2413

7

Current Projectsbull Use of natural remedies to alleviate enteric

pathogens in organic and conventionally raised poultry

bull Alternatives to antibiotics for controlling Salmonella and Campylobacter in poultry and poultry products

Selected Publicationsbull Donoghue AM Venkitanarayanan K Arsi K Woo‐

Ming A Upadhyaya I Kollanoor‐Johny A Darre MJ Upadhyay A Fanatico A and Donoghue DJ 2015 Organic Poultry Developing Natural Solutions for Reducing Pathogens and Improving Production Organic Agriculture Research Symp in press

bull Arsi K Donoghue AM Woo‐Ming A Blore PJ and Donoghue DJ 2015 Intracloacal inoculation an effective screening method for determining the efficacy of probiotic bacterial isolates against Campylobactercolonization in broiler chickens J Food Prot 78 209‐213

bull Arsi K Donoghue AM Venkitanarayanan K Kollanoor‐Johny A Fanatico AC Blore PJ and Donoghue DJ2014 The efficacy of the natural plant extracts thymol and carvacrol against Campylobacter colonization in broiler chickens J Food Safety 34 321ndash325

Poultry Production and Products Safety Research Unit

Mailing AddressUniversity Of ArkansasPOSC O‐303Fayetteville AR 72701

National Program(s)108 ndash Food Safety103 ndash Animal Health

CRIS Project(s)Alternative Intervention and Control Strategies for Foodborne Pathogens in Poultry and Poultry Products

Novel Therapeutic Diagnostic and Management Strategies to Reduce Antibiotic Use in Poultry Production

Production Systems StudiedPoultry

Laboratory and Field ExpertiseLab uses traditional microbiological culture and molecular biological techniques to study food borne pathogens Organic and conventional practices for poultry production

Research Interestsbull developing alternatives to antibiotic use in poultry bull developing strategies to reduce or eliminate pathogen

contamination with a focus on Campylobacter and Salmonella

bull developing sustainable and organic farming practices for poultry producers

David DonavanResearch Molecular Biologist

DavidDonovanarsusdagov

Ce 443-690-4251 Office 301-504-9150

Current Projectsbull Mastitis a cow‐side diagnosticbull Mastitis treatment with triple‐acting antimicrobialsbull Clostridium perfringens novel endolysins that are heat‐resistantbull Yeast expressed endolysins as an alternative to antibiotics in animal feedbull CRISPRCas9 genomic engineering of cow and pig embryos

Selected Publicationsbull Rodriacuteguez‐Rubio L Martiacutenez B Rodriacuteguez A Donovan DM Goumltz F et al The

phage lytic proteins from the Staphylococcus aureus bacteriophage vB_SauS‐phiIPLA88 display multiple active catalytic domains and do not trigger staphylococcal resistance PloS one 2013 8(5)e64671

bull Singh PK Donovan DM Kumar A Intravitreal injection of the chimeric phage endolysin Ply187 protects mice from Staphylococcus aureus endophthalmitis Antimicrobial agents and chemotherapy 2014 58(8)4621‐9

bull Swift SM Seal BS Garrish JK Oakley BB Hiett K et al A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens‐Specific Cell Wall Binding Domain Creates an Anti‐Clostridium Antimicrobial with Improved Thermostability Viruses 2015 7(6)3019‐34

Link to all publications httpwwwncbinlmnihgovsitesmyncbi1jOJlsCcVSxQTbibliography41565643publicsort=dateampdirection=ascending

Animal Biosciences and Biotechnology Laboratory

Mailing AddressRoom 104 10300 Baltimore AveBLDG 230 BARC‐EastBeltsville MD 20705

National ProgramNP101 Food Animal Production

CRIS Project TitleDeveloping Genetic Biotechnologies for Increased Food Animal Production including Novel Antimicrobials for Improved Health and Product Safety

Production Systems StudiedDairy cattle Swine poultry Aquaculture

Laboratory and Field Expertisebull Molecular biologist with

transgenic and knockout mouse background

bull Heterologous gene expression in yeast bacteria mice and cell culture

bull Induced Pluripotent Stem cell production via lentiviral transduction

bull Mouse colony animal husbandry and embryo transfer

Research InterestsDavid M Donovan PhD Research Scientist (Molecular Biologist) at the US Department of Agriculture received his PhD in 1987 in molecular genetics of the yeast Saccharomyces cerevisiae and has 22 years experience in heterologous gene expression He spent 15 years at the NIH culminating in Section Chief Transgenic and Knockout Mouse lab NIA In 2002 he joined the USDA where he has been developing antimicrobials for the treatment of mastitis pathogens including Staphylococcus aureus His enzyme antimicrobials harbor three unique synergistic lytic domains and a protein transduction domain to target intracellular pathogens and have been shown to be highly refractory to resistance development His constructs eradicate both extracellular S aureus [in a rat nasal colonization model and murine systemic infections] and intracellular pathogens ex vivo in bovine mammary epithelial cells and in both a mouse model of mastitis and osteomyelitis He is working to identify protein feed additives as alternative to antibiotic growth promotants

Thomas F DuceyMicrobiologist

ThomasDuceyarsusdagov

843-669-5203 x112

Current Projectsbull Microbial responses to wetland restoration as a part

of the Mid‐Atlantic Region Conservation Effects Assessment Project

bull Response of the microbial rhizosphere and arbuscular mycorrhizae fungi to clover cover crop and conservation tillage in cotton production

bull Isolation of E coli and Enterococcus species from swine wastewater poultry litter and agriculturally‐impacted groundwater for the determination of baseline antibiotic resistance levels in agricultural production systems

Selected Publicationsbull Ducey et al Soil physicochemical conditions

denitrification rates and nosZ abundance in NC coastal plain restored wetlands 2015 J Environ Qual 44 1011‐1022

bull Ducey et al Microbial community analysis of swine wastewater anaerobic lagoons by next‐generation DNA sequencing 2013 Anaerobe 2150‐57

Coastal Plain Soil Water and Plant Research Center

Mailing Address2611 West Lucas StreetFlorence SC 29501

National Program(s)211 ndash Water Availability and Water Management212 ndash Climate Change Soils and Emissions214 ndash Agricultural and Industrial Byproducts

CRIS Project(s)Managing Water Availability and Quality (NP 211)Improving Chemical Physical and Biological Properties of Degraded Sandy Soils (NP 212)Innovative Bioresource Management Technologies (NP 214)

Production Systems StudiedCrops Poultry and Swine

Laboratory and Field Expertisebull Classical Microbiology

bull DetectionEnumerationIsolationbull New species identification

bull Molecular Biologybull T‐RFLPARISAbull qPCRReal Time PCRbull High‐throughput DNA Sequencing

(Ion Torrent)

Research Interestsbull Southeastern US coastal plain wetland restoration

and its effect on microbial community composition and function

bull Animal wastewater treatment systems with a particular focus on pathogen reduction and antibiotic resistance gene elimination

bull Microbial community analysis and response to crop conservation and cover cropping management practices

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Annie DonoghueResearch Leader (Physiologist)

AnnieDonoghuearsusdagov479-575-2413

7

Current Projectsbull Use of natural remedies to alleviate enteric

pathogens in organic and conventionally raised poultry

bull Alternatives to antibiotics for controlling Salmonella and Campylobacter in poultry and poultry products

Selected Publicationsbull Donoghue AM Venkitanarayanan K Arsi K Woo‐

Ming A Upadhyaya I Kollanoor‐Johny A Darre MJ Upadhyay A Fanatico A and Donoghue DJ 2015 Organic Poultry Developing Natural Solutions for Reducing Pathogens and Improving Production Organic Agriculture Research Symp in press

bull Arsi K Donoghue AM Woo‐Ming A Blore PJ and Donoghue DJ 2015 Intracloacal inoculation an effective screening method for determining the efficacy of probiotic bacterial isolates against Campylobactercolonization in broiler chickens J Food Prot 78 209‐213

bull Arsi K Donoghue AM Venkitanarayanan K Kollanoor‐Johny A Fanatico AC Blore PJ and Donoghue DJ2014 The efficacy of the natural plant extracts thymol and carvacrol against Campylobacter colonization in broiler chickens J Food Safety 34 321ndash325

Poultry Production and Products Safety Research Unit

Mailing AddressUniversity Of ArkansasPOSC O‐303Fayetteville AR 72701

National Program(s)108 ndash Food Safety103 ndash Animal Health

CRIS Project(s)Alternative Intervention and Control Strategies for Foodborne Pathogens in Poultry and Poultry Products

Novel Therapeutic Diagnostic and Management Strategies to Reduce Antibiotic Use in Poultry Production

Production Systems StudiedPoultry

Laboratory and Field ExpertiseLab uses traditional microbiological culture and molecular biological techniques to study food borne pathogens Organic and conventional practices for poultry production

Research Interestsbull developing alternatives to antibiotic use in poultry bull developing strategies to reduce or eliminate pathogen

contamination with a focus on Campylobacter and Salmonella

bull developing sustainable and organic farming practices for poultry producers

David DonavanResearch Molecular Biologist

DavidDonovanarsusdagov

Ce 443-690-4251 Office 301-504-9150

Current Projectsbull Mastitis a cow‐side diagnosticbull Mastitis treatment with triple‐acting antimicrobialsbull Clostridium perfringens novel endolysins that are heat‐resistantbull Yeast expressed endolysins as an alternative to antibiotics in animal feedbull CRISPRCas9 genomic engineering of cow and pig embryos

Selected Publicationsbull Rodriacuteguez‐Rubio L Martiacutenez B Rodriacuteguez A Donovan DM Goumltz F et al The

phage lytic proteins from the Staphylococcus aureus bacteriophage vB_SauS‐phiIPLA88 display multiple active catalytic domains and do not trigger staphylococcal resistance PloS one 2013 8(5)e64671

bull Singh PK Donovan DM Kumar A Intravitreal injection of the chimeric phage endolysin Ply187 protects mice from Staphylococcus aureus endophthalmitis Antimicrobial agents and chemotherapy 2014 58(8)4621‐9

bull Swift SM Seal BS Garrish JK Oakley BB Hiett K et al A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens‐Specific Cell Wall Binding Domain Creates an Anti‐Clostridium Antimicrobial with Improved Thermostability Viruses 2015 7(6)3019‐34

Link to all publications httpwwwncbinlmnihgovsitesmyncbi1jOJlsCcVSxQTbibliography41565643publicsort=dateampdirection=ascending

Animal Biosciences and Biotechnology Laboratory

Mailing AddressRoom 104 10300 Baltimore AveBLDG 230 BARC‐EastBeltsville MD 20705

National ProgramNP101 Food Animal Production

CRIS Project TitleDeveloping Genetic Biotechnologies for Increased Food Animal Production including Novel Antimicrobials for Improved Health and Product Safety

Production Systems StudiedDairy cattle Swine poultry Aquaculture

Laboratory and Field Expertisebull Molecular biologist with

transgenic and knockout mouse background

bull Heterologous gene expression in yeast bacteria mice and cell culture

bull Induced Pluripotent Stem cell production via lentiviral transduction

bull Mouse colony animal husbandry and embryo transfer

Research InterestsDavid M Donovan PhD Research Scientist (Molecular Biologist) at the US Department of Agriculture received his PhD in 1987 in molecular genetics of the yeast Saccharomyces cerevisiae and has 22 years experience in heterologous gene expression He spent 15 years at the NIH culminating in Section Chief Transgenic and Knockout Mouse lab NIA In 2002 he joined the USDA where he has been developing antimicrobials for the treatment of mastitis pathogens including Staphylococcus aureus His enzyme antimicrobials harbor three unique synergistic lytic domains and a protein transduction domain to target intracellular pathogens and have been shown to be highly refractory to resistance development His constructs eradicate both extracellular S aureus [in a rat nasal colonization model and murine systemic infections] and intracellular pathogens ex vivo in bovine mammary epithelial cells and in both a mouse model of mastitis and osteomyelitis He is working to identify protein feed additives as alternative to antibiotic growth promotants

Thomas F DuceyMicrobiologist

ThomasDuceyarsusdagov

843-669-5203 x112

Current Projectsbull Microbial responses to wetland restoration as a part

of the Mid‐Atlantic Region Conservation Effects Assessment Project

bull Response of the microbial rhizosphere and arbuscular mycorrhizae fungi to clover cover crop and conservation tillage in cotton production

bull Isolation of E coli and Enterococcus species from swine wastewater poultry litter and agriculturally‐impacted groundwater for the determination of baseline antibiotic resistance levels in agricultural production systems

Selected Publicationsbull Ducey et al Soil physicochemical conditions

denitrification rates and nosZ abundance in NC coastal plain restored wetlands 2015 J Environ Qual 44 1011‐1022

bull Ducey et al Microbial community analysis of swine wastewater anaerobic lagoons by next‐generation DNA sequencing 2013 Anaerobe 2150‐57

Coastal Plain Soil Water and Plant Research Center

Mailing Address2611 West Lucas StreetFlorence SC 29501

National Program(s)211 ndash Water Availability and Water Management212 ndash Climate Change Soils and Emissions214 ndash Agricultural and Industrial Byproducts

CRIS Project(s)Managing Water Availability and Quality (NP 211)Improving Chemical Physical and Biological Properties of Degraded Sandy Soils (NP 212)Innovative Bioresource Management Technologies (NP 214)

Production Systems StudiedCrops Poultry and Swine

Laboratory and Field Expertisebull Classical Microbiology

bull DetectionEnumerationIsolationbull New species identification

bull Molecular Biologybull T‐RFLPARISAbull qPCRReal Time PCRbull High‐throughput DNA Sequencing

(Ion Torrent)

Research Interestsbull Southeastern US coastal plain wetland restoration

and its effect on microbial community composition and function

bull Animal wastewater treatment systems with a particular focus on pathogen reduction and antibiotic resistance gene elimination

bull Microbial community analysis and response to crop conservation and cover cropping management practices

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

David DonavanResearch Molecular Biologist

DavidDonovanarsusdagov

Ce 443-690-4251 Office 301-504-9150

Current Projectsbull Mastitis a cow‐side diagnosticbull Mastitis treatment with triple‐acting antimicrobialsbull Clostridium perfringens novel endolysins that are heat‐resistantbull Yeast expressed endolysins as an alternative to antibiotics in animal feedbull CRISPRCas9 genomic engineering of cow and pig embryos

Selected Publicationsbull Rodriacuteguez‐Rubio L Martiacutenez B Rodriacuteguez A Donovan DM Goumltz F et al The

phage lytic proteins from the Staphylococcus aureus bacteriophage vB_SauS‐phiIPLA88 display multiple active catalytic domains and do not trigger staphylococcal resistance PloS one 2013 8(5)e64671

bull Singh PK Donovan DM Kumar A Intravitreal injection of the chimeric phage endolysin Ply187 protects mice from Staphylococcus aureus endophthalmitis Antimicrobial agents and chemotherapy 2014 58(8)4621‐9

bull Swift SM Seal BS Garrish JK Oakley BB Hiett K et al A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens‐Specific Cell Wall Binding Domain Creates an Anti‐Clostridium Antimicrobial with Improved Thermostability Viruses 2015 7(6)3019‐34

Link to all publications httpwwwncbinlmnihgovsitesmyncbi1jOJlsCcVSxQTbibliography41565643publicsort=dateampdirection=ascending

Animal Biosciences and Biotechnology Laboratory

Mailing AddressRoom 104 10300 Baltimore AveBLDG 230 BARC‐EastBeltsville MD 20705

National ProgramNP101 Food Animal Production

CRIS Project TitleDeveloping Genetic Biotechnologies for Increased Food Animal Production including Novel Antimicrobials for Improved Health and Product Safety

Production Systems StudiedDairy cattle Swine poultry Aquaculture

Laboratory and Field Expertisebull Molecular biologist with

transgenic and knockout mouse background

bull Heterologous gene expression in yeast bacteria mice and cell culture

bull Induced Pluripotent Stem cell production via lentiviral transduction

bull Mouse colony animal husbandry and embryo transfer

Research InterestsDavid M Donovan PhD Research Scientist (Molecular Biologist) at the US Department of Agriculture received his PhD in 1987 in molecular genetics of the yeast Saccharomyces cerevisiae and has 22 years experience in heterologous gene expression He spent 15 years at the NIH culminating in Section Chief Transgenic and Knockout Mouse lab NIA In 2002 he joined the USDA where he has been developing antimicrobials for the treatment of mastitis pathogens including Staphylococcus aureus His enzyme antimicrobials harbor three unique synergistic lytic domains and a protein transduction domain to target intracellular pathogens and have been shown to be highly refractory to resistance development His constructs eradicate both extracellular S aureus [in a rat nasal colonization model and murine systemic infections] and intracellular pathogens ex vivo in bovine mammary epithelial cells and in both a mouse model of mastitis and osteomyelitis He is working to identify protein feed additives as alternative to antibiotic growth promotants

Thomas F DuceyMicrobiologist

ThomasDuceyarsusdagov

843-669-5203 x112

Current Projectsbull Microbial responses to wetland restoration as a part

of the Mid‐Atlantic Region Conservation Effects Assessment Project

bull Response of the microbial rhizosphere and arbuscular mycorrhizae fungi to clover cover crop and conservation tillage in cotton production

bull Isolation of E coli and Enterococcus species from swine wastewater poultry litter and agriculturally‐impacted groundwater for the determination of baseline antibiotic resistance levels in agricultural production systems

Selected Publicationsbull Ducey et al Soil physicochemical conditions

denitrification rates and nosZ abundance in NC coastal plain restored wetlands 2015 J Environ Qual 44 1011‐1022

bull Ducey et al Microbial community analysis of swine wastewater anaerobic lagoons by next‐generation DNA sequencing 2013 Anaerobe 2150‐57

Coastal Plain Soil Water and Plant Research Center

Mailing Address2611 West Lucas StreetFlorence SC 29501

National Program(s)211 ndash Water Availability and Water Management212 ndash Climate Change Soils and Emissions214 ndash Agricultural and Industrial Byproducts

CRIS Project(s)Managing Water Availability and Quality (NP 211)Improving Chemical Physical and Biological Properties of Degraded Sandy Soils (NP 212)Innovative Bioresource Management Technologies (NP 214)

Production Systems StudiedCrops Poultry and Swine

Laboratory and Field Expertisebull Classical Microbiology

bull DetectionEnumerationIsolationbull New species identification

bull Molecular Biologybull T‐RFLPARISAbull qPCRReal Time PCRbull High‐throughput DNA Sequencing

(Ion Torrent)

Research Interestsbull Southeastern US coastal plain wetland restoration

and its effect on microbial community composition and function

bull Animal wastewater treatment systems with a particular focus on pathogen reduction and antibiotic resistance gene elimination

bull Microbial community analysis and response to crop conservation and cover cropping management practices

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Thomas F DuceyMicrobiologist

ThomasDuceyarsusdagov

843-669-5203 x112

Current Projectsbull Microbial responses to wetland restoration as a part

of the Mid‐Atlantic Region Conservation Effects Assessment Project

bull Response of the microbial rhizosphere and arbuscular mycorrhizae fungi to clover cover crop and conservation tillage in cotton production

bull Isolation of E coli and Enterococcus species from swine wastewater poultry litter and agriculturally‐impacted groundwater for the determination of baseline antibiotic resistance levels in agricultural production systems

Selected Publicationsbull Ducey et al Soil physicochemical conditions

denitrification rates and nosZ abundance in NC coastal plain restored wetlands 2015 J Environ Qual 44 1011‐1022

bull Ducey et al Microbial community analysis of swine wastewater anaerobic lagoons by next‐generation DNA sequencing 2013 Anaerobe 2150‐57

Coastal Plain Soil Water and Plant Research Center

Mailing Address2611 West Lucas StreetFlorence SC 29501

National Program(s)211 ndash Water Availability and Water Management212 ndash Climate Change Soils and Emissions214 ndash Agricultural and Industrial Byproducts

CRIS Project(s)Managing Water Availability and Quality (NP 211)Improving Chemical Physical and Biological Properties of Degraded Sandy Soils (NP 212)Innovative Bioresource Management Technologies (NP 214)

Production Systems StudiedCrops Poultry and Swine

Laboratory and Field Expertisebull Classical Microbiology

bull DetectionEnumerationIsolationbull New species identification

bull Molecular Biologybull T‐RFLPARISAbull qPCRReal Time PCRbull High‐throughput DNA Sequencing

(Ion Torrent)

Research Interestsbull Southeastern US coastal plain wetland restoration

and its effect on microbial community composition and function

bull Animal wastewater treatment systems with a particular focus on pathogen reduction and antibiotic resistance gene elimination

bull Microbial community analysis and response to crop conservation and cover cropping management practices

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Rob DunganResearch Microbiologist

RobertDunganarsusdagov

208-423-6553

Current Projectsbull Monitoring antibiotic drugs in irrigation return waters in

south‐central Idahobull Investigating the impact of moisture content and

temperature and application rate of dairy manure solids and compost on the occurrence of antibiotic resistant bacteria and antibiotic resistance genes in soil

bull Defining antibiotic resistance in indicator organisms isolated from dairy and aquaculture production systems

Selected Publicationsbull Franklin AM DS Aga E Cytryn LM Durso JE McLain

A Pruden MC Roberts MJ Rothrock Jr DD Snow JE Watson and RS Dungan Antibiotics in Agroecosystems Introduction to Special Section 45377‐393 2016

bull Rothrock MJ PL Keen KL Cook LM Durso AM Franklin and RS Dungan How should we be determining background and baseline antibiotic resistance levels in agroecosystems research J Environ Qual 45420‐431 2016

Northwest Irrigation and Soils Research Unit

Mailing Address3793 North 3600 EastKimberly ID 83341

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Improving the Sustainability of Integrated Dairy‐Irrigated Crop Production Systems

Production Systems StudiedDairy

Laboratory and Field Expertisebull Collection of airborne

microorganismsbull Quantitative microbial risk

assessmentbull Molecular‐based detection and

quantification of pathogens and antibiotic resistance genes

Research Interestsbull Influence of long‐term dairy manure applications as well as

over application on the occurrence and transport of antibiotic resistance genes in soils under crop rotation

bull Heavy metal coselection of antibiotic resistance in agricultural soils as impacted by copper in dairy wastewater

bull Airborne transport of antibiotic resistant bacteria from dairy feedlots and housing

bull Determine factors that contribute to the prevalence of antibiotic resistance in aquaculture production systems

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Lisa DursoMicrobiologist

LisaDursoarsusdagov

402-472-9622

Current Projectsbull Fate of pathogens fecal indicators antibiotic

resistant bacteria and antibiotic resistance genes in feedlot runoff and agricultural soils

bull Assessing Epidemiological Cutoff (ECOFF) Values from agricultural E coli and Enterococcus

bull Long‐term survival of non‐O157 Shiga‐toxigenic E coli in runoff

Selected Publicationsbull Durso et al 2016 Assessment of selected antibiotic

resistances in ungrazed native Nebraska prairie soils J Environ Qual45454‐462

bull Durso and Cook 2014 Impacts of antibiotic use in agriculture what are the benefits and risks Curr Opinion Microbiol 1937‐44 2014

bull Durso et al 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7e48325

bull Durso et al 2011 Virulence‐associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach J Microbiol Methods 84278‐282

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Soil and Water

CRIS Project(s)

Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedBeef cattle swine

Laboratory and Field Expertisebull Primary isolation of E coli from

manure‐impacted samplesbull Culture and quantification of

fecal indicator organismsbull Bacterial characterization and

quantification using PCR and qPCR methods

bull Phenotypic assessment of antibiotic resistance using CLSI standard methods

Research Interestsbull Applied relationships between survival of antibiotic

resistant bacteria and persistence of antibiotic resistance genes in agriculturally ndashimpacted environments

bull Comparability of antibiotic resistance gene assays across methodological platforms production systems and sample types

bull Defining ldquoresistancerdquo for agricultural and environmental bacteria in a way that integrates human animal and environmental health

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Tom EdringtonResearch Animal Scientist

TomEdringtonarsusdagov

979-260-3757

Current Projectsbull Current research efforts are focused on

understanding Salmonella infection of the peripheral lymph nodes of cattle and swine and designingevaluating effective interventions to prevent uptake by or eliminate this pathogen from these nodes

Selected Publicationsbull Edrington TS KM Bischoff GH Loneragan and DJ

Nisbet 2014 Evaluation of feeding dried distillerrsquos grains containing virginiamycin on antimicrobial susceptibilities in fecal isolates of Enterococcus and Escherichia coli and prevalence of resistance genes in cattle J Anim Sci 921144‐1149

bull Edrington TS WE Fox TR Callaway RC Anderson DW Hoffman and DJ Nisbet 2009 Pathogen prevalence and influence of composted dairy manure application on antimicrobial resistance profiles of commensal soil bacteria Foodborne Path Dis 6217‐224

bull Edrington TS TR Callaway RC Anderson and DJ Nisbet 2008 Prevalence of multi‐drug resistant Salmonella on commercial dairies utilizing a single heifer raising facility J Food Prot 7127‐34

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)108 ndash Food Safety

CRIS Project(s)Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Production Systems StudiedBeef and Dairy cattle Swine

Laboratory and Field Expertisebull Sample collection in livestock

production and processing facilities

bull Detection and enumeration of Salmonella and E coli O157H7 using traditional culture based and PCR methods

bull Antimicrobial susceptibility testing of above pathogens using broth microdilutiontechniques

Research Interestsbull Conducts research on foodborne pathogens and factors

involved in their population dynamics in beef and dairy cattle and swine as related to pre‐harvest food safety

bull Develops and evaluates the efficacy of pre‐harvest interventions for control of Salmonella and E coliO157H7

bull Examines antimicrobial susceptibility and mechanisms of resistance in foodborne pathogens

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Jonathan FryeResearch Microbiologist

JonathanFryearsusdagov

706-546-3677

Current Projectsbull Analyzing 195 genome sequences of diverse AR and

MDR Salmonella isolated from animals bull Determining Salmonella susceptibility to biocides

used as interventions on‐farm in processing and in retail food environments and linkage to AR

bull Analyzing surface water for the prevalence of Salmonella determining whether water is a reservoir for Salmonella and waterrsquos role in AR development

Selected Publicationsbull Frye J G and C R Jackson 2013 Genetic mechanisms of

antimicrobial resistance identified in Salmonella enterica Escherichia coli and Enteroccocus spp isolated from US food animals Front Microbiol 2013 May 234135

bull Glenn L M R L Lindsey J P Folster G Pecic P Boerlin M W Gilmour H Harbottle S Zhao P F McDermott P J Fedorka‐Cray J G Frye 2013 Antimicrobial resistance genes in multi‐drug resistant Salmonella enterica isolated from animals retail meats and humans in the US and Canada Microb Drug Resist 2013 Jun19(3)175‐184

bull Frye J G R L Lindsey R J Meinersmann M E Berrang C R Jackson M D Englen J B Turpin and P J Fedorka‐Cray 2011 Related antimicrobial resistance genes detected in different bacterial species co‐isolated from swine fecal samples Foodborne Pathog Dis Jun8(6)663‐79

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressRoom 838 US National Poultry Research Center950 College Station RoadAthens GA 30605

National Program108 ndash Food Safety

CRIS Project and GrantsMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Determination of the Prevalence of Resistance to Biocides in Salmonella and Identification of the Genetic Mechanisms of Resistance

Production Systems StudiedPrimarily Chickens with Cattle Dairy Cattle Swine and Turkeys also investigated

Laboratory and Field Expertisebull PCR multiplex‐PCR RT‐PCR

microarrays PFGE sequencing WGS NGS bioinformatics

bull Developing detection assaysbull Surface water sampling and

bacterial isolation

Research Interestsbull Investigate Salmonella enterica one of the most

prevalent foodborne pathogens associated with poultry bull Identify the mechanisms of antimicrobial resistance (AR)

in Salmonella with a focus on multidrug‐resistance (MDR) and the role of mobile genetic elements of AR

bull Determine how AR develops in the preharvestenvironment and how Salmonella acquires AR

bull Study the genomic characteristics that lead to diverse serovars host specificity pathogenics and AR

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Kelli HiettLead ScientistMicrobiologist

KelliHiettarsusdagov706-546-3593706-540-2866

Current Projectsbull Perform proteomic comparisons of genetically distinct C

jejuni isolates that vary in their ability to colonize broiler chickens

bull Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C jejuni isolates and subsequently perform proteomic analyses to determine the mechanisms associated with die‐off

bull Perform microbiomemicrobial ecology analyses on poultry samples and poultry associated environmental samples collected from several small multi‐commodity antimicrobial growth promoter (AGP)‐free farms

Selected Publicationsbull Hiett KL Stintzi A Andacht TM Kuntz RL and Seal BS

Genomic differences between Campylobacter jejuni isolatesidentify surface membrane and flagellar function gene productspotentially important for colonizing the chicken intestine FunctIntegr Genomics 8407‐420 2008

bull Rothrock MJ Jr Hiett KL Gamble J Caudill AC Cicconi‐Hogan KM and Caporaso JG A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples J Vis Exp 94 e52161 doi10379152161 2014

Poultry Microbiological Safety and Processing Research Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Production Systems Studiedbull Poultry ndash primarily broiler chickensbull Small multi‐commodity

antimicrobial growth promoter (AGP)‐free farms

bull Producecompostenvironmental

Laboratory and Field Expertisebull Cultural and molecular detection

of foodborne pathogens with special emphasis on Campylobacter spp

bull Molecular epidemiology of pathogens across poultry production and processing environments

bull Molecular genetics and proteomics

bull Antimicrobial susceptibility tests (AST)

Research Interestsbull Utilize genomic and proteomic approaches to determine the

presence and expression of virulence fitness and antimicrobial resistance genes in Campylobacter species in poultry productionprocessing environments and produce farms

bull Develop refine and implement improved methods for the detection and recovery of zoonotic pathogens and emerging foodborne pathogens

bull Perform microbiomemicrobial ecology analyses on chicken gastrointestinal material to increase our basic knowledge of the microbial ecology of the broiler chicken gut

bull Perform microbial ecology analyses on the environment of small poultry farms and small produce farms

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Mark IbekweMicrobiologist

MarkIbekwearsusdagov

951-369-4828

Current Projectsbull Identification of factors fostering the dissemination

of transferable antibiotic resistances in agroecosystem

bull Shiga Toxin‐producing E coli detection using recombinase polymerase amplification (RPA)

bull Persistence of Escherichia coli O157H7 on plant roots grown under water and salinity stress regimes

Selected PublicationsIbekwe A M S E Murinda A K Graves 2011 Genetic Diversity and Antimicrobial Resistance of Escherichia colifrom Human and Animal Sources uncovers Multiple Resistances from Human Sources PLoS ONE 6(6) e20819 doi101371journalpone0020819Murinda S E A M Ibekwe S Syamil A Cruz S Park N Syahadatain F Amira L A Samad K Baquir K Muthaiyah B Santiago A Rusli S Balkcom2014 Real‐Time isothermal detection of Shiga toxinndashproducing Escherichia coli using recombinase polymerase amplification Foodborne Pathogens and Disease 11529‐536

US Salinity Laboratory

Mailing Address450 W Big Springs RdRiverside CA 92507

National Program(s)212‐Soil and Air

CRIS Project(s)Protection of Food and Water Supplies from Pathogen Contamination

Production Systems StudiedDairy cattle and Fresh produce

Laboratory and Field Expertisebull Sampling surface water

manure soil and leaf surfaces for pathogens

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Resistance gene characterization

Research InterestsMicrobial ecology and metagenomics of plant‐microbe interactions with human enteric pathogensMetagenomics based bacterial source tracking for water quality evaluationPersistence of human enteric pathogens in the pre‐harvest environmentMetagenomics and mobilome of antimicrobials inAgroecosystems

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Charlene JacksonResearch Microbiologist

CharleneJacksonarsusdagov

706-546-3604

Current Projectsbull Prevalence and identification of replicon families in

multi‐drug resistant enterococci from poultrybull Identification of antimicrobial resistance genes and

virulence factors in Enterococcus cecorum causing disease in poultry

bull Identification of extended‐spectrum beta‐lactamase (ESBL) resistance genes in E coli from food animals

Selected Publicationsbull Adenipekun EO Jackson CR Oluwadun A Iwalokun BA

Frye JG Barrett JB Hiott LM and Woodley TA 2015 Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos Nigeria Microb Drug Resist 21(3)358‐65 Corresponding author

bull Jackson CR Davis JA and Barrett JB 2013 Prevalence and characterization of methicillin‐resistant Staphylococcus aureus isolated from retail meat and humans in Georgia J Clin Microbiol 51(4)1199‐207

bull Furtula V Jackson CR Farrell EG Barrett JB Hiott LM and Chambers P 2013 Antimicrobial resistance in Enterococcus spp isolated from environmental samples in an area of intensive poultry production Int J Environ Res Public Health Special Issue Environmental Determinants of Infectious Disease Transmission 10(3)1020‐36 Corresponding author

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressUS National Poultry Research Ctr950 College Station RoadAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS ProjectMolecular Approaches for the Identification and Characterization of Antimicrobial Resistance in Foodborne Pathogens

Production Systems StudiedPoultry Cattle Dairy Cattle Swine

Laboratory and Field Expertisebull Isolation and detection of

commensal bacteria from food animals retail food and the environment

bull Detection of antimicrobial resistance genes and mobile genetic elements using molecular tools

bull Antimicrobial susceptibility testing

bull Development of molecular tools for identification of enterococci

Research Interestsbull Identify mechanisms of antimicrobial resistance and

genetic types of commensal bacteria (Enterococcus Escherichia coli Staphylococcus) from food animals

bull Evaluate the role of Enterococcus and generic E coli as reservoirs of antimicrobial resistance genes and mobile genetic elements

bull Determine linkage of antimicrobial resistance and resistance to biocides in Enterococcus and E coli from poultry

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Mark JenkinsMicrobiologist

MarkJenkinsarsusdagov301-504-8054

Current Projectsbull Improvement of coccidiosis vaccines through

administration of Eimeria oocysts‐gelatin beadsbull Development of in vitro assays for drug resistance in

avian Eimeriabull Study of Crypsovirus and its role in fecundity of

Cryptosporidium parvum

Selected PublicationsJenkins MC OBrien CN Fuller L Mathis GF Fetterer R (2014) A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella Vet Parasitol 206153‐158

bull Jenkins MC OBrien CN Santin M Fayer R (2015) Changes in the levels of Cryspovirus during in vitro development of Cryptosporidium parvum Parasitol Res 114 2063‐2068

bull Jenkins MC Parker C OBrien C Persyn J Barlow D Miska K Fetterer R (2013) Protecting chickens againstcoccidiosis in floor pens by administering Eimeria oocystsusing gel beads or spray vaccination Avian Dis 57622‐626

Animal Parasitic Diseases Unit

Mailing AddressRoom 100 10300 Baltimore AveBldg 1040 BARC‐EastBeltsville MD 20705

National Program(s)103‐Animal Health108 ndash Food Safety)

CRIS Project(s)ZOONOTIC PARASITES AFFECTING FOOD SAFETY AND PUBLIC HEALTH

DEVELOPMENT OF CONTROL AND INTERVENTION STRATEGIES FOR AVIAN COCCIDIOSIS

Production Systems StudiedPoultry Dairy Cattle

Laboratory and Field ExpertisePCR and RT‐PCR analysis of

Eimeria Cryptosporidium Neospora parasites from field and experimental studies

bull Cell culture assays for anti‐coccidial drug resistance in Eimeria

Research Interestsbull Control of avian coccidiosis through vaccinationbull Development of anticoccidial drug resistance in Eimeriabull Role of Cryspovirus in Cryptosporidium development

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Steven LehotayResearch Chemist

Current Projectsbull Development validation and implementation of

efficient and effective high‐throughput multiresiduemonitoring methods for veterinary drugs pesticides and environmental and other contaminants in foods and related sample types

bull Development and evaluation of analytical criteria needed using mass spectrometry to accurately identify chemicals in food for regulatory purposes

Selected Publicationsbull Lehotay SJ Sapozhnikova Y and HGJ Mol 2015

Current issues involving screening and identification of chemical contaminants in foods by mass spectrometryTrends Anal Chem 6962‐75

bull Lehotay SJ and JM Cook 2015 Sampling and sample processing in pesticide residue analysis J Agric Food Chem 634395‐4404

bull Schneider MJ Lehotay SJ and AR Lightfield 2015 Validation of a streamlined multiclass multiresiduemethod for determination of veterinary drug residues in bovine muscle Anal Bioanal Chem 4074423‐4435

Residue Chemistry and Predictive Microbiology Research Unit

Mailing AddressEastern Regional Research Center600 East Mermaid LaneWyndmoor PA 19038

National Program(s)108 ndash Food Safety

CRIS Project(s)Technologies for the Detection of Chemical and Biological Contaminants in Foods

Production Systems StudiedApplicable to all foods and related sample types

Laboratory and Field Expertisebull Analytical chemistrybull Chemical residuesbull Sample preparationbull Chromatographybull Mass spectrometrybull Quality Assurancebull Regulatory monitoring

Research InterestsImprovement in the analysis of pesticides veterinary drugs and other contaminants in food and environmental samples by addressing all aspects of the analytical process including sample preparation cleanup separations detection screening quantification identification confirmation and data processing using many types of analytical techniques applied in novel and useful ways Then transfer and implementation of the new methods for food safety monitoring and other applications

StevenLehotayarsusdagov

215-233-6433

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Torey LooftResearch Microbiologist

ToreyLooftarsusdagov

515-337-7140

Current Projectsbull Characterization of the effects of therapeutic and

sub‐therapeutic in‐feed antibiotics on the turkey gut bacterial membership function and antibiotic resistance and on susceptibility to Campylobacter jejuni colonization

bull The affects of ecological niches within the avian gut on Campylobacter jejuni gene expression and colonization

Selected Publicationsbull Looft T H K Allen T A Casey D P Alt T B Stanton

Carbadox has both temporary and lasting effects on the swine gut microbiota Front Microbiol 5276 2014

bull Looft T H K Allen Collateral effects of antibiotics on mammalian gut microbiomes Gut Microbes 3 463‐467 2012

bull Looft T T Johnson H K Allen D O Bayles D P Alt J Cole S Hashsham R Stedtfeld T Stedtfeld B Chai J Tiedje and T B Stanton In‐feed antibiotic effects on the swine intestinal microbiome Proc Natl Acad Sci U S A109 1691‐1696 2012

National Animal Disease Center

Mailing AddressPO Box 70 1920 Dayton AveAmes IA 50010

National Program(s)108 ndash Food Safety

CRIS Project(s)Animal Intestinal Microbiomes Foodborne Pathogens and Antimicrobials

Production Systems StudiedTurkey and Swine

Laboratory and Field Expertisebull Microbial ecology (16S and

metagenomic)bull Anaerobic bacterial culturingbull Transcriptomic analysisbull Genome sequencing

Research Interestsbull Characterize microbiomes of turkeys and investigate the

effects of antibiotic feed additives on the expression and transmission of fitness and antimicrobial resistance genes in intestinal microbial populations

bull Evaluate environmental and host influences on gut bacterial ecological niches and foodborne pathogen control strategies

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Joyce LoperResearch Plant Pathologist

JoyceLoperarsusdagov

541-738-4057

Current Projectsbull Holistic view of interactions between biological

control and pathogenic bacteria on floral surfaces PIs Stockwell Loper and Chang USDA‐AFRI‐NIFA

bull Antibiotics as signaling molecules Loper (PD) USDA‐AFRI‐NIFA

bull Comparative genomics of Pseudomonas spp DOE‐JGI

Selected Publicationsbull Loper JE Hassan KA Mavrodi DV Davis EW II Lim

CK Shaffer BT et al (2012) Comparative genomics of plant‐associated Pseudomonas spp Insights into diversity and inheritance of traits involved in multitrophicinteractions PLoS Genetics 8 e1002784

bull Stockwell VO Johnson KB Sugar D and Loper JE (2011) Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology 101 113‐123

bull Stockwell VO Johnson KB and Loper JE (1996) Compatibility of bacterial antagonists of Erwiniaamylovora with antibiotics used to control fire blight Phytopathology 86 834‐840

bull Loper JE Henkels MD Roberts RG Grove GG Willet MJ and Smith TJ (1991) Evaluation of streptomycin oxytetracylcine and copper resistance of Erwinia amylovora isolated from pear orchards in Washington state Plant Disease 75 287‐290

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330s

National Program 303mdashPlant Health

CRIS Project(s)5358‐12220‐004‐00DImproved strategies for management of soilborne diseases of horticultural crops

Production Systems StudiedHorticultural crops including small fruit nursery crops and tree fruit crops

Laboratory and Field Expertisebull Biological control of plant

disease (field and greenhouse)bull Genetics and genomics of

Pseudomonas spp bull Genomics‐guided discovery of

natural products toxins and other bacterial traits

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Plant microbiomebull Bacterial genetics and genomicsbull Comparative genomics to identify traits (ie antibiotic

resistance genes) in environmental bacteria

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Sara J LuptonResearch Chemist

SaraLuptonarsusdagov

701-239-1236

Current Projectsbull Plant uptake and animal bioavailability of

perfluorooctanoic acidbull Distribution of drugs and environmental

contaminants in cow milk fractionsbull ADME of a brominated diphenyl ether (BDE 99) in

milking goats

Selected Publicationsbull Lupton SJ OKeefe M Basu P Muniz‐Ortiz J 2015

Dioxins dioxin‐like compounds and PBDEs in the US domestic meat supply trends and levels 2003 to 2013 [abstract] 35th International Symposium on Halogenated Persistent Organic Pollutants [Dioxin 2015] August 23‐28 2015 Sao Paulo Brazil Paper No PAP019465

bull Lupton SJ Shelver WL Newman DJ Larsen S Smith DJ 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part I Tissue residue depletion Journal of Agricultural and Food Chemistry 62(30)7577‐7585

Animal Metabolism ndash Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)108 ndash Food Safety

CRIS Project(s)Current Chemical and biological residues in foodsNew (Feb 2016) Environmental Chemical Residues and Their Impact in the Food Supply

Production Systems StudiedCattle Goat Swine Sheep Chickens and Turkeys

Laboratory and Field Expertisebull Quantification of drug residues

in agricultural samplesbull Detection and quantification of

dioxin‐like compounds and PBDEs in meat

bull Absorption distribution metabolism and excretion studies of drugs and environmental contaminants in lab and farm animals

Research Interestsbull Update data on levels of dioxins and related compounds

in the domestic food supply to provide Food Safety agencies with an adequate profile of the situation and confirm the safety and competitiveness of US foods

bull Perform absorption distribution metabolism and excretion (ADME) studies for animal drugs and environmental contaminants in lab and food animal systems

bull Investigate sources which contribute to levels of these contaminants in food animals that are feed components dust or soils treated wood and identify intervention strategies that may reduce the levels

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Rick MeinersmannResearch Microbiologist

RickMeinersmannarsusdagov

706-546-3236

Current Projectsbull Population genetics of environmental and foodborne

Campylobacter and Listeriabull Role of bacterivorous protozoa in foodborne

pathogen communitybull Prevalence and distribution of antimicrobial

resistance in foodborne pathogensbull Whole genome sequence‐based typing of foodborne

pathogens

Selected Publications1 Meinersmann RJ Lindsey RL Bono JL Smith TP Oakley BB 2013 Proposed model for the high rate of rearrangement and rapid migration observed in some IncAC plasmid lineages Appl Environ Microbiol 794806‐14 2 Meinersmann RJ Berrang ME Little E 2013 Campylobacter spp recovered from the Upper Oconee River Watershed Georgia in a 4‐year study Microb Ecol 6522‐7 3 Snipen L Wassenaar TM Altermann E Olson J Kathariou S Lagesen K Takamiya M Knoslashchel S Ussery DW Meinersmann RJ 2012 Analysis of evolutionary patterns of genes in Campylobacter jejuni and C coli Microb Inform Exp 2(1)84 First MR Park NY Berrang ME Meinersmann RJ Bernhard JM Gast RJ Hollibaugh JT 2012 Ciliate ingestion and digestion flow cytometric measurements and regrowth of a digestion‐resistant Campylobacter jejuni J EukaryotMicrobiol 5912‐9

Bacterial Epidemiology and Antimicrobial Resistance Unit

Mailing AddressNational Poultry Research CenterRBRRC950 College Station RoadAthens GA 30605

National Program(s)Number ndash Name108 ndash Food Safety

CRIS Project(s)Microbial Ecology of Human Pathogens Relative to Poultry ProcessingMonitoring of Antimicrobial Resistance in Food Animal ProductionProduction Systems StudiedMostly chickens but we participate with NAHMS (APHIS) that does several animal commodities

Laboratory and Field Expertisebull DNA sequence analysesbull Confocal microscopy

Research Interestsbull Campylobacterbull Listeriabull Other foodborne pathogensbull Population genetics

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Dan MillerResearch Microbiologist

DanMillerarsusdagov

402-472-0741

Current Projectsbull Nutrient pathogen and antibiotic residue fate in

feedlot runoff applied to vegetative treatment areasbull Effect of antibiotics on soil and sediment

biogeochemical processesbull Treatment and inactivation of PEDv in swine manure

slurry applied to crop soils

Selected Publicationsbull Miller D N and V H Varel 2001 In vitro study of the

biochemical origin and production limits of odorous compounds in cattle feedlots J Anim Sci 792949‐2956

bull Boumlhlke J K R L Smith and D N Miller 2006 Ammonium transport and reaction in contaminated ground‐water Application of isotope tracers and isotope fractionation studies Water Resources Research 42W05411 doi1010292005WR004349

bull Durso L M D N Miller and B J Wienhold 2012 Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non‐agricultural metagenomes PLoS ONE 7 article no e48325

Agroecosystem Management Research Unit

Mailing Address251 Filley Hall ndash FICLincoln NE 68583

National Program(s)212 ndash Climate Change Soils and Emissions

CRIS Project(s)Assessing and Managing Antibiotic Resistance Nutrients and Pathogens in Animal‐Impacted Agroecosystems

Production Systems StudiedAnimalmdashbeef cattle swine and

dairyCroplandmdashcorn soybeanVegetative Treatment Systems

Laboratory and Field Expertisebull GCMS of fermentation

productsbull HPLC of antibioticsbull RNADNA extraction from

manure and soilbull Quantitative PCR of antibiotic

resistance genes

Research Interestsbull How do microbes working on microscopic scale affect

landscape‐level phenomena such as gas emissions aerobic and anaerobic decomposition and nutrient cycling

bull Can we enhance natural microbial processes to remediate contamination

bull How may antibiotics affect biogeochemical processes in future manure‐impacted ecosystems (soils sediments surface and subsurface waters)

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Patricia MillnerResearch Microbiologist

PatMillnerarsusdagov

301-504-5631

Current Projectsbull Manure Pathogen Survival in Soilsbull Development of Compost Maturity Assaybull Bioaerosols Manure and Poultry Litter bull Preventive Controls Fresh and Fresh Cut Produce

Production Post‐Harvest Handling and Washingbull Ammonia Capture from Poultry Litter and In‐Vessel

Composting Systemsbull Microbial Ecology and Phytonutrients in Microgreens

Organic and Conventional Systems

Selected Publicationsbull Ingram DT et al 2012 Use of zero‐valent iron biosand filters to reduce Escherichia coli O157H12 in irrigation water applied to spinach plants in a field setting J Appl Microbiol 112551‐560 bull Luo Y et al 2012 A pilot plant scale evaluation of a new process aid for enhancing chlorine efficacy against pathogen survival and cross‐contamination during produce wash Intl J Food Microbiol

158133‐139bull Zhou B Luo Y Nou X Millner P 2014 Development of an algorithm for feed‐forward chlorine dosing of lettuce wash operations and correlation of chlorine profile with Escherichia coli O157H7 inactivation J Food Protect 77558‐566bull Luo Y et al 2015 A novel microfluidic mixer‐based approach for determining inactivation kinetics of Escherichia coli O157 H7 in chlorine solutions Food Microbiol 49152‐160

Environmental Microbial amp Food Safety Laboratory

Mailing Address10300 Baltimore AvenueBuilding 001 BARC‐West Rm 140Beltsville MD 20705

National Program(s)108 ndash Food Safety216 Agricultural System Competitiveness and Sustainability

CRIS Project(s)Microbial Ecology and Safety of Fresh ProduceDefining Agroecological Principles and Developing Sustainable Practices in Mid‐Atlantic Cropping SystemsProduction Systems StudiedBeef Dairy Poultry SwineLeafy greens Tomatoes Cantaloupes

Laboratory and Field Expertisebull Compost Systems Maturity

Tests Uses in Organic and Conventional Systems and for Phytopathogen Biocontrol

bull Bioaerosols Dispersion Deposition Modeling

bull Microfluidic device assay of sanitizersdisinfectants

bull Sanitizing wash systems

Research Interestsbull Fresh amp Fresh‐Cut Produce Food Microbiology amp Safetybull Microbial Ecology of Animal Manures Composts and

Manure‐Amended Soils including Antibiotic Resistancebull Bioaerosol Dissemination and Deposition from Animal

Production and Composting Facilitiesbull Biocontrol Agents and Fugitive Ammonia Capture

Strategies

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Tom MoormanResearch Leader (microbiologist)

TomMoormanarsusdagov

515-294-2308

Current Projectsbull Modeling antibiotic transport in soils using RZWQMbull Transport of antibiotic resistance genes in drainage

water after manure applicationbull Antibiotics and antibiotic resistance genes in two

Iowa watershedsbull Nitrate and pathogen removal using woodchip

denitrification bioreactorsbull Long Term Agroecosystem Research Network (LTAR)

Selected Publicationsbull Lertpaitoonpan WL Moorman TB and Ong SK Effect

of swine manure on sulfamethazine degradation in aerobic and anaerobic soils Water Air Soil Pollut 22681

bull Garder JL Moorman TB and Soupir ML Transport and persistence of tylosin‐resistant Enterococci ermgenes and tylosin in soil and drainage water from fields receiving swine manure J Environ Qual 43 1484‐1493

bull Carstens KL Gross AD Moorman TB and Coats JR Sorption and photodegradation processes govern distribution and fate of sulfamethazine in freshwater‐sediment microcosms Environ Sci Technol 47 10877‐10883

National Laboratory for Agriculture and the Environment

Mailing Address2110 University Blvd NLAEAmes IA 50011‐3120

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Managing Agricultural Water Quality in Fields and Watersheds New Practices and Technologies

Production Systems StudiedSwine and Poultry

Laboratory and Field Expertisebull Tile and stream water sampling

and microbial analysis by cultural and molecular methods

bull Extraction and analysis of antibiotics by LC‐MS

bull qPCR of antibiotic resistance genes

Research Interestsbull Antibiotic resistance and animal agriculturebull Fate and behavior of agrochemicals including antibioticsbull Soil microbiology

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Walter MulbryMicrobiologist

WalterMulbryarsusdagov

301-504-6417

Current Projectsbull Fate and effect of antibiotics and feed additives

during composting and anaerobic digestion of dairy manure and poultry litter

bull Evaluation of methods to minimize ammonia and methane emissions during composting

Selected Publicationsbull Arikan O Mulbry W Rice C 2016 The Effect of

Composting on the Persistence of Four Ionophores in Dairy Manure and Poultry Litter Waste Management (in press)

bull Arikan O Mulbry W Lansing S 2015 Effect of Temperature on Methane Production from Field‐Scale Anaerobic Digesters Treating Dairy Manure Waste Management 43108‐113

bull Arikan OA Mulbry W Ingram D Millner P 2009 Minimally managed composting of beef manure at the pilot scale effect of manure pile construction on pile temperature profiles and the fate of oxytetracycline and chlorotetracycline Bioresource Technol 1004447‐4453

Sustainable Agricultural Systems Laboratory

Mailing AddressBld 001 Room 245 BARC‐West10300 Baltimore AveBeltsville MD 20705

National Program(s)212 ndash Soil and Air

CRIS Project(s)Biological Treatment of Manure and Organic Residuals to Capture Nutrients and Transform Contaminants

Production Systems StudiedDairy cows swine and broiler chickens

Laboratory and Field Expertisebull Nutrient and carbon analyses of

manures and compostsbull Microplate‐based methods for

nitrogen phosphorus and chloride analysis

bull Laboratory‐ to farm‐ scale facilities for composting and anaerobic digestion of dairy manure

bull Extraction and analysis of antibiotics and feed additives from manure and compost

Research Interestsbull Biological treatment of manure and organic wastes

composting anaerobic digestion algae‐based systemsbull Technologies to recover nutrients from manure and

agricultural wastewaterbull Technologies to reduce greenhouse gas emissions and

ammonia emissions from agricultural facilities bull Anaerobic digesters for small farmsbull Composting urban wastes and urban gardening

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Toni PooleResearch Microbiologist

ToniPoolearsusdagov

979-260-9360

Current Projectsbull Studies regarding persistence of antimicrobial

resistance plasmids in absence of selection pressure

Selected PublicationsPoole et al 2012 Competitive effect of commensal faecalbacteria from growing swine fed chlortetracycline‐supplemented feed on β‐haemolytic Escherichia coli strains with multiple antimicrobial resistance plasmids J Applied Microbiology 113659‐668

Poole et al 2011 Persistence of resistance plasmids carried by beta‐hemolytic Escherichia coli when maintained in a continuous‐flow fermentation system without antimicrobial selection pressure Foodborne Pathogens Dis 8535‐540

Poole TL and T L Crippen 2009 Conjugative plasmid transfer between Salmonella enterica and Escherichia coli within the gastrointestinal tract of the lesser mealworm beetle Alphitobius diaperinus (ColeopteraTenebrionidae) Poult Sci 881553‐1558

Food and Feed Safety Research Unit

Mailing Address2881 FampB RoadCollege Station TX 77845

National Program(s)Ie 108 ndash Food Safety

CRIS Project(s)Microbial interactions and management approaches to reduce pathogenic bacteria in poultry

Interventions to reduce foodborne pathogens in swine and cattle

Production Systems StudiedBeef cattle swine poultry

Laboratory and Field Expertisebull Plasmid conjugation and

transfer assaysbull PCR and qPCR

Research InterestsProblems related to antimicrobial resistance and preharvest food safety Studies in our unit involve the reduction of pathogen load in the gastrointestinal tracts of cattle swine and poultry Antimicrobial resistance studies encompass the mechanism of dissemination by multi‐drug resistant Salmonella E coli and Enterococci This research also includes the study of genetic factors such as incompatibility plasmids that confer antimicrobial resistance to bacteria

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Clifford RiceResearch Chemist

CliffordRicearsusdagov

301-504-6398 ext 446

Current Projectsbull Anaerobic and aerobic decomposition of feed

additives monensin lasalocid and enrofloxacinbull Allelopathic chemicals in Rye (Secale cereale) and

their fate in soil after cover croppingbull Use of the chiral markers in metolachlor to date

groundwater

Selected Publications1 Lozano N Rice CP Ramirez M Torrents A Fate of

triclosan and methyltriclosan in soil from biosolidsapplication Env Pollut 2012 160 103‐108

2 Netthisinghe AMP Cook KL Rice CP Gilfillen RA SistaniKR Soil nutrients bacteria populations and veterinary pharmaceuticals across backgounding beef feedlot J Environ Qual 2013 42 532‐544

3 Varel VH Wells JE Shelver W Rice CP Armstrong D Parker DB Effect of anaerobic digestion temperature on odor coliforms and chlortetracycline in swine manure or monensin in cattle manure J Applied Microbiology 2012

Sustainable Agricultural System Laboratory ARS‐BeltsvilleClifford P RiceMailing AddressRoom 219 10300 Baltimore AveBldg 001 BARC‐WestNational Program(s)214 Agricultural and Industrial Byproducts212 ndash Soil and Air304‐ndash Crop Protection and QuarantineCRIS Project(s)304‐Cover Crop‐Based Weed Management‐Allelopathy214 ndash Biological treatment of manure and organic residuals to capture nutrients and transform contaminants

Production Systems StudiedBeef cattle poultry and field crops

Laboratory and Field Expertisebull Stream sampling water fish

macroinvertebrates air sampling

bull Analytical measurements with HPLC‐MS‐MS and GCMS for trace environmental samples their collection and processing

Research Interestsbull Analytical issues involving bioactive compoundsbull Process studies on fate and transport of bioactive

compounds bull Analytical tools for following chemical transport and fate

of bioactive compounds that depend on chiralselectivity

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Mike RothrockResearch Microbiologist

MichaelRothrockarsusdagov

706-546-3072

Current Projectsbull Systems‐based study of foodborne pathogen ecology in

local antibiotic‐free pastured broiler flocks (large multi‐year field study)

bull Cultural isolation and characterization of Salmonella Campylobacter E coli and Listeria (including AST profiling)

bull Molecular characterization of communities (qPCR NGS)bull Comparison to physiochemical and management

metadata

bull Characterization of environmentally‐prevalent epidemiologically infrequent Salmonella serotypes and determination of their competitive advantage over more epidemiologically relevant serotypes including the role of antibiotic resistance within these serotypesstrains

Selected Publicationsbull Rothrock et al (2015) The characterization of Salmonella

enterica serotypes isolated from the scalder tank of a commercial poultry processing plant Recovery of a multi‐drug resistant Heidelberg strain Poultry Science 94(3) 467‐472

bull Rothrock et al (2016) Antibiotic resistance patterns of major zoonotic pathogens from a season‐long farm‐to‐fork study of all‐batural antibiotic‐free pasture‐raised broiler flocks in the Southeastern US JEQ 45(2)593‐603

US National Poultry Research CenterEgg Safety and Quality Unit

Mailing Address950 College Station RdAthens GA 30605

National Program(s)108 ndash Food Safety

CRIS Project(s)Reduction of Invasive Salmonella enterica in Poultry through Genomics Phenomics and Field Investigations of Small Multi‐Species Farm Environments(under OSQR review)

Production Systems StudiedCommercial BroilerPoultryLocal All Natural Pasture‐raised Broiler ProductionProcessing

Laboratory and Field Expertisebull Cultural isolation of zoonotic

pathogensbull Use of NARMS to characterize these

pathogens based on their AST profilesbull DNA isolation from complex

environmental matrices (soils feces organs carcasses)

bull qPCR and community analyses of poultry and swine farmsmanure

bull Microbiomic (16S) community analyses

Research Interestsbull Zoonotic pathogen ecology and the environmental drivers

of pathogen ecology in alternative poultry management systems (but I am interested in other alternative animal production systems as well)

bull Using system‐based approaches to combine management physiochemical and microbiological data to address complex agricultural questions

bull Antibiotic resistance potential of microbial communities and isolates in agroecosystems devoid of antibiotic use (eg background antibiotic resistance)

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

John W SchmidtResearch Microbiologist

JohnWSchmidtarsusdagov

402-762-4226

Current Projectsbull Comparison of the occurrences of antimicrobial

resistant bacteria and antimicrobial resistance genes in cattle feces ground beef and pork chops from animals raised with and without antimicrobials

bull Occurrence of antimicrobial resistance in cattle manure and manure‐impacted soil

bull Impact of chlortetracycline metaphylaxis administered to weaning cattle on the occurrence of antimicrobial‐resistant bacteria

Selected Publicationsbull Schmidt JW Agga GE Bosilevac JM Brichta‐Harhay

DM Shackelford SD Wang R Wheeler TL and Arthur TM Occurrence of antimicrobial‐resistant E coliand Salmonella enterica in the beef cattle production and processing continuum Appl Environ Microbiol 81713‐725 2015

bull Agga GE Arthur TM Brichta‐Harhay DM Durso LM and Schmidt JW Antimicrobial‐resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste PLOS ONE 10e0132586 2015

Meat Safety and Quality Research Unit

Mailing AddressUS Meat Animal Research CtrPO Box 166Clay Center NE 68933

National Program(s)108 ndash Food Safety

CRIS Project(s)Pathogen Mitigation In Livestock and Red Meat Production

Exploring Genomic Differences and Ecological Reservoirs to Control Foodborne Pathogens

Production Systems StudiedBeef cattle Swine and Sheep

Laboratory and Field Expertisebull Sampling meat animal

production and processing environments

bull Detection and enumeration of pathogens and antimicrobial resistant bacteria

bull Antimicrobial susceptibility tests

bull Mobile genetic element and resistance gene characterization

Research Interestsbull Identify the biological mechanisms responsible for the

occurrence of antimicrobial resistant bacteria in food‐animal production environments

bull Determine the impact of antimicrobial uses in food‐animal production on the levels of antimicrobial‐resistant bacteria and antimicrobial resistance genes

bull Evaluate the efficacy of pre‐ and post‐harvest pathogen mitigation technologies against antimicrobial‐resistant bacteria and antimicrobial resistance genes

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Weilin ShelverResearch Chemist

WeilinShelverarsusdagov

701-239-1425

Current Projectsbull Validation of the usefulness of rapid screening tests in ante‐

mortem matrices (urine plasma serum saliva milk etc) for predicting post‐mortem tissue residues and(or) animal exposures to non‐steroidal anti‐inflammatory drugs

bull Application of a rapid lateral flow assay to detect antibiotic residues in swine urine to predict kidney violations

bull Determination of the partitioning of antibiotic residues of food safety concern into cream curd whey and water fractions during milk processing

Selected Publicationsbull Smith DJ WL Shelver RE Baynes L Tell R Gehring M

Li T Dutko JW Schroeder G Herges and JE Riviere 2015 Excretory Secretory and Tissue Residues after Label and Extra‐label Administration of Flunixin Meglumine to Saline‐ or Lipopolysaccharide‐Exposed Dairy Cows J AgricFood Chem 634893‐901

bull Shelver WL SJ Lupton DJ Newman S Larsen and DJ Smith 2014 Depletion of penicillin G residues in heavy sows after intramuscular injection Part II application of kidney inhibition swab tests J Agric Food Chem 627586‐92

Animal Metabolism‐Agricultural Chemicals Research Unit

Mailing Address1605 Albrecht Blvd NFargo ND 58102

National Program(s)( 108 ndash Food Safety)

CRIS Project(s)bull METABOLIC FATE OF CHEMICAL

AND BIOLOGICAL CONTAMINANTS

bull CHEMICAL AND BIOLOGICAL RESIDUES IN FOODS

Production Systems StudiedCattle Goat Swine and Sheep

Laboratory and Field Expertisebull Generation of antibodies for

use in immunochemical analysisbull Evaluation and validation of

rapid screening methods (microbial inhibition antibody cell or receptor based assays)

bull Development and evaluation of mass spectrometry methods (GC or LC based)

Research Interestsbull Develop inexpensive rapid sensitive diagnostic tools (capable of

being used in the field) to screen samples for agrochemicals and environmental contaminants to improve monitoring for food safety (immunochemical receptor or bacterial inhibition based)

bull Develop and (or) validate sensitive specific and accurate instrumental techniques (usually GC or LC based) to detect and quantify chemicals in food animals food animal products or other foods

bull Develop and validate detection methods (including novel techniques and on site methods) for new and emerging xenobiotic residues

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Virginia StockwellResearch Plant Pathologist

VirginiaStockwellarsusdagov

541-738-4078

Horticultural Crops Research Unit

3420 NW Orchard AveCorvallis OR 97330

National Program 303mdashPlant Health

CRIS Project5358‐220000‐039‐00DExotic and Emerging Plant Diseases of Horticultural Crops

Production Systems StudiedHorticultural crops including tree fruits ornamentals and small fruits

Laboratory and Field Expertisebull Biological control of plant

diseases (field and greenhouse)bull Integrated disease management

(field)bull Monitoring emergence of

antibiotic‐resistant bacterial plant pathogens (field and laboratory)

bull Genomics of Pseudomonas spp Pantoea spp and Erwinia amylovora

Current Projectsbull One Health Washington Antimicrobial Stewardship

Workgroup bull Microbiome studies of raspberry flowers and fruits

Selected Publicationsbull Stockwell VO and Duffy B 2012 Use of antibiotics in plant

agriculture World Organisation for Animal Health OIE Scientific and Technical Review Special Issue Antimicrobial Resistance in Animal and Public Health Rev Sci Tech Off Int Epiz 31199‐210

bull Stockwell VO Johnson KB Sugar D and Loper JE 2011 Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear Phytopathology101 113‐123

bull Rezzonico F Stockwell V and Duffy B 2009 Plant‐agricultural streptomycin formulations do not carry antibiotic resistance genes Antimicrob Agents Chemother 53 3173ndash3177

bull Stockwell VO Johnson KB and Loper JE 1996 Compatibility of bacterial antagonists of Erwinia amylovorawith antibiotics used to control fire blight Phytopathology 86 834‐840

bull McManus P S Stockwell V O Sundin G W and Jones A L 2002 Antibiotic use in plant agriculture Annual Review of Phytopathology 40 443‐465

Research Interestsbull Biological control of plant diseasesbull Bacterial pathogens of plantsbull Bacterial genetics and genomicsbull Plasmid acquisition and maintenance in environmental

bacteriabull Resistance mitigation

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

JoAnn Van KesselResearch Animal Scientist

JoannVankesselarsusdagov

301-504-8287

Current AR Projects

bull Phenotypic characterization of antimicrobial resistance in bacteria from dairy animals

bull Characterization of genomic resistance determinants in bacteria and genomic determinants that influence gut colonization capacity

Selected Publications

bull Van Kessel JS Sonnier JL Zhao S Karns JS 2013 Antimicrobial resistance of Salmonella enterica isolates from bulk tank milk and milk filters in the United States Journal of Food Protection Journal of Food Protection 7618‐25

bull H Cao JS Karns AK Pradhan and JS Van Kessel 2015 Antimicrobial Resistance of Salmonella and E coli from Pennsylvania Dairy Herds In preparation

Environmental Microbial and Food Safety Laboratory

Mailing Address10300 Baltimore AveBuilding 173 BARC‐East Room 202Beltsville MD 20705

National Program(s)108 ndash Food Safety

CRIS Project(s)Microbial Ecology Antimicrobial Resistance and Genomics of Zoonotic Foodborne Pathogens in Dairy Cattle

Production Systems StudiedDairy

Laboratory and Field Expertisebull Isolation and characterization of Salmonella spp Campylobacterspp and L monocytogenes from milk feces water etcbullAntimicrobial susceptibility testing

Research Interests

bull Ecology of zoonotic bacteria in dairy animals and their environment

bull Characterizing bacterial pathogens to understand how these pathogens infect colonize and persist in dairy cattle

bull Characterizing antimicrobial resistance in bacteria from dairy animals and determining factors that contribute to colonization of the host gut

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Tim WelchMicrobiologist

TimWelcharsusdagov

304-724-8340 x 2136

Current Projectsbull Identification of the factors necessary for virulence

regulation of the Yersinia ruckeri flagellar secretion system and characterization of the role of this regulation in virulence

bull Development of a live attenuated vaccine carrier strains capable of en masse delivery of foreign antigens to fish

bull Characterization of the role of IncAC MDR plasmids as a source of self transmissible resistance to florfenicol

Selected Publicationsbull Welch TJ Good CM Mortality associated with

Weissellosis (Weissella sp) in USA farmed rainbow trout Potential for control by vaccination Aquaculture 388 pp 1282‐137 2013

bull Welch TJ Verner‐Jeffreys DW Dalsgaard I Wiklund T Evenhuis JP Cabrera JA Hinshaw JM Drennan JD LaPatra SE Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe Appl Environ Microbiol 77(10)3493‐9 2011

bull Welch TJ et al Multiple antimicrobial resistance in plague an emerging public health risk PLoSONE 2(3)e309 2007

Cool and Cold Water Aquaculture Research Unit

Mailing Address11861 Leetown RoadKearneysville WV 25430

National Program(s)106‐ Aquaculture

CRIS Project(s)Integrated Research to Improve On‐Farm Animal Health in Salmonid Aquaculture

Production Systems StudiedAquaculture

Laboratory and Field Expertise

bull Genetic manipulation of bacteria and plasmids

bull Identification and characterization of bacterial virulence factors

bull Development of disease challenge models

bull Outbreak investigation and identification of emerging bacterial pathogens

Research Interestsbull Pathogen characterization and development of vaccines

for aquaculturebull Investigating the role of gene regulation in bacterial

pathogenesis and identification of virulence regulated genes

bull Identification and characterization of antimicrobial plasmids that threaten drug use in aquaculture

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Jim WellsResearch Microbiologist

JimWellsarsusdagov

402-762-4174

Current Projectsbull Developing a NextGen sequencing‐based method to

identify and quantify antibiotic resistance genes in complex microbial samples

bull Determining the microbial community structure in different gastrointestinal habitats and the potential effect of animal diet and dietary supplements

bull Examining associations between host genotypes and pathogen shedding to identify host genes responsible for pathogen colonization

Selected Publicationsbull Wells J E Berry E D Guerini M N and Varel V H

Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens J Appl Microbiol 118295‐304 2015

bull Wells J E Berry E D Kalchayanand N Rempel L A Kim M and Oliver W T Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs J Appl Microbiol 1181489‐1497 2015

Meat Safety amp Quality Research Unit

Mailing AddressUS Meat Animal Research CenterState Spur 18DClay Center NE 68933

National Program(s)108 ndash Food Safety (animal and plant products)

CRIS Project(s)Assessment of genotypic and phenotypic factors for foodbornepathogen transmission and development of intervention strategies

Understanding composition of bovine colonic microbiota and predisposition to EHEC as complex polygenic traits in beef cattle

Production Systems StudiedBeef Cattle and Swine

Laboratory and Field Expertisebull Experimental design and

sample collection from animal production systems

bull Analyses of pathogenic and commensal microbial populations

bull Knowledge‐based interpretation of complex microbial habitats

Research Interestsbull Determine how animal production systems and

management decisions impact the generation and dissemination of pathogens and antibiotic resistance

bull Evaluate the impact of gastrointestinal microbiology on pathogen shedding antibiotic resistance animal well‐being and animal performance

bull Identify animal production alternatives to dietary sub‐therapeutic antibiotics to sustain animal well‐being and performance

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Terry WhiteheadResearch Microbiologist

TerryWhiteheadarsusdagov

309-681-6272

Current Projectsbull Using condensed tannins to reduce production of

odors and emissions (ie hydrogen sulfide methane) from stored swine manure

bull Microbial ecology of the swine GI tract (feces) and stored manure

bull Investigating antibiotic resistance in commensal bacteria from swine feces and stored manure

Selected Publicationsbull Whitehead TR and Cotta MA Stored Swine Manure

and Swine Feces as Reservoirs of Antibiotic Resistance Genes Letters in Applied Microbiology 2013 Lett Appl Microbiol 56264‐267

bull Whitehead TR Johnson CN Cotta MA Moore E and Lawson PA Savagea faecisuis gen nov sp nov a Tylosin‐ and Tetracycline‐Resistant Bacterium Isolated from a Swine Manure Storage Pit 2015 Antonie van Leeuwenhoek 108 151‐161

bull Whitehead TR and Cotta MA Examination of the Cultivatable Aerobic Microflora of Swine Feces and Stored Swine Manure on Various Media and Antibiotics 2016 J Environ Qual 45 604‐608

Bioenergy Research Unit

Mailing AddressNCAUR1815 N University StPeoria IL 612604

National Program(s)212 Climate Change Soils and Emissions

CRIS Project(s)Understanding the Role of Commensal Bacteria in Antibiotic Resistance from Stored Livestock Manure and Gastrointestinal Tract

Production Systems StudiedSwine

Laboratory and Field Expertisebull Sampling underground stored

swine manure and feces in swine barns

bull Isolation and enumeration of commensal anaerobic and aerobic bacteria including antibiotic resistant bacteria

bull PCR identification of antibiotic resistance genes in bacterial isolates and total DNA from swine ecosystems

bull Identifying methods for reducing odor and emissions from stored swine manure

Research Interestsbull Identifying methods for reducing production of odors

and gaseous emissions from stored swine manurebull Isolating identifying and characterizing commensal

bacteria from swine GI tract (feces) and stored swine manure

bull Determining relative levels of antibiotic resistance in the swine GI tract and stored manure antibiotic resistance genes in bacterial isolates and movement of resistance genes between bacteria

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Clinton WilliamsSoil Scientist

ClintonWilliamsarsusdagov

520-316-6379

Current Projectsbull Investigation into Effect of Soil Moisture Depletion on

Vegetable Crop Uptake of Micro‐contaminants Under Recycled Water Irrigation

bull The occurrence and fate of antibiotics found in treated municipal wastewater used for groundwater recharge

bull Animal Feeding Operations Effluents Effect of Redox Status on the Dissipation of Contaminants of Emerging Concern

Selected Publicationsbull Williams CF JE Watson SD Nelson and CE Walker

Sorption Desorption of lincomycin from three arid‐region soils J Environ Qual 421460‐1465 2013

bull Mclain JE CF Williams Sustainability of water reclamation long‐term recharge with reclaimed wastewater does not enhance antibiotic resistance in sediment bacteria Sustainability 61313‐1327 2014

Water Management and Conservation Research

Mailing Address21881 North Cardon LaneMaricopa AZ 85238

National Program(s)211 ndash Water Availability and Watershed Management

CRIS Project(s)Reuse of Treated Municipal Waste Water for Irrigation as a Means to Increase Alternative Water Supplies

Production Systems StudiedIrrigation ground water recharge environmental services CAFOrsquos wetlands and municipal wastewater treatment

Laboratory and Field Expertisebull Quantification of antimicrobials

and pharmaceuticals from environmental samples

bull Low input treatment systems for removal of trace organics

bull Connection between antimicrobial resistance and environmental concentration

Research Interestsbull Quantify the fate and transport of antibiotics in the

environmentbull Low input treatment methods for pharmaceuticals

personal care products and trace organics bull Linking the environmental occurrence and concentration

of antibiotics to the development of antimicrobial resistance

bull Uptake of pharmaceuticals by food crops

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport

Bryan WoodburyAgricultural Engineer

BryanWoodburyarsusdagov

402-762-4275

Current Projectsbull Spatial variability of antimicrobial and their residues

in fields receiving runoff or manure amendmentsbull Determine the fate of and identify treatment options

for antimicrobials in beef feedlot runoff and manure amended soils

bull Development of geophysical tools for mapping and measuring the spatial variability of antimicrobials in agricultural systems

Selected Publicationsbull Mantz AR DN Miller MJ Spiehs BL Woodbury and

LM Durso Persistence of erythromycin resistance gene erm(B) in cattle feedlot pens over time Agric Food Analysis Bacteriol 3(4)312‐320 2013

bull Joy SR SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Parker DB Marx and X Li Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure slurry Environ Sci Technol 4712081‐12088 2013

bull Soni B SL Bartelt‐Hunt DD Snow JE Gilley BL Woodbury DB Marx and X Li Narrow grass hedges reduce Tylosin and associated antimicrobials resistance genes in agricultural runoff J Environ Qual 44(3) 895‐902 2015

Nutrition and Environmental Management Research Unit

Mailing AddressUS Meat Animal Research CenterPO Box 166Clay Center NE 68933

National Program(s)212 ndash Soil and Air

CRIS Project(s)Management of Manure Nutrients Environmental Contaminants and Energy From Cattle and Swine Production Facilities

Production Systems StudiedBeef and Swine

Laboratory and Field Expertisebull Geophysical methods for

detecting transport of environmental contaminants in agricultural systems

bull Spatial measures of contaminants in the environment

bull Soil and water sampling for environmental contaminants

bull Automated sampling systems

Research Interestsbull Development of control systems and management

practices for mitigating the impact of animal feeding operations on the environment

bull Design of field‐scale tools and technologies for monitoring contaminant fate and transport