amr research at the agricultural research service · environmental amr mitigation strategies....

AMR Research at theAgricultural Research Service

Develop antimicrobial-resistance solutions for healthy people, healthy animals and a healthy environment

United States Department of AgricultureAgricultural Research ServiceUnited States Department of AgricultureAgricultural Research ServiceUnited States Department of AgricultureAgricultural Research Service

United States Department of AgricultureAgricultural Research Service

Roxann Motroni DVM, PhDNational Program Leader for Animal HealthOffice of National ProgramsAgricultural Research Service

Kim Cook, PhDNational Program Leader for Food SafetyOffice of National ProgramsAgricultural Research Service

Overview of ARS• More than 90 locations (4 overseas

labs)• $1.2B budget in FY18• 16 National Programs

• ~690 research projects • ~1,600 scientists• ~8,000 employees

• 25 ongoing projects in AMR• FY17 Funding ~$21.5M

• Antibiotic Drug Resistance and Antimicrobial Resistance (Food Safety Funding) (AMR) - $13,925,000

• Antibiotic and Antimicrobial Resistance (Non-Food Safety Funding) - $3,608,000

• Alternative to Antibiotics (Non-Food Safety Funding) (ATA) - $3,954,000


Four National Program Areas

Nutrition, Food Safety and Quality

Animal Production and Protection Crop Production and Protection

Natural Resources and Sustainable Agriculture Systems

• Water Availability and Watershed Management

• Soil and Air

• Biorefining

• Grass, Forage, and Rangeland Agroecosystems

• Sustainable Agricultural Systems Research

• Food Animal Production

• Animal Health

• Veterinary, Medical, and Urban Entomology

• Aquaculture

• Plant Genetic Resources, Genomics, and Genetic Improvement

• Plant Diseases

• Crop Protection and Quarantine

• Crop Production

• Human Nutrition

• Food Safety (Animal and Plant Products)

• Quality and Utilization of Agricultural Products

ARS Mission and role in AMR Research

• ARS Mission:• ARS delivers scientific solutions to national and global agricultural challenges.

• ARS Role in AMR Research• ARS contributes solution oriented, hypothesis-driven research that benefits

agriculture and ensures safe, secure food supply• Perform basic and applied research that informs through peer-review publication,

subject matter expertise and information sharing

https://www.ars.usda.gov/nutrition-food-safetyquality/food-safety-animal-and-plant-products/docs/antimicrobial-resistance-amr/


ARS Researches many areas of AMR in Agriculture

Natural Resources and Agriculture Systems (NRSAS)

Nutrition, Food Safety and Quality (NFSQ)

Animal Production and Protection (APP)

Nutrition, Food Safety and Quality (NFSQ)

Animal Production and Protection (APP)

USDA Antimicrobial Resistance Action Plan (2014)

• Objective 1: Determine and/or model patterns, purposes, and impacts of antibiotic use in food-producing animals.

• Objective 2: Monitor antibiotic drug susceptibilities of selected bacterial organisms in food-producing animals, production environments, and meat and poultry.

• Objective 3: Identify feasible management practices, alternatives to antibiotic use, and other mitigations to reduce AMR associated with food-producing animals and their production environments.


Research Highlights from USDA AMR Action Plan





Mitigation Approaches for Foodborne Pathogens in Cattle and Swine for Use During Production and Processing

National Program 108: Food Safety, US Meat Animal Research Center, Clay Center, NE

• Demonstrated that a 5-day in-feed prophylactic chlortetracycline treatment reduced illness in cattle entering feedlot with no long-term impacts on levels of antibiotic-resistant bacteria and antibiotic resistance genes (Miller et al., 2018)

• Examined the fecal contents of 360 fed cattle raised "conventionally" (no restrictions on antibiotic use other than regulatory compliance) and 359 fed cattle "raised without antibiotics". Individual antibiotic resistance levels were either similar between production systems or slightly elevated in conventional cattle. (Vikram et al., 2017)



Reduction of Invasive Salmonella enterica in Poultry through Genomics, Phenomics and Field Investigations of Small Multi-Species Farm Environments

National Program 108: Food Safety, US. National Poultry Research Center, Athens, GA

• Examining antibiotic-free, pastured poultry management systems (Rothrock et al., 2015)

• Even without antibiotics, foodborne pathogens (namely Salmonella and Listeria) isolated from various points along the farm-to-fork continuum are MDR, with some resistant to up to 7 ABs (using the NARMS panels).

• Ongoing work includes collaborations with UGA and UCDavis to examine (1) if number/type of other farm animals on the farm or the concentrations of metals within the feces/soil are correlated with resistance on these AB-free farms and (2) using GIS to geospatially and temporally map these resistances from the 11 farms studied over 4 years.

Highlight: ARS On-Farm Pilot Studies• Technology development: DARTE-QM (Diversity of Antibiotic

Resistance genes and Transfer Elements-Quantitative Monitoring)• A high-throughput DNA sequencing method to sequence hundreds of

resistance genes, mobile genetic elements and phylogenetic markers• Applications

• Large-scale monitoring of various samples (manure, soil, water)• Efficacy of AMR mitigation strategies to affect spread of resistance

• Primers for 300 targets have been designed and initial trial runs have been completed

• 2016-2018- $1M USDA-NIFA grant – ISU (A. Howe & M. Soupir) USDA ARS (H. Allen & T. Moorman) Grinnell (S. Hinsa)

14


Highlight: DARTE-QMNational Program 108: Food Safety, National Animal Disease Center, Ames, IA

Research Focus: Ecology of AMREvaluating Trends in Resistance to

Antimicrobials and Biocides

• Nigeria, Egypt, Pakistan• Antimicrobial susceptibility of

E. coli, Salmonella and Staphylococcus• Isolates from eggs, poultry, cattle, swine and

clinical samples

International Collaborations: Under-Developed Countries

• Trends in poultry, dairy, swine, turkey and cattle

• At processing, on farm, at slaughter, at regional and watershed scale

• organic, range-fed, conventional

Antimicrobial Susceptibility

Resistance to Biocides


Dr. Charlene Jackson Dr. Jonathan Frye


Priority Animal Disease Vaccine and Therapeutic DevelopmentNational Program 103: Animal Health

• Streptococcus suis (Brockmeier et al. 2018)• Liamocins (Bischoff et al., 2015; Bischoff et al. 2018)

• Nanoparticle vaccines for Eimeria (Jenkins et al. 2018)

• Mastitis (Lippolis et al. 2017; Powell et al. 2018)


Environmental AMR Mitigation StrategiesNational Program 212: Soil and Air

• Development and implementation of woodchip bioreactors, reduce transport of tested antibiotic drugs 70-80% (Ames, IA) (Ilhan et al., 2012)

• Hydrothermal carbonization eliminates 100% of antibiotic resistant bacteria and their genes (Florence, SC) (Ducey et al. 2017).

• Composting of swine manure can effectively decrease the concentration of AR genes in swine manure (Bowling Green, KY)

• Assessing ARG removal performance for 7 full-scale anaerobic digesters treating dairy manure in Wisconsin (Marshfield, WI)

Grand Challenge

““The urgent progress needed today toaddress the most challenging problems requires leveraging capabilities across the scientific and technologicalenterprise in a convergent research approach.”

Recommendation 1: Transdisciplinary science and systems approaches should be prioritizedto solve agriculture’s most vexing problems.

ARS Grand Challenge

• What research questions should an ARS AMR Grand Challenge address?

• How can ARS research inform risk assessments, surveillance and antibiotic stewardship activities?

• How can ARS better work with academia and industry to address these challenges?


Thank You!

Roxann Brooks Motroni

National Program Leader for Animal Health: NP103

[email protected]

Kim Cook

National Program Leader for Food Safety: NP108

[email protected]

Cyril G. Gay

National Program Leader for Animal Health: NP103

[email protected]

Dave Knaebel

National Program Leader for Soil and Air: NP212

[email protected]

mailto:[email protected]

mailto:[email protected]

Characterizing “baseline” resistance in soils

Measuring antibiotic resistance in ungrazedprairie soils, Nebraska

Dr. Lisa Durso, Lincoln NE


Assessing and Managing Antibiotic Resistance, Nutrients, and Pathogens In Animal-Impacted Agroecosystems

National Program 212: Soil and Air, Agroecosystem Management Research, Lincoln, NE

• ARB and ARG are ubiquitous in all soils, so it is important to measure background/baselines levels when evaluating ag impacts.

• In cattle feedlots, Bacteroidetes and Clostridia are the bacteria most frequently carrying antibiotic resistance genes.

• Specific ARG classes are non-randomly distributed across taxa (some kinds of bacteria more likely than others to carry certain types of ARGs)

• The amount of resistance measured in any sample depends on the specific ARB/G target.

• Individual ARGs each have their own ecologies.

Impact of spatiotemporal, environmental, and wildlife factors on AMR and pathogens at watershed scale (34,000 acres)

Migratory waterfowl and other wildlife

Pest flies and mosquitoesAir, soil, water, feces

Chemicals, enzymes

Immune-derivedproducts

Phyto-chemicals

Microbial Products

Vaccines

BrockmeierVaccine

platforms in swine

Carroll Yeast to reduce

impacts of Bovine resp

disease & liver abscess in

cattle

Lillehoj CD molecules and cytokines

to control disease in

poultry

Swayne/AfonsoAvian influenza/

Newcastle vaccine for poultry

AndersonPhage to reduce

Salmonella in cattle

WelkerPre-biotic Chinese

tea additive for disease resist. &

growth in farmed fish.

LunneyCytokines to

improve swine health

DonoghuePlant products to

reduce Salmonella & Campy in

poultry AksoyChitosan to

control disease in fish

JenkinsCoccidiosis in

chicken

Anderson Sodium chlorate

to improve livestock food

safety

DunganCopper

footbaths in dairies

amr research at the agricultural research service · environmental amr mitigation strategies....

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