interpreting, reporting and communication of wgs data · • illustrate wgs data and clusters,...
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Interpreting, Reporting and Communication of WGS Data
Dave BoxrudEnterics Unit Supervisor
March 7, 2019
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General Foodborne Surveillance Philosophy
Identify clusters
Lab
Investigate clusters
Epi
What kinds of analysis are we creating/receiving?
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Genomic Characterization• Taxonomic ID and
serotyping/serogrouping• Kraken, SeqSero, Serotype
Finder, srst2 • Virulence factor and Plasmid
detection • ARIBA
• Antibiotic resistance gene detection
• ARIBA
Subtyping and phylogenetic comparisons• hqSNP analysis
• CDC LyveSet (locally or from CDC)• NYSDOH-Wadsworth Salmonella
Enteritidis and Typhimurium pipeline• NCBI Pathogen Detection
• wgMLST analysis • PulseNet Listeria Pilot lab• MentaLiST
• MLST analysis• stringMLST
How the results will be formatted and
communicated
How is the data communicated?
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Communication Methods
Project initiation
• In-person meetings to discuss:
What/why samples will be
sequenced
What kinds of data can/will
analysis provide
How the results will be
interpreted
How long will analysis take
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• PFGE-any 2 isolate match within 60 days
• WGS cluster-needs to be determined
What is a cluster for WGS?
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• SE-5 OBs, ≤3 SNPs within OB
• STM-12 outbreaks analyzed, ≤ 2 SNPs within OB, 1 exception (complicated outbreak)
• Campylobacter
• Exception is emerging Salmonella I 4,5, [12]:i:- associated with porcine exposure clone shows less diversity
• General rule (using LyveSet and NY pipeline) is 0-5 SNPs within 60 days
• Once a cluster/outbreak is identified, can consider expending SNP differences and time
Retrospective Outbreaks
MDH00219MDH00225- In-vivo, same as E2001001070
MDH00215 -Sporadic 4/19/01MDH00247 --Sporadic 8/6/12
MDH00204 - Sporadic 5/14/01MDH00221- Sporadic 5/14/01
MDH00203 - Sporadic 7/11/00MDH00214 - Sporadic 3/12/01
MDH00206 - Sporadic 8/23/00MDH00217 - Sporadic 6/10/13
MDH00237 Sporadic 6/22/11MDH00236 - Sporadic 5/7/11MDH00207 - Sporadic 8/31/2000
MDH00233 - Sporadic 12/7/2001
MDH00248 - Sporadic 6/10/13
MDH00205 - Sporadic 8/22/2000MDH00216 - Sporadic 4/30/2001
MDH00224 -Sporadic 6/11/2001MDH00254 MDH00252MDH00253MDH00234
MDH00226 - Sporadic 6/21/2001MDH00231 - Sporadic 7/16/2001
MDH00202 - Sporadic 7/7/2000MDH00208 - Sporadic- Same time, PFGE, and MLVA as Outbreak 1MDH00209MDH00210MDH00211
MDH00222- In-vivo, same as E2001001070
MDH00228- In-vivo, same as E2001001070
MDH00223
MDH00220MDH00218
MDH00213- Sporadic- Same PFGE and time as Outbreak 1MDH00232- Sporadic 10/17/01MDH00227MDH00230MDH00251MDH00229
MDH00235- Sporadic 10/3/05MDH00243- Sporadic, same PFGE and time as Outbreak 5MDH00245- Sporadic 6/26/12MDH00249MDH00250
MDH00246-Sporadic 7/30/12MDH00255- OH Sample 1 MDH00256- OH Sample 2
MDH00241- Sporadic, same PFGE and time as Outbreak 5MDH00239MDH00242MDH00244- Environmental sample from Outbreak 5MDH00238MDH00240
Defined Outbreak Samples
Outbreak 1- Sept 2000
Outbreak 2- May 2001
Outbreak 3- Aug 2001
Outbreak 4- Nov 2003
Outbreak 5- Aug 2008
Outbreak 6- Spring 2014
Outbreak 7- Spring 2014
0-2 SNPs
0-2 SNPs
0-2 SNPs
1SNP0 SNPs
0-1 SNPs
0-3 SNPsTaylor et al. J Clin Micro Oct 2015.
Retrospective Typhimurium Outbreaks
• Analyzed 12 outbreaks
• 11 OBs differed by ≤1 SNP
• Outbreak 12, n=3, 2 isolates 0 SNPs apart, 1 16 SNPs different
• Melon outbreak
• Likely increased diversity due to environment/longer outbreak
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Campy-White Lily restaurant – Salad, 2002
2002 Confirmed foodborne salads/cross-contamination White Lily Restaurant E2002002685 jejuni2002 Confirmed foodborne salads/cross-contamination White Lily Restaurant E2002002698 jejuni2002 Confirmed foodborne salads/cross-contamination White Lily Restaurant E2002002697 jejuni2002 Confirmed foodborne salads/cross-contamination White Lily Restaurant E2002002742 jejuni
E2002002697 E2002002698 E2002002685 E2002002742E2002002697 0
E2002002698 0 0
E2002002685 0 0 0
E2002002742 0 0 0 0
Campy-Chipotle-apple valley, lettuce, 20092009 Confirmed Foodborne lettuce/cross-contamination Chipotle - apple valley E2009004973 jejuni2009 Confirmed Foodborne lettuce/cross-contamination Chipotle - apple valley E2009005362 jejuni2009 Confirmed Foodborne lettuce/cross-contamination Chipotle - apple valley E2009005203 jejuni2009 Confirmed Foodborne lettuce/cross-contamination Chipotle - apple valley E2009005204 jejuni2009 Confirmed Foodborne lettuce/cross-contamination Chipotle - apple valley E2009005263 jejuni2009 Confirmed Foodborne lettuce/cross-contamination Chipotle - apple valley E2009009246 jejuni2009 Confirmed Foodborne lettuce/cross-contamination Chipotle - apple valley E2009006096 jejuni2009 Confirmed Foodborne lettuce/cross-contamination Chipotle - apple valley E2009005387 jejuni2009 Confirmed Foodborne lettuce/cross-contamination Chipotle - apple valley E2009005525 jejuni2009 Confirmed Foodborne lettuce/cross-contamination Chipotle - apple valley E2009005524 jejuni
E2009004973 E2009005203 E2009005204 E2009005263 E2009005362 E2009005387 E2009005524 E2009005525 E2009006096 E2009009246E2009004973 0E2009005203 0 0E2009005204 0 0 0E2009005263 0 0 0 0E2009005362 0 0 0 0 0E2009005387 0 0 0 0 0 0E2009005524 0 0 0 0 0 0 0E2009005525 0 0 0 0 0 0 0 0E2009006096 0 0 0 0 0 0 0 0 0E2009009246 5804 5741 5288 6152 4971 4869 6003 5587 6240 0
Non-WGS Outbreak #1: Chicken at a Restaurant
July 17, 2018
− Two Campylobacter jejuni cases interviewed through routine surveillance
− Both reported eating a chicken liver pâté dish from a restaurant in Minneapolis with meal dates of June 23 and June 30
− 3rd case interviewed on July 20 and reported eating a liver pâté dish at the restaurant on July 3
− Minneapolis Health Department (MHD) notified and investigation initiated
Not Your Ordinary Chicken Liver Pâté Dish…
EH Investigation
• No temperatures taken during food prep
• Cooked liver measured at 145° F
• Restaurant advised not to sell the dish until approved to do so by MHD
EH Investigation
• Chefs instructed to take final cooking temperatures and ensure minimum cook temperature of 165° F
• Restaurant required to send action plan to MHD showing correction in recipe
• Foodborne illness consumer warning printed on restaurant’s online menu
WGS Analysis
• Isolates from the two cases sequenced and were not closely related to each other (11,706 SNPs apart)
WGS Data
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How is the data communicated?
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cgMLST
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Lab
Epis
St. Paul
What are allele codes
WGS with cgMLST
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• Increase knowledge on cgMLST
How does Bionumerics
work
What do previous outbreaks look
like using cgMLST
How does cgMLST
compare to SNP
What is cgMLST
How the results will be formatted and
communicated
WGS with cgMLST
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• In-person meetings to discuss:
What/why samples will be
sequenced
What kinds of data can/will
analysis provide
How the results will be
interpreted
How long will analysis take
SNP/cgMLST Comparison
Organism N SNP Range Allele Range Allele CodeS. Enteritidis 6 0-2 ? ?S. Enteritidis 5 0-1 ? ?
S. Typhimurium 7 0-3 ? ?S. Heidelberg 6 0-2 ? ?E. Coli 0157 8 0-3 ? ?
Campy jejuni 5 0-2 ? ?
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• Lab/epi team meeting-show epi BN 7.6
• Illustrate WGS data and clusters, discuss timing
• Determine what to communicate-allele code, MLST type, AST, cluster info, etc
• Determine best communication methods• Stat-PFGE inbox email/phone call
• LIMS (new LIMS in 2019)
• Spreadsheets
• Try for a while, meet, adjust/perfect-reduce friction
Anticipated Communication Outcomes with Epi
Turn Around Time
• It needs to improve
• Maintain high quality
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How do we speed up getting an
isolate
How to Improve TAT
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• Lab meetings to
• discuss:How can we do the sequencing
faster
How can we do the analysis faster
How do we measure our
TAT
How long will analysis take
Isolation Timeline Salmonella
ResultsCIDT
0 to 1 d
SpecimenReceived at PHL*
Identification of isolated pathogen
Stool sample
collecteddays
WGS Completed
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External Partners
Identify clusters
Lab
Investigate clusters
Epi FDA
USDA
CDC
Thank You
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