Interpreting, Reporting and Communication of WGS Data · • Illustrate WGS data and clusters,...

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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