WGS Surveillance and Cluster Detection in New York State – past

experiences and future plans

2019 PulseNet / OutbreakNet Joint East Coast Regional Meeting 1/16/19

Deborah BakerWadsworth Center, NYSDOHDeborah.baker@health.ny.gov

Current NYS WGS Cluster Reporting Guidelines

Method of Analysis

Cluster size

Threshold Timeframe

Listeria BioNumerics 7.6 2 0-30 alleles (wgMLST)

Unlimited

E. coli In-house pipeline 2 0-20 SNPs 365 days

S. Typhimurium In-house pipeline 2 0-10 SNPs 90 days

S. Enteritidis In-house pipeline 3 0-5 SNPS 60 days

2016 - 2018 Reported Clusters2016 2017 2018

E. coli PFGE clusters 34 31 37E. coli WGS clusters 13 21 21

Listeria PFGE clusters 18 16 Listeria WGS clusters 7 9 22

Salmonella PFGE clusters (all serotypes) 123 138 145

Salmonella Enteritidis WGS clusters 13 19 11Salmonella Typhimurium WGS clusters ---- 24 29

NYS Listeria outbreak investigation

Timeline

8/1/2014 Cluster A

10/30/2014 Additional

case Cluster A

12/2/2016 Cluster B

1/17/2017Environmental

sampling

1/20/2017 Additional

case Cluster B

6/19/2017 Cluster C

9/14/17 Food samples collected

10/10/2017 Environmental

sampling

Listeria investigation spanning 3 years – 3 separate clusters?

Isolates in CDC PulseNet database with PFGE pattern combination GX6A16.0677 / GX6A12.0770 collected between 2014 - 2017

Cluster A6/2014 – 10/2014

NYS Environmental sampling

Cluster C 5/2017

PNUSAL000806PNUSAL000888PNUSAL001130PNUSAL002278PNUSAL002634PNUSAL002709PNUSAL002802FDA00011776PNUSAL003099CFSAN071131CFSAN071132CFSAN071133CFSAN071134

GX6A16.0677GX6A16.0677GX6A16.0677GX6A16.0677GX6A16.0677GX6A16.0677GX6A16.0677GX6A16.0677GX6A16.0677GX6A16.0677GX6A16.0677GX6A16.0677GX6A16.0677

GX6A12.0770GX6A12.0770GX6A12.0770GX6A12.0770GX6A12.0770GX6A12.0770GX6A12.0770GX6A12.0770GX6A12.0770GX6A12.0770GX6A12.0770GX6A12.0770GX6A12.0770

BloodBloodBloodBloodBloodBloodBloodEnvironmental SwabBloodSwabSwabSwabSwab

2014-06-022014-06-172014-10-192016-06-232016-10-202016-11-042017-01-042017-05-022017-05-302017-10-102017-10-102017-10-102017-10-10

Cluster B6/2016 – 1/2017

*

*

* Out-of-state isolates

Three separate PFGE clusters due to temporal distribution

PFGE-AscI PFGE-ApaI

Hi Deb, These two NY cases are not closely related to the CA case, they are more than 60 alleles different. With that said, they are closely related to some NY isolates sequenced in 2014 and given cluster code 1410NYGX6-1. These fall all within 2 allele differences.

Key WGS_id Outbreak IsolatDate NY___IDR1400018203-01 PNUSAL000806 1410NYGX6-1 6/2/2014 NY___IDR1400021850 PNUSAL000888 1410NYGX6-1 6/17/2014 NY___IDR1400033631 PNUSAL001130 1410NYGX6-1 10/19/2014 NY___IDR1600030928-01 PNUSAL002278 6/23/2016 NY___IDR1600051367-01 PNUSAL002709 11/4/2016

This cluster was not followed by CDC epis as there was not much epi data on the 2014 cases. Did you all ever identify a source? I’d suspect they are all epidemiologically linked. Thanks, Steven G. Stroika PulseNet National Database Manager CDC/NCEZID/DFWED/EDLB/PulseNet PulseNet: (404) 639-4558 P:(404) 639-0779 F:(404) 718-1095

BioNumerics 7.6 wgMLST Analysis

Salmonella PFGE report

• Isolates span almost a full year

• Two separate PulseNet clusters• Two different, but closely-related PFGE

pattern combinations

• Local cluster naming

1712MLEXH-1 EXHX01.4071/EXHA26.0531

1712MLEXH-1 EXHX01.4071/EXHA26.0531

1810MLEXH-1EXHX01.7220/EXHA26.5334

1712MLEXH-1 EXHX01.4071/EXHA26.0531

E. coli In-house Pipeline Report

Cluster spanning 2 years

Out-of-state matches detected using NCBI Pathogen Detection Browser (records created on NCBI < 120 days,

Future PlansWorkflow• 4 PFGE staff will transition to WGS (1 staff member already exclusively WGS) for a total of 5

laboratory staff• 4 are currently certified for WGS Analysis

• New York State will discontinue PFGE for all organisms by March, 2019

• Batch DNA extractions during off-peak season – 3 days / week

• Wadsworth Center has core facility for NGS sequencing• Challenge – uncertain timeframe for completion of sequencing

• QiaCube HT on order – will allow batch extractions for 8-96 samples

• Plans to order plate reader for quantification during next ELC cycle

Additional Future Plans…hypotheticallyAnalysis and Reporting • Internal cluster naming• Utilize allele codes to search for matches• Use line lists for reporting to Epi

• Dendrograms too labor-intensive for routine reporting

Unknowns????• How long will analysis process take for large batches of isolates• Refining cluster thresholds

https://pixabay.com

https://pixabay.com

Current NYS WGS Cluster Detection Guidelines

Method of Analysis

Cluster size

Threshold Timeframe

Listeria BioNumerics 7.6 2 0-30 alleles (wgMLST)

Unlimited

E. coli In-house pipeline 2 0-20 SNPs 365 days

S. Typhimurium In-house pipeline 2 0-10 SNPs 90 days

S. Enteritidis In-house pipeline 3 0-5 SNPS 60 days

AcknowledgementsWadsworth Center• Kim Musser• Nellie Dumas• Lisa Mingle• William Wolfgang• Samantha Wirth• Lisa Thompson• Michelle Dickinson• Amy Saylors

• Pascal LaPierre• Erica Lasek-Nesselquist• Applied Genomic Technologies Core

New York State Bureau of Communicable Disease Control• Madhu Anand• Alexandra Newman• Amy Robbins• Katherine Purcell• Paula Huth• Kadri Ajileye

New York Integrated Food Safety Center of Excellence

New York State Dept. of Agriculture and Markets

WGS Surveillance and Cluster Detection in New York State – past experiences and future plansCurrent NYS WGS Cluster Reporting Guidelines2016 - 2018 Reported ClustersNYS Listeria outbreak investigationListeria investigation spanning 3 years – 3 separate clusters?Slide Number 6BioNumerics 7.6 wgMLST AnalysisSlide Number 8Slide Number 9E. coli In-house Pipeline ReportSlide Number 11Future PlansSlide Number 13Current NYS WGS Cluster Detection GuidelinesAcknowledgements