Impact of WGS in New York2018 Genome Trackr Meeting

September 27, 2018

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Division of Food Laboratory

Albany, NY

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Food Laboratory sections:• Food and Dairy Microbiology: analyze over 20,000

food samples/yr. ~ 2,500 of these for foodborne pathogens and the remainder for other indicators

• Food and Dairy Chemistry: analyze over 5,000 food samples/yr. ~ 1,500 for chemical hazards

• Pesticide residues: analyze over 2,500 produce samples/yr. for 165 different pesticide residues and pharmaceutical products

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Division of Food Laboratory • PulseNet Ag laboratory • Genome Trakr laboratory• FDA certified for milk testing laboratory• Member of Food Emergency Response

Network (FERN)• Participant of the Pesticide Data Program

(USDA) • Participant of MFRPS and RRT programs

Division of Food Laboratory2008 Accredited to• ISO/IEC 17025 Standard• AOAC ALACC Criteria: Guidelines for Laboratories

Performing Microbiological and Chemical Analysis of Food, Dietary Supplements, and Pharmaceuticals

https://www.a2la.org/scopepdf/2749-01.pdfhttps://www.a2la.org/scopepdf/2749-02.pdf

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Where do the samples come from?• Within Ag and Markets (surveillance)

• Division of Food Safety Inspection • Division of Milk Control/Dairy Services• Division of Plant Industry

Collected by field staff from farms, food processing plants, food/feed/fertilizer manufacturers, distribution centers, farmers markets, and retail stores.

What do we test? • Primarily testing for specific health hazards and/or

accuracy of labeling

• Focus on high risk, ready-to-eat food, feed, andenvironmental samples

• Collaborate and coordinate work with other agencies (FDA, USDA, EPA, NYSDOH, etc.)

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Where do the samples come from?

• NE Region• Other states

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Outbreaks, Recalls & Others Investigations• Listeria monocytogenes in potato salad (2011)• Salmonella in chicken livers (2011)• E. coli O157:H7 associated with produce (2013)• Listeria monocytogenes in imported seafood (2012-13)• Salmonella in pet foods/treats (2013)• Salmonella in chia seeds (2014)• Listeria monocytogenes in soft cheese (2016-17)• Listeria monocytogenes in deli markets (2018) • Listeria monocytogenes in tuna salad (2018)• Listeria monocytogenes in raw milk (2018)

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From PFGE to WGS

• 2007: Joined PulseNet • 2015: Joined Genome Trakr• 2015 - 2016: Training and Implementation • 2017: Received WGS grant• 2017 - 2018: Interactions with others

concerning WGS analysis (Cornell, Wadsworth and Seed lab)

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Where do isolates are coming from?

• Foodborne pathogens isolated in-house (L. monocytogenes, Salmonella, E. coli, and Campylobacter)

• Salmonella from chicken and historical isolates

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Where do isolates are coming from? • International collaboration

Different strains of Salmonella from environment and chicken

WGS Isolates WGS analysis

WGS analysis

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Examples of Investigations• Listeria monocytogenes in raw milk cheese

• End of February 2017: Joint investigation with FDA • At least 100 environmental samples were sent to FDA laboratory• 6 samples were taken and sent to NYSDAM Food Laboratory. Three samples positive.

• March 2017 • March 3: Firm issues recall of product (Ouleout cheese)

• Isolates PFGE patterns matched to clinical isolates (NYDAM Food Laboratory)• March 7: Nationwide recall of all product

• Isolates WGS matches sequence to ≤3 SNPs difference to those of the clinical isolates (NYDAM Food Laboratory)

Five of the eight ill people in the outbreak were New York residents. A Florida resident became sick after eating the cheese during a visit to New York. The outbreak involved one resident each in Connecticut and Vermont, and those were the two that died.

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Examples of Investigations (cont.)• Listeria monocytogenes in raw milk cheese (again!)

• October 2017: L. monocytogenes isolated from herbal jack raw cheese. One clinical PFGE match (FL)• Product was recalled and destroyed

• November 2017: NYSDAM Environmental swabs were collected but no L. monocytogenes was isolated

• January 2018: Public Health laboratories stopped uploading L. monocytogenes PFGE

• April 2018: Joint investigation with FDA. No L. monocytogenes was isolated from cheese• June 2018: NYSDAM Environmental swabs were collected but no L. monocytogenes was isolated

• August 2018: NYSDAM collected cheddar raw cheese and L. monocytogenes is isolated• Product was recalled and destroyed

• August 2018: NYSDAM collected more samples but no L. monocytogenes was isolated

• September 2018: Active investigation

Raw milk cheddar (Oct 2017) 0 SNP

Raw milk cheddar (Aug 2018) 19 SNPs

Clinical (June 2018) 1 SNP

Clinical (March 2018) 0 SNP

Listeria monocytogenes in raw milk cheese

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Examples of Investigations (cont.)• Listeria monocytogenes in tuna salad

• NYDOH notified NYSDAM of one clinical case of listeriosis. Per patient interview, potential food and retail establishment were determined as potential source of contamination.

• August 2018: NYSDAM collected food (5) and environmental samples (15) from a deli. L. monocytogenes was isolated from 1 food and 4 environmental samples.

Clinical (July 2018) 0 SNP

Tuna salad (Aug 2018) 0 SNP

Floor drain close to salad prep area 45 SNPs

Cheese cutting board 20 SNPs

Shopping cart wheel found close to salad prep area 0 SNP

Slicing machine 20 SNPs

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Investigations involving Environmental Sampling• From February 2016 – October 2017

• Environmental and food sampling as part of investigation of Listeria monocytogenes in deli market.

• Swabs are collected from different zones.

• When positive samples are identified, Food Safety inspectors return to the establishment and request compliance of the “Listeria protocol”.

• Establishment removed/destroyed contaminated equipment.

Listeria monocytogenes in a deli place

Turkey Breast (2017) 0 SNP

Deli Meat (2016) 2 SNP

Cheese Tray Zone 1 (2016) 0 SNP

Cheese Tray Zone 1 (2016) 0 SNP

Slicer A2 Zone 1 (2016) 2 SNP

Slicer A1 Handle (2016) 2 SNP

Rolling Metal Zone 3 (2016) 0 SNP

Wrapping Paper Holder (2016) 2 SNP

Auto-Slicer Zone 2 (2016) 1 SNP

Cheese Cooler Zone 3 (2016) 0 SNP

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Listeria monocytogenes in a raw milk farm

Raw Milk 9 (April 2018) 77 SNP

Raw Milk 6 (Jan 2018) 76 SNP

Raw Milk 9 (Jan 2018) 12 SNP

Raw Milk 10 (Feb 2018) 61 SNP

Raw Milk 8 (April 2018) 77 SNP

Prep Rag 2 (April 2018) 14 SNP

Prep Rag 1 (April 2018) 13 SNP

Raw Milk 4 (Feb 2018) 57 SNP

Raw Milk 10 (March 2018) 0 SNP

Prep Pail (April 2018) 0 SNP

Prep Pail (April 2018) 0 SNP

Acknowledgements

Thank you!

Maria Ishida, PhDDirector of Food Laboratory

NYS Department of Agriculture and MarketsEmail: Maria.Ishida@agriculture.ny.gov