Impact of WGS in New York...Auto-Slicer Zone 2 (2016) 1 SNP Cheese Cooler Zone 3 (2016) 0 SNP 21...
Transcript of Impact of WGS in New York...Auto-Slicer Zone 2 (2016) 1 SNP Cheese Cooler Zone 3 (2016) 0 SNP 21...
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: [email protected]