GenomeTrakr database: WGS network for foodborne pathogen traceback

Transcription

1 GenomeTrakr database: WGS network for foodborne pathogen traceback Conference for Food Protection WGS workshop April 16, 2016 Ruth E. Timme, PhD Research Microbiologist GenomeTrakr data manager

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3 GenomeTrakr Labs U.S. States with Federal, State, or University Labs, and countries other than the U.S., that are part of the GenomeTrakr Network {;:[ NCBI Data Curation Site 3

4 Total Number of draft genomes in the GenomeTrakr database **CDC contributing clinical isolates Average Number of Sequences Added Per Month in 2013 = 169 Average Number of Sequences Added Per Month in 2014 = 1,076 Average Number of Sequences Added Per Month in 2015 = 2,362 Number of Sequences (as of the last day of the quarter) Public Health England uploads more than 8,000 Salmonella sequences First sequences uploaded in Feb

5 A Growing Regulatory Role: CFSAN USA:WI environmental: food-contact surface PNUSAL USA Peritoneal fluid acites CFSAN Canada cantaloupe PNUSAL USA:NY Blood FDA * * USA:VA * Facility swab Timeline: Virginia, 2015 Listeria monocytogenes March- April 2015, first matches May 5 th, FDA contacts VA lab May- June, more matches OB VA-WGS * * USA:VA * mung bean sprouts VA-WGS * * USA:VA * soybean sprouts PNUSAL * * USA * Wound PNUSAL * * USA * Blood VA-WGS * * USA:VA * Facility swab PNUSAL * * USA * Blood 0.06 VA-WGS * * USA:VA * soybean sprouts VA-WGS * * USA:VA * soybean sprouts

6 A Growing Regulatory Role: CFSAN USA:WI environmental: food-contact surface PNUSAL USA Peritoneal fluid acites CFSAN Canada cantaloupe PNUSAL USA:NY Blood FDA * * USA:VA * Facility swab June 22 nd, voluntary recall 58 SNPs from OB OB VA-WGS * * USA:VA * mung bean sprouts VA-WGS * * USA:VA * soybean sprouts PNUSAL * * USA * Wound PNUSAL * * USA * Blood VA-WGS * * USA:VA * Facility swab 0-4 SNPS PNUSAL * * USA * Blood 0.06 VA-WGS * * USA:VA * soybean sprouts VA-WGS * * USA:VA * soybean sprouts

7 Timeline for TradiKonal Approach to Foodborne Illness InvesKgaKon Identify illnesses and get PFGE pattern from clinical samples CDC Identify contaminated food and confirm that product or environmental sample PFGE pattern matches the clinical sample pattern CDC/ FDA/FSIS Number of Cases Contaminated food enters commerce Source of contamination identified too late to prevent most illnesses Days

8 TARGET: Timeline for Foodborne Illness InvesKgaKon Using Whole Genome Sequencing 40 FDA, CDC, FSIS, and States use WGS in real-time and in parallel on clinical, food, and environmental samples Source of contamination identified early through WGS combined database queries Number of Cases Contaminated food enters commerce Averted Illnesses Days

9 Immediate benefits of WGS to industry, growers, and distributers. Earlier intervenkon means: 1) Reduced amount of recalled product; 2) fewer sick pakents 3) less impact overall and minimal damage to brand recognikon.

10 The Fresh- cut Tomato Supply Chain, for example, Is complex

11 WGS- based monitoring can pinpoint root causes in the Fresh- cut Tomato Supply Chain

12 Benefits to industry, growers, and distributers (conenued). Regular teseng throughout network: 1) idenefies specific suppliers that are introducing contaminants; 2) idenefies whether contaminant is resident to a facility or transient; 3) knowledge of where contaminant is coming from allows industry to fix the problem based on scienefic evidence. ShiX costs to the supplier who has introduced the contaminant. How oxen is the root cause of the problem lex unresolved to occur again at a later date? 12

13 Acknowledgements FDA Center for Food Safety and Applied NutriKon Center for Veterinary Medicine Office of Regulatory Affairs NaEonal InsEtutes of Health NaKonal Center for Biotechnology InformaKon State Health and University Labs Alaska Arizona California Florida Hawaii Maryland Minnesota New Mexico New York South Dakota Texas Virginia Washington USDA/FSIS Eastern Laboratory CDC Enteric Diseases Laboratory INEI- ANLIS Carlos Malbran Inst., ArgenEna Centre for Food Safety, University College Dublin, Ireland Food Environmental Research Agency, UK Public Health England, UK WHO Illumina Pac Bio CLC Bio APHL 13