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  1. Whole Genome Sequencing (WGS) Program

GenomeTrakr Network


The GenomeTrakr network is the first distributed network of laboratories to utilize whole genome sequencing for pathogen identification. It consists of public health and university laboratories that collect and share genomic and geographic data from foodborne pathogens. The data, which are housed in public databases at the National Center for Biotechnology Information (NCBI), can be accessed by researchers and public health officials for real time comparison and analysis that promises to speed foodborne illness outbreak investigations and reduce foodborne illnesses and deaths.

Real Time Food Safety Applications of the GenomeTrakr Network

Collaboration with NCBI

With its mission of providing publicly accessible information and tools that enhance understanding of how genetic processes impact health and disease, NCBI has played a key role in the development and success of GenomeTrakr. NCBI collects, houses, and analyzes foodborne pathogen whole genome sequences to reveal their relatedness to one and other. It also provides analytical tools that can be used by public health officials, researchers, and members of industry, to conduct their own analyses of genomic sequences. Since 2013 the genomic information NCBI houses has been used by public health officials to support more than 837 actions intended to protect consumers from foodborne illness. Examples of public health actions supported by genomic data analyzed by NCBI include investigations of multistate outbreaks of: E. coli infections linked to flour (2017); Salmonella Typhimurium infections linked to dried coconut (2018); and Salmonella Concord infections linked to tahini (2018-19). WGS findings have also prompted FDA to issue numerous warning letters and companies to recall products, including pet food. GenomeTrakr data can be accessed for review and analysis via NCBI’s Pathogen Detection portal.

FDA/CDC Real Time Listeria Project

Further integrating the marriage of clinical, food, and environmental pathogen analysis, FDA has partnered with CDC in an effort to sequence every clinical, food, and environmental isolate of Listeria monocytogenes collected in the U.S. CDC is primarily sequencing clinical samples while FDA and the state laboratories are sequencing food and environmental samples. The genomic sequences and corresponding collection information for the samples are publicly available via the NCBI website.

Minn./Wash./NY/FDA Real Time Salmonella Enteritidis Project

State labs in Minnesota, Washington, and New York have paired with FDA to conduct real time sampling of Salmonella Enteritidis isolates from clinical, food, and environmental samples. The genomic sequences and corresponding collection information for the samples are publicly available in the GenomeTrakr database maintained by NCBI.

Additional Foodborne Pathogen Sequencing

GenomeTrakr member labs initially focused their whole genome sequencing efforts primarily on Salmonella and Listeria pathogen isolates. However, performing whole genome sequencing on other foodborne pathogens will further leverage the public health benefits that can be derived from the open sharing of the genomic information. To this end FDA and its partners are also sequencing E. coli, Campylobacter, Vibrio, Cronobacter, etc. isolates, as well as parasites and viruses. Many public health laboratories have pathogen isolates from past outbreaks stored in their freezers. These isolates hold a treasure trove of genomic information waiting to be unlocked by whole genome sequencing. FDA encourages those labs to sequence those isolates and upload the genomic information to the GenomeTrakr database at NCBI.

Joining and Using the GenomeTrakr Network

For information about joining the GenomeTrakr network as a sequencing lab, providing isolates to a current member lab for sequencing, or using the GenomeTrakr database as a research tool, please contact FDA at GenomeTrakr@fda.hhs.gov.

Contributing Labs:

U.S. FDA Labs
Gulf Coast Seafood Laboratory, Dauphin Island, AL
Arkansas Regional Laboratory, Jefferson, AR
San Francisco District Laboratory, Alameda, CA
Pacific Regional Laboratory—Southwest, Irvine, CA
Denver District Laboratory, Denver, CO
Southeast Regional Laboratory, Atlanta, GA
CFSAN Research Laboratories at Moffett Campus, Bedford Park, IL
CFSAN Molecular Methods and Subtyping Lab, College Park, MD
ORA-CFSAN Method Development and Validation Laboratory at MOD1, Laurel, MD
Winchester Engineering & Analytical Center, Winchester, MA
Northeast Regional Laboratory, Jamaica, NY
Forensic Chemistry Center, Cincinnati, OH
Pacific Regional Laboratory—Northwest, Bothell, WA

State Health and University Labs
Alaska State Public Health Laboratory, Anchorage, AK
Arizona Department of Health Services with the Translational Genomics Research Institute, Phoenix, AZ
California Department of Public Health, Richmond, CA
Colorado Department of Public Health and Environment, Denver, CO
NOVA Southeastern University, Fort Lauderdale, FL
Florida Department of Health, Jacksonville, FL
Florida Department of Agriculture and Consumer Services, Tallahassee, FL
Hawaii Department of Health, Pearl City, HI
State Hygienic Laboratory at the University of Iowa, Coralville, IA
Kentucky Cabinet for Health and Family Services, Frankfort, KY
Maryland Department of Health and Mental Hygiene, Baltimore, MD
Joint Institute for Food Safety and Applied Nutrition, College Park, MD
Massachusetts State Public Health Laboratory, Jamaica Plain, MA
Michigan Department of Agriculture and Rural Development, East Lansing, MI
Michigan Department of Health and Human Services, Lansing, MI
Minnesota Department of Health, Saint Paul, MN
Missouri Department of Health and Senior Services, Jefferson City, MO
Nevada Department of Health and Human Services with University of Nevada - Reno, Reno NV
New Hampshire Department of Health and Human Services, Concord, NH
New Jersey Department of Health and Senior Services, Trenton, NJ
New Mexico State University, Food Safety Laboratory, Las Cruces, NM
New York State Department of Agriculture & Markets, Albany, NY
New York State Department of Health - Wadsworth Center, Albany, NY
Cornell University, Ithaca, NY
North Carolina State University, College of Veterinary Medicine, Raleigh, NC
Animal Diseases Diagnostic Laboratory, Ohio Department of Agriculture, Reynoldsburg, OH
Pennsylvania Department of Health with Pennsylvania State University, University Park, PA
Rhode Island Department of Health, Providence, RI
South Carolina Department of Health and Environmental Control, Columbia, SC
South Dakota Department of Health with South Dakota State University, Brookings, SD
Texas Department of State Health Services, Austin, TX
Vermont Agency of Human Services, Colchester, VT
Virginia Department of Health, Richmond, VA
University of Washington, Seattle, WA
Washington State Department of Agriculture, Olympia, WA
Washington State Department of Health Public Health Laboratories, Shoreline, WA

U.S. Hospital Labs
Brigham and Women's Hospital, Boston, MA

U.S. Department of Agriculture (USDA) Food Safety Inspection Service (FSIS) Field Services Labs
Eastern Laboratory, Athens, GA

Centers for Disease Control and Prevention (CDC) Labs
Enteric Diseases Laboratory, Atlanta, GA

Other Labs located in the U.S
Gladstone Institutes, San Francisco, CA
IEH Laboratories & Consulting Group, Lake Forest Park, WA

Labs located outside of the U.S.
INEI-ANLIS “Carlos Malbran Institute,” Buenos Aires, Argentina
Doherty Institute, Melbourne, Australia
Institute of Clinical Pathology and Medical Research, Westmead Hospital, Sydney, Australia
University of New South Wales, Sydney, Australia
Austrian Agency for Health and Food Safety, Vienna, Austria
Health Canada, Ottawa, Canada
Laboratoire de sante publique du Quebec, Sainte-Anne-de-Bellevue, Canada
Danish Technical University, Kongens Lyngby, Denmark
Statens Serum Institute, Copenhagen, Denmark
Justus Liebig University, Giessen, Germany
University Hospital Muenster, Muenster, Germany
Centre for Food Safety, University College Dublin, Dublin, Ireland
National Salmonella, Shigella, and Listeria Reference Laboratory, Galway, Ireland
Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "Giuseppe Caporale" (IZSAM), Teramo, Italy
Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria (SENASICA), Mexico City, Mexico
University of Birmingham, Birmingham, United Kingdom
NHS Lothian, Edinburgh, United Kingdom
Public Health England, London, United Kingdom
University of Oxford, Oxford, United Kingdom
Animal and Plant Health Agency, Surrey, United Kingdom
Food Environmental Research Agency (Fera), York, United Kingdom

Collaborations with Independent Academic Researchers:
In addition to state labs, university labs, federal labs, and labs located outside of the U.S., the GenomeTrakr network has collaborative relationships with a number of independent researchers, including graduate students, who supply foodborne pathogen isolates and/or perform whole genome sequencing on the isolates.

Data Curation:
Data curation and bioinformatic analyses and support are provided by the National Center for Biotechnology Information (NCBI) in Bethesda, MD.

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