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.
- GenomeTrakr Fast Facts
Includes updates on the number of pathogens sequenced
- Video overview of how foodborne pathogens are isolated from a food sample and sequenced
- GenomeTrakr: Pushing Back the Frontiers of Outbreak Response
- Access the GenomeTrakr Database at NCBI
- Joining and Using the GenomeTrakr Network
Real Time Food Safety Applications of the GenomeTrakr Network
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 shigatoxin producing 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.
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 FoodWGS@fda.hhs.gov.
U.S. FDA Labs
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
Winchester Engineering & Analytical Center, Winchester, MA
ORS-CFSAN Molecular Methods and Subtyping Lab, College Park, MD
ORA-CFSAN Method Development and Validation Laboratory at MOD1, Laurel, MD
Northeast Regional Laboratory, Jamaica, NY
Forensic Chemistry Center, Cincinnati, Ohio
Pacific Regional Laboratory—Northwest, Bothell, WA
State Health and University Labs
Alaska State Public Health Laboratory, Anchorage, AK
Arizona State Public Health Laboratory, Phoenix, AZ
Florida Department of Health, Jacksonville, FL
Hawaii Department of Health, Pearl City, HI
Maryland Department of Health and Mental Hygiene, Baltimore, MD
Minnesota Department of Health, Saint Paul, MN
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
South Dakota Department of Health, Pierre, SD
Texas Department of State Health Services, Austin, TX
Virginia Department of Health, Richmond, VA
Washington State Department of Health Public Health Laboratories, Shoreline, WA
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
Labs located outside of the U.S.
INEI-ANLIS “Carlos Malbran Institute,” Buenos Aires, Argentina
Centre for Food Safety, University College Dublin, Dublin, Ireland
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 and bioinformatic analyses and support are provided by the National Center for Biotechnology Information (NCBI) in Bethesda, MD.