Detecting contamination and controlling outbreaks of foodborne illness are national priorities. These tasks require accurate tools to distinguish which illnesses are related to the same contamination event – that way, investigators can begin to identify the responsible food, companies and regulatory agencies can take effective control measures, and consumers can make informed choices about which foods to avoid.
The projects listed here represent major national, international, and public-private partnerships in which FDA participates.– Additional research by the Whole Genome Sequencing group can be found on the Research page.
- GenomeTrakr Network
- Global Microbial Identifier
- FDA/CDC Real Time Listeria Project
- Minn./Wash./NY/FDA Real Time Salmonella Enteritidis Project
GenomeTrakr is a network of State and Federal Public Health Laboratories collecting and sharing 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.
The data captured by the GenomeTrakr network could serve as a model for other national and international research platforms, such as the Global Microbial Identifier . 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.
Access the GenomeTrakr Database at NCBI: http://www.ncbi.nlm.nih.gov/bioproject/183844
US FDA field labs
Winchester Engineering & Analytical Center, Winchester, MA
Forensic Chemistry Center, Cincinnati, Ohio
Northeast Regional Laboratory, Jamaica, NY
Southeast Regional Laboratory, Atlanta, GA
Arkansas Regional Laboratory, Jefferson, AR
Pacific Regional Laboratory—Southwest, Irvine, CA
Denver District Laboratory, Denver, CO
San Francisco District Laboratory, Alameda, CA
Pacific Regional Laboratory—Northwest, Bothell, WA
ORA-CFSAN Method Development and Validation Laboratory at MOD1, Laurel, MD
State Health Labs
Arizona State Public Health Laboratory, Phoenix, AZ
Florida Department of Health, Jacksonville, FL
New York State Dept. of Health - Wadsworth Center, Albany, NY
Washington State Department of Health Public Health Laboratory, Shoreline, WA
Minnesota Department of Health, Saint. Paul, MN
Maryland Dept. of Health and Mental Hygiene, Baltimore, MD
Virginia Department of Health, Richmond, VA
The Global Microbial Identifier (GMI) will use the growing collections of genomic data to do worldwide epidemiological surveillance and perform standardized identification of microbes (including bacteria, parasites, and fungi). Eventually the genomic information from every new outbreak sample can be compared to the information in this global network of genomic databases to determine where similar outbreaks have occurred before, or if new types of pathogens are emerging.
The GMI will provide user-friendly interfaces for genomic researchers in academia, industry, and government. The GMI will enable faster, cheaper, and more accurate microbial identification, tracing, disease control, and research – locally and globally.
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.
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.