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U.S. Department of Health and Human Services


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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 – additional research by the Whole Genome Sequencing group can be seen on the Research page.

Genome Trakr Network
Genome Trakr is a new pilot network of State and Federal Public Health Laboratories collecting and sharing genomic data from foodborne pathogens Researchers around the US will be able to analyze and compare data in real time, speeding up investigations and contamination control. These archived data will become the foundation for other national and international research platforms, such as the Global Microbial Identifier disclaimer icon.
Access Genome Trakr Database at NCBI: http://www.ncbi.nlm.nih.gov/bioproject/183844 disclaimer icon

Contributing labs:

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

Global Microbial Identifier
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 every new outbreak sample can be compared with to 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.

Learn more about the GMI disclaimer icon 

100K Pathogen Genome Project

  • FDA CFSAN is providing food pathogen strains for sequencing. FDA scientists will guide the project and provide technical support.
  • UC-Davis is performing the genome sequencing and coordinating the overall effort.
  • Agilent Technologies of Santa Clara, Calif., is supplying expertise, instrumentation, and funding. The company that manufactures equipment for electronic and bio-analytical measurement.
  • CDC is providing its foodborne disease expertise, strains to be sequenced, and other information. CDC experts will also serve on the steering committee for the project.
  • Dept. of Agriculture will submit important bacterial strains from its regulatory testing program for sequencing.

 Learn more about the 100K Genome project. disclaimer icon