Food Genome Database Planned

FDA, CDC, Agilent Technologies, and the University of California, Davis are collaborating on the 100K Genome Project to build a free, public database of 100,000 foodborne pathogen genomes, enabling faster pinpointing of illness outbreaks.

The next step in the ongoing U.S. effort to limit outbreaks of foodborne illnesses, which are occurring about 1,000 times per year, is a new collaboration involving the U.S. Food and Drug Administration, the University of California, Davis, Agilent Technologies Inc., and the Centers for Disease Control and Prevention to create a free, public database of 100,000 foodborne pathogen genomes. Once it is established about five years from now, it will enable faster identification of bacteria responsible for outbreaks of foodborne illnesses.

FDA announced the collaboration July 12, saying in its announcement that the typical public health response time in outbreaks will be "days instead of weeks." Allowing open access to the database will foster the creation of tests to identify bacteria in a sample "within a matter of days or hours, significantly faster than the approximately one week it now takes between diagnosis and genetic analysis," it said. FDA is providing more than 500 completed Salmonella genome draft sequences and thousands more important food pathogen strains for sequencing; the agency's scientists also will help with guiding the project and providing technical assistance when needed.

The database was conceived by the university, Agilent, and FDA and is called "The 100K Genome Project." It will include the genomes of important pathogens such as Salmonella, Listeria, and E. coli. "This important project will harness the cutting-edge technology of genome sequencing to advance our understanding of and response to foodborne outbreaks," said FDA Commissioner Dr. Margaret A. Hamburg. "FDA is pleased to contribute scientific and technical expertise necessary to create and maintain this foodborne pathogen database which will be fully accessible and have long-lasting impact on protecting public health."

"Each year in the United States, there are more than 48 million cases of foodborne illness," said Mike McMullen, president of Agilent's Chemical Analysis Group. "A problem of this magnitude demands an equally large countermeasure. We see this project as a way to improve quality of life for a great many people, while minimizing a major business risk for food producers and distributors."

USDA's Food Safety and Inspection Service will collaborate on the project. "This initiative shows great promise as we look to improve our ability to identify and track down potential sources of foodborne outbreaks," said USDA Under Secretary for Food Safety Dr. Elisabeth Hagen. "FSIS intends to submit important bacterial strains from our regulatory testing program for sequencing at UC Davis, and we look forward to the benefits this public database could provide federal, state and local public health agencies."

The gene sequencing will be coordinated by UC Davis, which is providing access to its collection of bacteria samples. UC Davis is forming a consortium to support the project with federal, state, and local public health laboratories, food manufacturers, industries, and academic organizations participating. Organizations interested in joining should contact Bart Weimer, the UC Davis program director, at bcweimer@ucdavis.edu.

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