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FDA, UC Davis, Agilent Technologies and CDC to Create Publicly Available Food Pathogen Genome Database

Published: Friday, July 13, 2012
Last Updated: Friday, July 13, 2012
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Genetic code sequencing of 100,000 food pathogens will provide roadmap to help identify causes of outbreaks.

The U.S. Food and Drug Administration (FDA), the University of California, Davis,Agilent Technologies Inc., and the Centers for Disease Control and Prevention (CDC) announced today a collaboration to create a public database of 100,000 foodborne pathogen genomes to help speed identification of bacteria responsible for foodborne outbreaks.
The database will provide a roadmap for development of tests to identify pathogens and provide information about the origin of the pathogen. The tests have the potential to significantly reduce the typical public health response time in outbreaks of foodborne illness to days instead of weeks.
Open access to the database will allow researchers to develop tests that can identify the type of bacteria present 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.
Conceived by UC Davis, Agilent, and FDA and called “The 100K Genome Project,” the collaboration will be a five-year effort to sequence the genetic code of approximately 100,000 important foodborne pathogens and make this information available in a free, public database. The sequencing will include the genomes of important foodborne 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 Margaret A. Hamburg, M.D. “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.
The FDA is providing more than 500 already completed Salmonella whole-genome draft sequences, thousands of additional important food pathogen strains for sequencing, and bioinformatic support. FDA scientists also will participate in guiding the project and providing technical assistance when needed.
Agilent is providing scientific expertise, instrumentation, and funding to support a portion of UC Davis activities.
“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.”
With the goal of making the food supply safer for consumers, the new database will significantly speed testing of raw ingredients, finished products, and environmental samples taken during investigation of foodborne illness outbreaks. This type of information also enables scientists to make new discoveries that drive the development of new methods to control disease-causing bacteria in the food chain.
The CDC will provide its foodborne disease expertise, strains to be sequenced and other information for use in the project. CDC experts will also serve on the steering committee for the project.
“Protecting the American population from foodborne illness is a public health priority and requires the combined efforts of public and private partners,” said Beth Bell, MD, director of CDC’s National Center for Emerging and Zoonotic Infectious Diseases. “We welcome the opportunity to join in an initiative that shows promise for advancing our technological capacity for foodborne disease surveillance and outbreak response.”
Identifying the pathogens responsible for foodborne illnesses and outbreaks is only one part of the public health response. Food safety officials still need to be able to determine which food or ingredient is contaminated and where it came from. This can be a challenge, especially when multi-ingredient foods are involved or the same ingredient is sourced from multiple suppliers around the world.
When used as part of an overall surveillance and outbreak investigation system, the genetic information in the new database, in combination with geographic information about the pathogens, will help public health officials more quickly pinpoint the source of contamination responsible for a foodborne outbreak.
The U.S. Department of Agriculture’s Food Safety and Inspection Service (FSIS) will also 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 genomic sequencing will be coordinated by UC Davis, which is also providing access to its collection of bacteria samples. The sequencing will be done at the newly formed BGI@UC Davis genome sequencing facility.
“This landmark project harnesses UC Davis’ partnership with BGI, a world leader in genomics, to mine information about the most deadly foodborne pathogens,” said Harris Lewin, vice chancellor for research at UC Davis. “It will revolutionize our basic understanding of these disease-causing microorganisms.”
As sequences are completed they will be stored in the National Institutes of Health’s National Center for Biotechnology Information’s public database.
As part of its efforts for the collaboration, UC Davis is currently forming a consortium to support the 100K Genome Project. The consortium participants will draw from a variety of stakeholders including Federal, state, and local public health laboratories, food manufacturers, industries, and academic organizations. Organizations interested in joining the collaboration can contact Bart Weimer, the UC Davis program director at

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