FDA: Sequencing project will help solve foodborne outbreaks

Jul 12, 2012 (CIDRAP News) – The US Food and Drug Administration (FDA) said today that a big genome sequencing project it is launching with private and public partners will help speed up the identification of bacteria that cause foodborne disease outbreaks.

The aim of the project is to create a public database of the genomes of about 100,000 foodborne pathogen isolates, including strains of important agents such as Salmonella, Listeria, and pathogenic Escherichia coli, the FDA said.

"The database will provide a roadmap for development of tests to identify pathogens and provide information about the origin of the pathogen," the agency said. "The tests have the potential to significantly reduce the typical public health response time in outbreaks of foodborne illness to days instead of weeks."

The FDA's major partners in the project are the University of California, Davis (UC Davis); Agilent Technologies, Inc.; and the Centers for Disease Control and Prevention (CDC). The effort—conceived by UC Davis, the FDA, and Agilent—is called the 100K Genome Project. It's expected to take 5 years.

"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," the FDA said.

The FDA said it is providing more than 500 completed Salmonella whole-genome sequences, thousands of additional important food pathogen strains for sequencing, and bioinformatic support. FDA scientists also will help guide the project and provide technical assistance when needed.

Agilent is providing scientific expertise, instrumentation, and funding to support a portion of UC Davis activities, the FDA said. The CDC will provide its foodborne disease expertise, isolates to be sequenced, and other information, and CDC experts will serve on the steering committee for the project.

Another partner will be the US Department of Agriculture's (USDA's) Food Safety and Inspection Service (FSIS), the announcement said. The agency will submit bacterial strains from its testing program for sequencing, said Elizabeth Hagen, USDA under secretary for food safety.

The genomic sequencing will be coordinated by UC Davis, which is also providing access to its collection of bacteria samples, the FDA reported. 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, in the press release. BGI, a Chinese firm, was formerly known as the Beijing Genomics Institute. Lewin predicted that the project would "revolutionize our basic understanding of these disease-causing microorganisms."

The FDA said the new database "will significantly speed testing of raw ingredients, finished products, and environmental samples taken during investigation of foodborne illness outbreaks."

The statement adds, "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."

Completed sequences will be stored in the public database of the National Institutes of Health's National Center for Biotechnology Information, the agency said.

UC Davis is currently working to form a consortium to support the project, with participants such as public health laboratories, food manufacturers, and academic organizations, officials said.

See also:

Jul 12 FDA press release
http://www.fda.gov/NewsEvents/Newsroom/PressAnnouncements/ucm311661.htm

Related FDA consumer update
http://www.fda.gov/ForConsumers/ConsumerUpdates/ucm311086.htm

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