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Sequencing of 100,000 Pathogens to Help Solve Foodborne Outbreaks

Published: Friday, August 24, 2012
Last Updated: Friday, August 24, 2012
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New collaboration of Federal agencies with UC Davis and Agilent Technologies.

Federal agencies has announced a new collaboration with the University of California, Davis (UC Davis) and Agilent Technologies to create a public database of 100,000 foodborne pathogen genomes to help speed identification of bacteria responsible for foodborne outbreaks.

The goal of the project is to create an open access database for researchers across industry and academia to advance development of tests for food pathogen identification and origin determination.

Such tests have the potential to significantly reduce the typical public health response time in outbreaks of foodborne illness to hours or days instead of weeks.

The five-year effort, dubbed “The 100K Genome Project”, was conceived by UC Davis, Agilent, and the Food and Drug Administration (FDA).

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.

Hamburg continued, “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.

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.

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 genomic sequencing will be coordinated by UC Davis and performed at the newly formed BGI@UC Davis genome sequencing facility.

Agilent is providing scientific expertise, instrumentation, and funding to support a portion of these activities.

The CDC and FDA will provide guidance for the project, scientific expertise, and thousands of important food pathogen strains to be sequenced.

The U.S. Department of Agriculture’s Food Safety and Inspection Service (FSIS) will also collaborate on the project, contributing important bacterial strains from their regulatory testing program.

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.


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