Food Engineering

Publicly available food pathogen genome database in the works

July 24, 2012
The genus Salmonella has approximately 2,000 serotypes that are known to cause disease in humans. Source: CDC.

The FDA, University of California at Davis, Agilent Technologies Inc. and the Centers for Disease Control and Prevention (CDC) are collaborating 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 road map for developing 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, “The 100K Genome Project” 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.

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.

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 the investigation of foodborne illness outbreaks. This type of information also enables scientists to make 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.

The USDA’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,” says 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.

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 should contact Bart Weimer, the UC Davis program director at