The Food and Drug Administration(FDA) and the Centers for Disease Control (CDC) are collaborating with the University of California Davis and Agilent Technologies, a chemical analysis/engineering company from Santa Clara, California, to sequence the genetic codes of 100,000 types of lethal food-borne bacteria.  This project, designated “The 100k Genome Project,” will allow the FDA to more easily identify pathogens and in much shorter time periods from weeks to days, or even hours.

The 100k Genome Project is a five-year effort to discern the genetic codes of subtypes of important pathogens like salmonella, listeria, and e coli, all of which were responsible for widespread outbreaks from a range of food products in recent years.  This will enable the FDA to pinpoint the genetic codes of 100,000 types of lethal food-borne bacteria so that the agency can respond quickly to deadly contamination outbreaks. The FDA is contributing more than 500 completed salmonella whole-genome draft sequences, as well as other food bacteria strains.  The CDC and U.S. Department of Agriculture’s Food Safety and Inspection Service will also be providing strains to be sequenced.

The actual sequencing will occur mostly at the newly formed genome sequencing facility at U.C. Davis.  Once sequenced, the genomes of the genetic codes will be stored in a public database maintained by the National Institute of Health’s National Center for Biotechnology Information. The Department of Agriculture’s Food Safety and Inspection Service, which is responsible for inspecting meat in the US, will also cooperate in the effort.

The United States has been no stranger to food-safety incidents .  With the 100+ people allegedly sickened from the salmonella bacteria tied to raw tuna this year and the 25 people who allegedly died from listeria-infected cantaloupe last year (not to mention the more recent cantaloupe-related outbreak), there is no doubt that food-borne bacteria incidents have been noticed by the media and the population at large.

A problem of this magnitude demands an equally large countermeasure,” said Mike McMullen, president of Agilent’s Chemical Analysis Group, “we see this project as a way to improve for quality of life for a great many people, while minimizing major business risk for food producers and distributers.”

According to the FDA, this newly created database will provide a roadmap for the  development of tests to identify pathogens and provide information about the origin of each pathogen. It will also hopefully accelerate the testing of raw ingredients, finished products, and environmental samples examined during outbreak investigations.

Open access to this information 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.

“Right now, we spend a lot of time after an outbreak trying to figure out what country is it from, and how is it spreading,” said Dr. Steven Musser, director of the FDA’s Office of Regulatory Science for Food Safety, “the hope of this outbreak is to cut down on that time, and in turn be able to identify and address the infected food faster, saving as many people as possible from unnecessary illness or death from food-borne pathogens.”

The FDA, however, warns that the creation of this database addresses only one aspect of the outbreak response and public health officials still must identify the food or ingredient contaminated and where the outbreak originated.