New Partnership Aims to Sequence 100,000 Foodborne Pathogen Genomes

The U.S. Food and Drug Administration and Centers for Disease Control and Prevention have partnered with the University of California-Davis and Agilent Technologies to create a publicly available database that will eventually contain the genomes of at least 100,000 foodborne pathogens.

Known as The 100K Genome Project, the initiative is aimed at reducing public health response time to foodborne illness outbreaks by guiding the development of tests to identify pathogens and helping to pinpoint their origins.

“Since people have started sequencing organisms, only about 2,000 bacteria have been sequenced, and of those, only about 700 in the public domain are food pathogens,” said Steven Musser, PhD, director of the FDA’s Office of Regulatory Science. For example, Salmonella, one of the most common pathogens associated with foodborne outbreaks, has approximately 2,700 known serotypes, but fewer than 2% of those have been sequenced. “We’re going to increase the number of publicly available food pathogen sequences by a factor of more than 100.”

The FDA has jumpstarted the database, which is housed at UC-Davis’ newly formed BGI@UC Davis genome sequencing facility, with more than 500 already completed Salmonella whole-genome draft sequences, thousands of additional important food pathogen strains for sequencing, and bioinformatic support. The CDC will also provide strains to be sequenced. Agilent is providing scientific expertise, instrumentation, and funding. As sequences are completed, they will be stored in the public database at the National Institutes of Health’s National Center for Biotechnology Information.

Anyone can submit samples to the project for sequencing by contacting UC-Davis program director Bart Weimer, PhD, with information about the strain you would like to submit.

“The highest priority for us are strains that have a specific geographic location,” said Dr. Musser. “If you can tell us that you’ve isolated this strain from a stream in Mexico or a pond in Minnesota, for example. We do need human and animal samples, but those are secondary. The primary focus of the project is to allow us to eventually be able to track the source or geographic region that a food pathogen comes from using whole-genome sequencing.”

Sequencing on this scale can only be done with a lot of players, said Dr. Musser. “We wouldn’t have been able to do this had we not partnered with Agilent and UC-Davis and the rest of the consortium. Working full time here in my lab, using several sequencers, we’ve only been able to sequence 500 pathogen genomes over the past three years. For a big database like this, which is essential to improve food safety, it had to be a partnership.”

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