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100K Genome Project Launched to Sequence Genomes of Foodborne, Waterborne Pathogens

NEW YORK (GenomeWeb News) – A public-private collaborative project to sequence the genomes of 100,000 infectious microorganisms has been launched.

The University of California, Davis today announced the start of the project aimed at speeding the diagnosis of foodborne illnesses. Along with the university, Agilent Technologies and the US Food and Drug Administration are partners in the launch of the 100K Genome Project. Other collaborators include the US Centers for Disease Control and Prevention and the US Department of Agriculture.

The project will conduct high-throughput next-generation sequencing to investigate the genomes of targeted microorganisms, with whole genome sequencing to be carried out on a small number of microorganisms for use as a reference genome. Most bacterial strains will be sequenced and assembled as draft genomes. The strategy, UC Davis said, is intended to identify sets of genetic biomarkers associated with certain important pathogen traits.

The five-year microbial pathogen project will result in a free, public database with the sequence information for each pathogen's genome, including Salmonella, Listeria, and E. coli, as well as the most common foodborne and waterborne viruses, UC Davis said.

The completed gene sequences will be stored in the National Institutes of Health's National Center for Biotechnology Information's public database.

The project will also provide a roadmap for developing tests to identify pathogens and trace their origins more quickly. Using the database, scientists will be able to develop new methods of controlling disease-causing bacteria in the food chain, UC Davis said.

Bart Weimer, a professor at the UC Davis School of Veterinary Medicine, will be the director of the 100K Genome Project.

"It's becoming more and more apparent that the persistence and pervasiveness of these organisms in the food supply stem from their genetic flexibility, which enables specific strains of bacteria to adapt in food, the environment, and animals," he said in a statement. "The lack of information about food-related bacterial genomes is hindering the research community's ability to improve the safety and security of the world food supply.

"The data provided by the 100K Genome Project will make diagnostic tests quicker, more reliable, more accurate and more cost-effective," he added.

The project will be conducted at a sequencing facility located at UC Davis. It and BGI announced a deal last year to share resources and conduct large-scale sequencing and functional genomics. In the fall, they further announced a deal to create a sequencing facility at the university.

"This landmark project harnesses UC Davis' partnership with BGI … to mine information about the most deadly foodborne pathogens," Harris Lewin, vice chancellor for research at UC Davis, said in a statement. "It will revolutionize our basic understanding of these disease-causing microorganisms."

The FDA is providing more than 500 completed Salmonella whole genome draft sequences to the project as well as thousands of additional important food pathogen strains for sequencing, and bioinformatics support. Scientists at the agency will help guide the work and provide technical assistance as needed.

CDC will provide expertise in foodborne disease, strains to be sequenced and other information. CDC experts will also serve on the steering committee for the project.

The Department of Agriculture's Food Safety and Inspection Service, meanwhile, intends to submit bacterial strains to UC Davis for sequencing, and Agilent is contributing scientific expertise, instrumentation, and funding.

The university added that it is forming a consortium to include additional partners in the project.

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