UC Davis, Agilent, FDA announce genome project

The 100K Genome Project to sequence microorganism genomes

Kelsey Kaustinen
DAVIS, Calif.—A new initiative was announced today betweenthe University of California, Davis (UC Davis), Agilent Technologies and theU.S. Food and Drug Administration (FDA). The five-year project will sequencethe genomes of 100,000 infectious microorganisms in hopes of speeding thediagnosis of food-borne illnesses. Prof. Bart Weimer of the UC Davis School ofVeterinary Medicine will serve as director of the 100K Genome Project, and thesequencing will take place at the recently established BGI@UC Davis facility.Additional collaborators on the undertaking include the U.S. Centers forDisease Control and Prevention (CDC) and the U.S. Department of Agriculture'sFood Safety and Inspection Service.
 
Through the project, the partners will create a free, publicdatabase consisting of sequence information for each pathogen's genome,including pathogens such as Salmonella, Listeria and E. coli.
 
 
"It's becoming more and more apparent that the persistenceand pervasiveness of these organisms in the food supply stem from their geneticflexibility, which enables specific strains of bacteria to adapt in food, theenvironment and animals," said Weimer in a press release. "The lack ofinformation about food-related bacterial genomes is hindering the researchcommunity's ability to improve the safety and security of the world foodsupply. The data provided by the 100K Genome Project will make diagnostic testsquicker, more reliable, more accurate and more cost-effective."
 
 
The initiative targets a serious issue, as outbreaks offood-borne diseases continue worldwide. In the United States alone, 48 millionpeople come down with food-borne diseases each year, and 3,000 die from them,according to the CDC.
 
 
All the participants will have active roles in the project.The FDA will provide more than 500 complete Salmonella whole-genome draftsequences, as well as thousands of food pathogen strains for sequencing andbioinformatic support. FDA scientists will have a hand in guiding the projectand providing technical assistance, with members of the CDC also serving thesteering committee and providing additional disease expertise and strains forsequencing.
 
 
The U.S. Department of Agriculture's Food Safety andInspection Service will be responsible for providing bacterial strains forsequencing by UC Davis, which will coordinate the sequencing and provide accessto its collection of bacterial samples and bioinformatic analysis capabilities.Agilent Technologies, for its part, will contribute funding, additionalinstrumentation and expertise, and UC Davis will also form a consortium thatwill include additional partners for The 100K Genome Project.
 
Next-generation sequencing technologies at the BGI@UC Davisfacility will be used to examine the pathogens' genomes, with some being sequencedfor their entire genomes and others sequenced and assembled as draft genomes.As the various sequences are completed, they will be stored in the NationalInstitutes of Health's National Center for Biotechnology Information's publicdatabase.
 
 
"A problem of this magnitude demands an equally largecountermeasure," Mike McMullen, president of Agilent's Chemical Analysis Group,said in a press release regarding the project. "We see this project as a way toimprove quality of life for a great many people, while minimizing a majorbusiness risk for food producers and distributors." 
 
 
 
SOURCE: UC Davis press release

Kelsey Kaustinen

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