F.D.A. moving forward to implement whole genome sequencing

by Keith Nunes
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Listeria in a dish, food safety
In 2018, the C.D.C. will start using whole genome sequencing to identify such pathogens as salmonella, campylobacter and E. coli.
 

WASHINGTON — The Food and Drug Administration “is laying the foundation for the use of whole genome sequencing to protect consumers from food borne illness...”, Steven Musser, Ph.D., deputy director for scientific operations in the Center for Food Safety and Applied Nutrition, wrote in a blog post on the F.D.A.’s web site Sept. 14. Members of the agency, including Dr. Musser, recently attended the Codex Alimentarius Commission meeting in Geneva and one point of discussion was how to share whole genome sequencing technologies globally.

“In the last few years, W.G.S. has fundamentally changed the way that we detect, identify and monitor microbiological food safety hazards within the United States,” the F.D.A. said. “This technology is rapid, precise, cost-effective, easy-to-use, and can be applied universally to all food borne pathogens.”

Steve Musser, F.D.A.
Steven Musser, Ph.D., deputy director for scientific operations in the Center for Food Safety and Applied Nutrition

Recognizing the breadth of the global food supply chain, Dr. Musser wrote that W.G.S. is an effective monitoring tool, but that such efforts require international coordination and collaboration. In 2012, the F.D.A. launched the GenomeTrakr, which consists of a network of laboratories sequencing food borne pathogens and uploading them to a public database. Dr. Musser wrote that one approach to sharing W.G.S. data may be through the agency’s GenomeTrakr.

“We are certain that the public health benefit of W.G.S. will only become more evident with every food borne pathogen’s genomic sequence that is shared,” Dr. Musser wrote. “Already, GenomeTrakr has collected more than 142,000 sequenced strains, has made them freely available to anyone in the world, and continues to demonstrate how a large database of this kind is being used effectively for food safety within the United States, and throughout the world.

“As the food supply becomes increasingly global, the use of W.G.S. in a way that crosses national borders will ultimately help keep us all safe from foodborne illness.”

In 2013, the Centers for Disease Control and Prevention in Atlanta started a pilot project that used W.G.S. to track Listeria. In 2018, the program will be expanded to identify such pathogens as salmonella, campylobacter and E.coli.

Robert Tauxe, C.D.C.
Robert Tauxe, Ph.D., director of the division of foodborne, waterborne and environmental diseases at the C.D.C.

“We are finding and solving more outbreaks, but finding them when they are smaller,” said Robert Tauxe, Ph.D., director of the division of foodborne, waterborne and environmental diseases at the C.D.C., during a March 1 panel discussion about W.G.S. technology at the Global Food Safety Conference in Houston. “Whole genome sequencing is a major step forward in outbreak detection and investigation.”

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