FDA sees whole genome sequencing as foundation of future food safety

September 15, 2017

The FDA is making the case for using whole genome sequencing (WGS) as part of global food safety efforts. Agency officials recently attended a meeting of the Codex Alimentarius Commission in Geneva, Switzerland, and participated in a panel discussion on how best to share WGS globally to fight foodborne illnesses.

Using WGS reveals the genetic fingerprint of diseases, offering clues about their geographic source, antimicrobial resistance and other key markers that help scientists respond more effectively to food contamination.

“In the last few years, WGS has fundamentally changed the way that we detect, identify and monitor microbiological food safety hazards within the United States, “wrote the FDA on its FDA Voice blog. “This technology is rapid, precise, cost-effective, easy to use and can be applied universally to all foodborne pathogens.”

Recently, public health institutions, including FDA, WHO (the World Heath Organization) and FAO (the Food and Agriculture Organization of the United Nations), have been working to raise awareness about the importance of WGS and the benefits of sharing both sequence information and metadata. In 2012, FDA started the GenomeTrakr, a now-international network of laboratories sequencing microbial foodborne pathogens and uploading the data to a common public database in real time.

Deputy Director for Scientific Operations in the FDA’s Center for Food Safety and Applied Nutrition (CFSAN), Steven Musser, and Eric Stevens, staff fellow in FDA’s Division of Microbiology at CFSAN, attended the meeting in Switzerland.

“We all understand that food is a global commodity, with complex shipping and distribution networks that can easily result in contaminated food being sold in more than one country,” they wrote. “Thus, the most effective use of WGS in foodborne disease surveillance requires coordination and collaboration, and the panel emphasized the global health benefit of every country sharing their data.”

They said one option would be sharing the data through FDA’s GenomeTrakr. They added that the system has collected more than 142,000 sequenced strains and has made them freely available to anyone in the world.


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