Whole genome sequencing could impact food safety interventions

by Keith Nunes
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In 2018, the CDC will start using whole genome sequencing to identify such pathogens as salmonella, campylobacter and E. coli.

HOUSTON — A panel discussion at the Global Food Safety Conference about collaborative ways industry, academia and regulators may address Listeria control quickly turned to a discussion about whole genome sequencing technology and what it may mean for the future of food safety.

Robert Tauxe, Ph.D., director of the division of foodborne, waterborne and environmental diseases at the Centers for Disease Control and Prevention (CDC) in Atlanta, said that in 2013 the agency started a pilot project with the CDC that used whole genome sequencing. He said the results showed there was more to be learned about Listeria and more to be found.

Robert Tauxe, Ph.D., director of the division of foodborne, waterborne and environmental diseases for the CDC.

“We are finding and solving more outbreaks, but finding them when they are smaller,” he said during the March 1 session.

Tauxe went on to note the use of whole genome sequencing at the CDC will be expanded in 2018 to identify other such pathogens as SalmonellaCampylobacter and E. coli.

“Whole genome sequencing is a major step forward in outbreak detection and investigation,” he said.

The CDC’s use of the technology may put food and beverage manufacturers in a bind, because regulators will have access to a more powerful technology to detect and trace outbreaks. A question arose during the panel session regarding how food manufacturers may use the technology, but not face greater regulatory scrutiny based on the findings.

Mickey Parish, senior science adviser for the Food and Drug Administration’s Center for Food Safety and Applied Nutrition, said the agency would encourage industry to adopt whole genome sequencing for their own internal purposes.

Mickey Parish, senior science adviser for the FDA's Center for Food Safety and Applied Nutrition

“We recognize they may want to take baby steps by looking at spoilage organisms initially to become more comfortable with the technology,” he said. “From there move toward the pathogen area.

“We are using it for regulatory purposes. Therefore a prudent firm might decide that if FDA is using it in this way we need to use it to stay ahead.”

Matthew Stasiewicz, Ph.D., an assistant professor of food microbiology at the University of Illinois, Urbana-Champaign, said research he has conducted involving searching for and identifying the sources of 30 delis across the country said whole genome sequencing may improve the identification of persistent Listeria monocytogenes in food environments.

Matthew Stasiewicz, Ph.D., assistant professor of food microbiology at the University of IIIinois

“Whole genome sequencing can inform if a persistent strain is more likely,” he said. He added that the process may also help operators generate hypotheses about where the pathogen may be originating.

Parish added that the FDA has created a council focused on whole genome sequencing to discuss the technology and its uses with industry stakeholders.

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