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FDA Explores NGS for Outbreaks but Says Technology Not Yet Cost-Effective for Routine Use

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By Julia Karow

The US Food and Drug Administration has been exploring next-gen sequencing to study disease outbreaks in greater detail, but an agency official said the technology is not yet cost effective for routine investigations.

Last month, scientists from the FDA's Center for Food Safety and Applied Nutrition published in the New England Journal of Medicine a retrospective analysis of a recent salmonellosis outbreak, using 454 sequencing technology, which helped them define the scope of that outbreak more precisely.

But according to Eric Brown, one of the paper's authors, the technology is still too expensive for routine outbreak investigations, and whole-genome sequencing may not always be needed. Brown is the acting director of the division of microbiology in the FDA's Office of Regulatory Science at the CFSAN.

For the paper, the scientists analyzed by 454 shotgun sequencing 35 samples of Salmonella enterica serotype Montevideo, collected from suppliers, patients, and food sources.

The Montevideo serotype was associated with a disease outbreak in 2009 and 2010 that affected almost 300 people in 44 states and the District of Columbia. Using conventional subtyping, it was traced back at the time to red and black pepper in a New England spiced meat processing facility.

But conventional technology, in particular pulsed-field gel electrophoresis, which Brown said is still the FDA's "primary laboratory tool for identifying and linking clusters," was unable to distinguish between bacteria found in the spiced meat and isolates from a previous outbreak that was linked to contaminated pistachios.

Sequencing, however, showed clearly that the spiced meat outbreak strain is unrelated to Montevideo strains from other outbreaks, both domestic and international.

Brown said that he and his colleagues have used 454 sequencing in another retrospective study – this of a 2010 salmonellosis outbreak linked to egg shells – and that "the method again retrospectively delineated strains that had previously been indistinguishable under current protocols."

However, "at this point in time, the technology is not cost effective for routine outbreak investigation," he said. "Additionally, in certain situations, whole-genome sequencing is simply not needed."

He said the FDA scientists are currently discussing "next-generation molecular tests for specific situations" with the Centers for Disease Control, the US Department of Agriculture's Food and Safety Inspection Service, and "other federal partners."

The FDA's Center for Food Safety and Applied Nutrition first brought in next-gen sequencing in 2009, Brown said, "largely to enhance our ability to design more effective DNA-based detection and typing approaches," but also to test the technology's potential to define and track the sources of foodborne outbreaks caused by bacteria like Salmonella and E. coli more precisely. The center currently has two 454 GS FLX instruments in house.

"Although this method has significant implications for our future work and we are very excited about the possibilities, the current testing process does not permit the use of this technology in real time during outbreak investigations," he said.

But as next-gen sequencing "continues to improve both in terms of time for analyses as well as cost … we anticipate that there will be a role for whole-genome sequencing during certain foodborne outbreaks."


Have topics you'd like to see covered in In Sequence? E-mail the editor at jkarow [at] genomeweb [.] com.

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