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FDA Applied Next-Gen Sequencing to Retrospectively Analyze Food-Borne Pathogens


By Turna Ray

This article was originally posted on March 10.

Next-generation sequencing techniques helped the US Food and Drug Administration to retrospectively analyze foodborne illnesses caused by a hard-to-locate bacteria strain, the agency announced earlier this month. However, the speed and cost of such technology will have to improve before the FDA uses next-generation sequencing to characterize food-borne illnesses and determine treatment strategies bases on test results in real time.

According to the FDA, in early 2010 an outbreak of Salmonella enterica serotype Montevideo made 300 people sick in 44 states and the District of Columbia. As part of the agency's investigation, the FDA recalled several lots of red and black pepper spice rubs produced by Mincing Overseas Spice Company and Wholesome Spice Company and supplied to Daniele International between late 2009 and early 2010. Daniele International, used them in their ready-to-eat salamis, which they also recalled after reports of sickness.

Field investigators collected 35 samples of the red and black pepper meat rub from suppliers, disparate food sources, and people suspected of consuming the contaminated salamis. Then they analyzed these 35 genomes of S. enterica Montevide by shotgun sequencing to identify the source of the contamination.

"Test results showed a recent common origin of the outbreak strain [at] a single food facility. The results also indicated a single source: a spiced meat rub" found on certain salamis, the agency said in a statement. "The findings supported the information gathered in the field phase of the investigation and suggest an important role for this novel tool in augmenting future outbreak investigations."

An FDA spokesperson told PGx Reporter that due to the time required to complete the testing using current sequencing methods, this method is not currently used in real time during outbreaks. "After the Montevideo outbreak, it was used retrospectively to trace the evolution of the outbreak strain," the spokesperson said in an e-mail. "As the technology continues improve both in terms of time for analyses, as well as cost (which continues to drop), we anticipate that this DNA sequencing approach will be useful for FDA’s response during foodborne outbreaks."

The agency is planning to work closely with the Centers for Disease Control and Prevention and the US Department of Agriculture "to assess what tests can and should be used in specific situations during outbreak investigations." In their analysis, the FDA used 454 Life Sciences' GS-FLX titanium technology. Each sample required one week to analyze, according to the FDA spokesperson.

According to a Letter to the Editor published by the FDA in the New England Journal of Medicine discussing the use of next-generation sequencing during the Montevideo outbreak, the FDA turned to the technology to identify the source of contamination when standard epidemiological methods failed to parse out which facility was producing the tainted pepper rub. "Pulsed-field gel electrophoresis was unable to distinguish spiced-meat food and clinical samples from isolates that were associated with a previous contamination of pistachios," researchers from the FDA and elsewhere wrote in the NEJM letter.

Ultimately, using sequencing techniques, investigators were able to narrow it down to one processing plant, where they collected a Montevideo serotype isolate from a drain swab.

"It has long been accepted that food facilities can become endemically contaminated with resident pathogens and that pathogenic reservoirs within a facility may serve as regular sources of contamination. In this particular case, a good traceback investigation, coupled with conventional subtyping, led investigators to the responsible facility," investigators wrote in the NEJM.

"NGS confirmed this finding and provided additional evidence that delimited the scope of the outbreak. Moreover, NGS data pointed to a domestic origin for the Montevideo strain associated with this outbreak, underscoring the utility of this technique in revealing subtle genotypic differences essential to the traceback of bacterial pathogens as they emerge in the food supply," the letter stated.

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