FDA is Using Whole Genome Sequencing to Stop Foodborne Illnesses

FDA is Using Whole Genome Sequencing to Stop Illnesses

FDA is Using Whole Genome Sequencing to Stop Illnesses


The U.S. Food and Drug Administration (FDA) is implementing whole genome sequencing to quickly detect and stop the spread of foodborne illnesses, Business Insider reports. The process offers huge advantages over the previous method, where samples from sick patients were tested to see if infections were caused by the same pathogen. Once enough matches appeared, the sick individuals were interviewed by epidemiologists to see if a common food was responsible for the outbreak. This method, however, does not conclusively find the cause and is time-consuming. “While all of this was going on, more contaminated product was getting out into the public,” said Dr. Steven Musser, deputy director for scientific operations at the U.S. Food and Drug Administration’s Center for Food Safety and Applied Nutrition, according to Business Insider.

The FDA is now having state and federal labs map out the exact genome of strains of foodborne pathogens such as Listeria and Salmonella. The National Institutes of Health houses a public database, known as GenomeTrakr where all the sequences are uploaded. Whole genome sequences allows scientists to distinguish a pathogen from related species, as well as slight mutations within the same strain.

In addition to sequencing common pathogens, the FDA has started sequencing pathogens found during routine plant inspections and adding them to the database. This allows patients within an outbreak to be quickly identified, and potentially detect the source of an outbreak. The FDA also wants manufacturers to submit samples of pathogens found during internal plant inspections, but many are unwilling to do so, according to public health officials, food manufacturers and recall experts interviewed by Business Insider.

The new method proved itself to be superior during a 2014 salmonella outbreak affecting peanut butter made by nSpired Natural Foods of Oregon. At the time, the FDA had just employed a network of state, federal and academic laboratories to do whole genome sequences. Additinally, pathogens found during factory inspections were also being sequenced. When people became ill, the FDA collected samples and found that the DNA of pathogens from two sick patients were “almost indistinguishable” from salmonella the FDA found at nSpired Foods, according to Dr. Eric Brown, director of FDA’s Division of Microbiology. The peanut butter was quickly recalled, with only 6 individuals getting sick.

Dr. David Lipman, director of the National Center for Biotechnology Information, said “You catch things far earlier” Business Insider reports. “It can be two cases. If you see a match, Bam! You’ve got em.”

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