FDA Applies Genome Sequencing in Outbreak Investigation

The U.S. Food and Drug Administration recently put whole genome sequencing technology — which maps the entire DNA sequences of microbes to distinguish one strain from another — to use in its investigation into a Listeria outbreak linked to Roos Foods.  Earlier this year, one person died and seven others were sickened after eating cheese made by the company. After Roos issued a recall, FDA linked the outbreak bacteria to those found in the food facility and in samples of the finished cheese using whole genome sequencing.  On March 11, 2014, FDA suspended the food facility registration of Roos Foods.  “This was the first time we used whole genome sequencing to match the environmental and food samples with the CDC’s human biological samples, and it helped support the agency in taking regulatory action,” says Eric Brown, director of FDA’s Division of Microbiology. “We were able to suspend food production at a facility to minimize an outbreak.”  The agency’s Consumer Update explains that FDA researchers also used the technology in 2012 to examine a completed Salmonella outbreak in Southwest India and genetically link the bacteria to the area surrounding the source of the outbreak.  FDA has collaborated with the National Center for Biotechnology Information at the National Institutes of Health to develop a global database of pathogen genome sequences. Labs in the GenomeTrackr network have already contributed the genomes of more than 5,000 isolates for Salmonella, Listeria and E. coli.  Whole genome sequencing for food safety is one project nominated for a “People’s Choice” award within the U.S. Department of Health and Human Services. The project has the potential to replace many lab methods for detecting and investigating foodborne illness and can cut the time needed to identify and characterize pathogens.