Whole Genome Sequencing Part 2: Regulatory and Public Health Uses

In Part 1 of this blog series, I went back to Genetics 101 to provide a brief crash course on whole genome sequencing (WGS). Now that we better understand the technology, it is easier to understand how it can be utilized in the world of food safety.

To begin with, the Food and Drug Administration (FDA), Food Safety and Inspection Service (FSIS), and Centers for Disease Control and Prevention (CDC) are using WGS to analyze all samples collected by their respective agencies, and to develop a library of results. There are currently 12,900 whole genome sequences of Salmonella spp., 4,000 of Listeria spp., and hundreds of genomes of diverse E. coli O157:H7, STEC, and Vibrio parahaemolyticus from shellfish in this library. The library is expanding, with more than 800 isolates being uploaded each month.

We have already seen public health authorities use whole genome sequencing in outbreak investigations when other methods, such as pulse field gel electrophoreses (PFGE) did not provide sufficient detail to identify which case patients should be part of the cluster of illnesses and to identify likely sources. The CDC has been budgeted $5 million per year over the next 5 years to update the state public health laboratories to run WGS. Currently 26 public health laboratories are running genome sequencing (GS) as a matter of course.

If there is a GS match among patients, there is little doubt that there was a single common source causing all the illnesses. If the “fingerprint” matches a regulatory sample, the public health authorities have a “prime suspect.” If the authorities can demonstrate that the facility was present “at the scene of the crime” (through food consumption histories), the “verdict” may be a recall and other regulatory actions.

On the regulatory front, the FDA has already indicated its intent to use GS in analyzing its regulatory verification samples. FDA is relying on the library of samples and the “fingerprints” of all pathogens found in your product and in your plant when they take samples. FDA will cross reference the library to determine if any positive pathogens found at a plant have resulted in illnesses (resulting in potential linking of product to outbreak), or to assist in determining there is an on-going issue at the plant (matches to previous regulatory samples). As previously described, FSIS is running WGS on all samples collected by the Agency and submitting the results to the Library. However, FSIS is only considering WGS results in outbreak situations at this time. FSIS does anticipate moving to its use for regulatory purposes over the next few years. The CDC is also contributing human isolates to the library and working to advance WGS in public health.

As the technology advances, and the library increases, it is important to recognize that a day may come when adulteration is defined by SNPs identified with virulence, not by species of microorganisms.

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