Regulatory agencies and public-health authorities have increasingly used whole genome sequencing (WGS), a laboratory process that can determine the DNA sequence of microorganisms, as part of pathogen surveillance programs and foodborne outbreak investigations. In recent meetings with industry, the Food Safety and Inspection Service (FSIS) has been sharing how the agency will continue to use WGS to help meet its public health mission.
One critical component of the agency’s 2017-2021 Strategic Plan is modernization, which among other initiatives, includes WGS. The agency is making the capital investment in WGS and the necessary personnel expertise to build its infrastructure capacity, so the nearly 10,000 isolates FSIS collects yearly can be sequenced by 2018. This is critical, as FSIS has indicated it intends to rely less on non-WGS techniques for pathogen surveillance and outbreak investigations in the next decade. That means the agency will become less dependent on culture enrichments and begin consolidating its various techniques for bacterial characterization to a single workflow. In other words, the data collected by serotyping, PFGE (pulsed field gel electrophoresis), and any of FSIS’s antimicrobial susceptibility testing will eventually be replaced by WGS. But the agency has confirmed epidemiological data will always be considered in conjunction with WGS analysis when it comes to outbreak investigations.