Transition to Whole Genome Sequencing Surveillance: The Impact on National Outbreak Detection and Response for , , Shiga Toxin-Producing , and Clusters in Canada, 2015-2021.

Between 2017 and 2019, pulsed-field gel electrophoresis was replaced by whole genome sequencing (WGS) for identifying enteric disease clusters in Canada. The number and characteristics of all clusters of , , Shiga toxin-producing (STEC), and spp. between 2015 and 2021 were analyzed. Following the transition to WGS, an increase in the number of , STEC, and clusters was noted, whereas the number of clusters of decreased. Unlike previous subtyping methods, WGS provided increased resolution to identify discrete clusters of Enteritidis. This led to the identification of a number of outbreaks linked to frozen raw breaded chicken products and ultimately a change in food safety policy to reduce the number of illnesses associated with these products. Other pathogens did not experience a similar increase in the number of outbreaks detected. Although WGS did provide increased confidence in the genetic relatedness of cases and isolates, challenges remained in collecting epidemiological data to link these illnesses to a common source.