Between 2017 and 2019, Canadian public health laboratories transitioned to whole genome sequencing (WGS) from pulsed-field gel electrophoresis for identifying foodborne illness outbreaks in the country. A recent study by researchers at the Public Health Agency of Canada aimed to identify the impact of WGS on national outbreak detection and response for significant foodborne pathogens by analyzing PulseNet Canada surveillance data for 2015–2021.

The study focused on Listeria monocytogenes, Salmonella, Shiga toxin-producing Escherichia coli (STEC), and Shigella. All PulseNet surveillance data for clusters of these pathogens, containing two or more human clinical isolates and identified between 2015 and 2021, were included in the analysis.

Following the implementation of WGS for L. monocytogenes in January 2017, there was a decrease in the number of L. monocytogenes clusters detected (prior to WGS, 53 percent of listeriosis isolates were associated with clusters, versus 21 percent after WGS implementation). However, the detection of Salmonella, STEC, and Shigella clusters increased.

The increase in Salmonella clusters was primarily associated with S. Enteritidis, the most common serotype in Canada. Prior to the introduction of WGS, S. Enteritidis accounted for 14 percent of clusters, which increased to 27 percent post-WGS implementation. Moreover, the percentage of clusters that resulted in a source identified increased from three (2 percent) to 25 (4 percent) in the pre-WGS and post-WGS periods, respectively—mostly attributed to fresh and/or frozen, raw, breaded chicken products. According to the researchers, enabled by WGS, the increased identification of S. Enteritidis clusters inked to frozen, raw, breaded chicken products has led to revised food safety policies aimed at reducing the number of illnesses associated with these products in Canada.

Regarding STEC, there was an overall increase in the number of clusters identified pre-WGS (106) and post-WGS (237). Identification of Shigella clusters also increased, from 33 pre-WGS to 60 post-WGS.

Overall, the researchers conclude that the transition to WGS as the primary subtyping technique for enteric disease surveillance has improved foodborne illness outbreak detection and response in Canada.