Implementation of PoreSippR for rapid detection and risk-characterization of Verotoxigenic E. coli

Funding period: 2022–2024
Leads: Catherine Carrillo and Burton Blais
Total GRDI funding: $40,000

This project will use leading edge sequencing technology (PoreSippR) for real-time identification and risk profiling of Verotoxigenic Escherichia coli (VTEC). VTEC toxins are thought to be an important factor for assessing the risk of these organisms. Characterizing toxins can be challenging with current sequencing methods because of a lack of comprehensive toxin databases available to researchers and the difficulty in sequencing these genes. In fact, in a recent study involving international participants, none of the laboratories was able to type VTEC toxins on the basis of whole genome sequencing data. Strains recovered in Canadian Food Inspection Agency food testing programs often have unusual variants of toxins that are incorrectly classified using automated tools.

This project will solve this problem by providing a comprehensive public database of curated verotoxin genes and a method for rapid VTEC profiling based on long-read sequencing (PoreSippR). The ultimate goal is to ensure the availability of a method for risk characterization of VTEC recovered from foods that will meet broader Canadian food safety regulatory needs.