,Foodborne pathogens are a significant cause of illness and infection with Shiga toxin-producing Escherichia coli (STEC) has the potential to produce life-threatening complications. The current methods to identify STEC in meat involve culture-based, molecular, and proteomic assays and take at least four days to complete. This time could be reduced by using long-read whole genome sequencing to identify foodborne pathogens. Therefore, the goal of this project was to evaluate using long-read sequencing to detect STEC in ground beef. The objectives of the project included: establishing optimal sequencing parameters, determining the limit of detection of all STEC virulence genes of interest in pure cultures and spiked ground beef, and evaluating selective sequencing to enhance STEC detection in ground beef. Sequencing libraries were run on Oxford Nanopore Technologies’ MinION sequencer. Optimal sequencing output was obtained using the default parameters in MinKNOW, except for setting the minimum read length to 1 kb. All genes of interest (eae, stx1, stx2, fliC, wzx, wzy, rrsC) were detected in DNA extracted from STEC pure cultures within 1 hour of sequencing, and 30X coverage was obtained within 2 hours. All virulence genes were confidently detected in STEC DNA quantities as low as 12.5 ng. In STEC inoculated ground beef, software-controlled selective sequencing improved virulence gene detection; however, several virulence genes were not detected due to high bovine DNA concentrations in the samples. Growth enrichment of inoculated meat samples in mTSB resulted in a 100-fold increase in virulence gene detection as compared to the unenriched samples. The results of this project suggest that further development of long-read sequencing protocols may result in a faster, less labor-intensive method to detect STEC in ground beef. The sequencing data from this project has been uploaded.,

4331 samples of ready-to-eat meat were tested for bacterial pathogens and indicators. 99.7% of the samples were satisfactory.

A targeted survey on bacterial pathogens in raw milk cheese analyzed 2,009 samples for Escherichia coli (E. coli) O157. Of the 2,009 samples, 1,723 samples were tested for generic E. coli, Salmonella species (spp.), Staphylococcus aureus (S. aureus) and Listeria monocytogenes (L. monocytogenes). No Salmonella spp., E. coli O157 or generic E. coli were found in any of the samples. S. aureus was found in 6 samples and L. monocytogenes was found in 2 samples. The CFIA conducted appropriate follow-up activities which resulted in recalls.

A targeted survey on bacterial pathogens in bean sprouts and seed sprouts analyzed 3,221 samples for Salmonella, E. coli O157:H7, and generic E. coli. Some of these samples were also tested for non-O157 Verotoxigenic E. coli (VTEC). E. coli O157:H7 was not found in any samples. Six samples were found to contain non-O157 VTEC. Salmonella was found in three samples. The CFIA conducted appropriate follow-up activities for the Salmonella contaminated samples resulting in product recalls and/or the implementation of corrective actions by the processing facilities. No reported illnesses were in association with any of the Salmonella positive samples.