Funding period: 2020-2025
Leads: Burton Blais and Catherine Carrillo
Total GRDI funding: $125,500
Genomics and whole genome sequencing (WGS) technology are poised to have an increasingly important role as routine analytical tools in the CFIA's Food Microbiology Laboratory. Our laboratory has been focusing on strategies for the integration of genomics in regulatory food testing, and as a result we have developed a number of bioinformatics tools supporting the detection and recovery of pathogenic bacteria, such as Shiga-Toxigenic Escherichia coli (STEC) from foods. This project builds on previous research by continuing to develop and apply genomics tools for the characterization of STEC and Shigella strains involved in outbreaks of food-borne illness. A key goal is to inform the customization of selective enrichment strategies that favour the recovery of outbreak strains from food samples during food safety investigations.
Research tool/process
- Custom selective enrichment of STEC from foods: Isolation of STEC from outbreak-associated foods is often problematic due to the lack of selectivity of cultural enrichment broths. We have devised a workflow enabling specific recovery of STEC outbreak strains from foods which involves predicting the antimicrobial resistance of specific strains based on genome analysis. We have evaluated performance of this approach 12 different antibiotics representing several classes, and with different strains of STEC. The technique works extremely well for the recovery of STEC strains from different types of food matrices (ground beef, leafy greens, sprouts) with various levels and diversities of background bacteria. This represents a powerful tool enabling CFIA food microbiology testing labs to increase the probability of recovering STEC causing foodborne illness outbreaks during active investigations.
- Method for recovery of Shigella sonnei from foods: S. sonnei is rarely recovered from foods, even in cases where foods have been linked to an outbreak. To address we have optimized a method for recovery of S. sonnei from foods that leverages antimicrobial resistance (trimethoprim) that is found in over 96% of S. sonnei. This method was shown to be highly effective under “worst-case-scenario” conditions in which S. sonnei is cultivated with bacteria that produce substances that inhibit their growth. Methods that can leverage widespread antimicrobial resistance, including genomically-informed custom enrichment, will be invaluable for ensuring the safety of foods.
Publications
- Yao L, Cooper A, Gill A, Koziol A, Wong A, Blais BW, Carrillo CD. 2024 Overcoming microbial inhibition of Shigella sonnei in food enrichments through the exploitation of genomically-predicted antibiotic resistance profiles for the development of enrichment media. Journal of Food Protection. 87(7): 100302 DOI: https://doi.org/10.1016/j.jfp.2024.100302
- Yao L, Cooper A, Lau CHF, Wong A, Blais BW, Carrillo CD. 2024. Strain-specific recovery of S. sonnei from artificially contaminated baby carrots: Enhancing food-safety investigations with a customized Shigella sonnei detection method based on genomically-predicted antibiotic resistance traits. Journal of Food Protection. 87(7): 100300 DOI: https://doi.org/10.1016/j.jfp.2024.100300
- Yao L. Genomic approaches to improve the recovery of bacterial pathogens in foods. Thesis for Doctor of Philosophy in Biology, Carleton University, Ottawa, Ontario. 17 January 2024. DOI: https://doi.org/10.22215/etd/2024-15928
Contact us
For additional information, please contact:
Genomics R&D Initiative
Email: info@grdi-irdg.collaboration.gc.ca