Whole genome sequence benchmark datasets for validation of bioinformatics workflows

Funding period: 2020-2024
Leads: Burton Blais and Catherine Carrillo
Total GRDI funding: $85,000

The food microbiology testing laboratory has a key role in supporting regulatory food safety investigations, whether stemming from a contamination incident identified through routine monitoring or a food-borne illness outbreak event. Such investigations typically involve the concerted actions of food inspection and public health authorities at different levels of government, and the main role of the laboratory is to confirm the presence of a specified contamination in food and provide data indicating its scope and source. CFIA food microbiology testing programs primarily targeting Salmonella enterica, Listeria monocytogenes and verotoxigenic Escherichia coli (VTEC) routinely include Whole Genome Sequencing (WGS) analysis of bacterial isolates using bioinformatics workflows for 1) gene marker discovery (e.g., virulence and AMR gene determination), and 2) high resolution typing. The purpose of this project is to develop curated benchmark WGS datasets to meet CFIA requirements for validation of bioinformatics test routines. The ultimate goal is to include these curated datasets as part of the Microbiological Methods Committee requirements for the validation of bioinformatics-based and current molecular methods within the purview of the Compendium of Analytical Methods.