SRA

The comprehensive analysis of priority food pathogens, such as verotoxigenic Escherichia coli (VTEC), using whole genome sequencing (WGS)-based approaches can be a powerful tool to support food safety risk management decisions. Virulence profiling of foodborne isolates (e.g., determination of shigatoxin subtype in VTEC) can be a very useful factor in risk analyses. We have developed bioinformatics tools enabling determination of the shigatoxin subtype using WGS data from foodborne VTEC isolates.One approach is based on an in silico PCR algorithm requiring genome assembly to replicate a reference PCR-based method developed by the Statens Serum Institut (SSI). Another technique is an assembly-independent approach we have named V-Typer in which raw sequencing reads are mapped to a database of known verotoxin subtype sequence variants. These tools were evaluated in parallel alongside wet lab techniques such as the SSI reference PCR method and a recently described PCR-based pyrosequencing technique.