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The availability of benchtop high-throughput sequencing instruments has made whole genome sequencing (WGS) of bacteria an option for routine investigation of outbreaks. Here we report the application of WGS to a familial EHEC outbreak (E. coli O121:H19) with a sheep farm as the suspected source. Sheep and human bacterial isolates were compared using SNP variation and the presence/absence of genes and gene variants. We also compared WGS typing to best current practice methodology (PFGE, MLVA). We conclude that WGS can provide improved typing resolution, which was crucial in the presented case.

Rapid whole genome sequencing investigation of a familial outbreak of E. coli O121:H19 with a sheep farm as the suspected source