Comparison of single nucleotide variants identified by Illumina and Oxford Nanopore technologies in the context of a potential outbreak of Shiga Toxin producing Escherichia coli

Shiga toxin-producing Escherichia coli (STEC) O157 is a zoonotic, foodborne pathogen defined by the presence of phage-encoded Shiga toxin genes (stx). Symptoms range from severe bloody diarrhoea to Haemolytic Uremic Syndrome (HUS). The STEC O157:H7 genome is typically 5.4 Mb in size, and a high proportion (>10%) of the genome comprises mobile elements, and prophage. The genome also typically including plasmids.

During a foodborne outbreak investigation, there is often a need for a rapid typing result in order to confirm a microbiological link between an isolate in the implicated food and the outbreak strain isolated from clinical cases. Oxford Nanopore Technologies (ONT) offers a range of rapid sequencing platforms from the portable MinION to the more high throughput sequencers, GridION and PromethION.

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