Nanopore sequencing reveals the hidden intra-outbreak accessory genome variation of Shiga toxin-producing E. coli (STEC) O157:H7
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Shiga toxin-producing Escherichia coli (STEC) are a group of zoonotic, foodborne pathogens defined by the presence of phage-encoded Shiga toxin genes (stx). STEC cause gastrointestinal disease in humans and symptoms include severe bloody diarrhoea, abdominal pain and nausea. In 5-15% of cases infection leads to Haemolytic Uremic Syndrome (HUS), characterised by kidney failure and/or cardiac and neurological complications.
STEC O157:H7 genomes range from 5.4Mbp to 5.6Mbp in size, and a high proportion (9-15%) is comprised of mobile genetic elements and prophages. Due to the limitations of short read sequencing technologies in handling the homologous regions of the STEC chromosome, information and context regarding inter and intra variation in prophages, structural variation and context surrounding plasmid content is lost.