Journal
MICROBIAL GENOMICS
Volume 6, Issue 3, Pages -Publisher
MICROBIOLOGY SOC
DOI: 10.1099/mgen.0.000334
Keywords
Escherichia coli O157:H7; bacteriophage; Shiga toxin; whole-genome sequencing
Categories
Funding
- National Institute for Health Research (NIHR) Health Protection Research Unit in Gastrointestinal Infections at the University of Liverpool (UK)
- PHE
- University of East Anglia (UK)
- University of Oxford (UK)
- Quadram Institute (UK)
- BBSRC (Biotechnology and Biological Sciences Research Council, UK)
- BBSRC [BB/P02095X/1, BBS/E/D/20002173] Funding Source: UKRI
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Over the last 35 years in the UK, the burden of Shiga toxin-producing Escherichia coli (STEC) O157:H7 infection has, during different periods of time, been associated with five different sub-lineages (1983-1995, Ia, I/IIa and I/IIb; 1996-2014, Ic; and 20152018, IIb). The acquisition of a stx2a-encoding bacteriophage by these five sub-lineages appears to have coincided with their respective emergences. The Oxford Nanopore Technologies (ONT) system was used to sequence, characterize and compare the stx-encoding prophages harboured by each sub-lineage to investigate the integration of this key virulence factor. The stx2a-encoding prophages from each of the lineages causing clinical disease in the UK were all different, including the two UK sub-lineages (Ia and I/IIa) circulating concurrently and causing severe disease in the early 1980s. Comparisons between the stx2a-encoding prophage in sub-lineages I/IIb and IIb revealed similarity to the prophage commonly found to encode stx2c, and the same site of bacteriophage integration (sbcB) as stx2c--encoding prophage. These data suggest independent acquisition of previously unobserved stx2a-encoding phage is more likely to have contributed to the emergence of STEC O157:H7 sub-lineages in the UK than intra-UK lineage to lineage phage transmission. In contrast, the stx2c--encoding prophage showed a high level of similarity across lineages and time, consistent with the model of stx2c being present in the common ancestor to extant STEC O157:H7 and maintained by vertical inheritance in the majority of the population. Studying the nature of the stx-encoding bacteriophage contributes to our understanding of the emergence of highly pathogenic strains of STEC O157:H7.
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