Comparison of Shiga toxin-encoding bacteriophages in highly pathogenic strains of shiga toxin-producing Escherichia coli O157:H7 in the UK

Daniel A. Yara, David R. Greig, David L. Gally, Timothy J. Dallman, Claire Jenkins*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

27 Citations (Scopus)
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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 2015– 2018, 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.

Original languageEnglish
Article number000334
JournalMicrobial Genomics
Issue number3
Publication statusPublished - 25 Feb 2020

Bibliographical note

Funding Information: The research was part funded by the National Institute for Health Research (NIHR) Health Protection Research Unit in Gastrointestinal Infections at the University of Liverpool (UK), in partnership with PHE, in collaboration with the University of East Anglia (UK), the University of Oxford (UK) and the Quadram Institute (UK). C.J., T.J.D. and D.R.G. are based at PHE. The views expressed are those of the authors and not necessarily those of the National Health Service, the NIHR, the Department of Health nor PHE. D.A.Y. was funded by a Doctoral Training Partnership PhD studentship from the BBSRC (Biotechnology and Biological Sciences Research Council, UK; The funders had no role in study design, data collection and analysis, decision to publish nor preparation of the manuscript.

Open Access: This is an open-access article distributed under the terms of the Creative Commons Attribution License.

Publisher Copyright: © 2020 The Authors.

Citation: Yara, Daniel A., et al. "Comparison of Shiga toxin-encoding bacteriophages in highly pathogenic strains of Shiga toxin-producing Escherichia coli O157: H7 in the UK." Microbial genomics 6.3 (2020).



  • Bacteriophage
  • Escherichia coli O157:H7
  • Shiga toxin
  • Whole-genome sequencing


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