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

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

doi:10.1099/mgen.0.000334

Abstract

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.

Highlights

Shiga toxin-producing Escherichia coli (STEC) serotype O157:H7 is a zoonotic pathogen that causes gastrointestinal symptoms in humans
The stx2a-encoding prophages in the UK lineages associated with severe disease appear to be acquired independently and most likely from different geographical and/ or environmental sources
We provide further evidence that stx2c-encoding prophages exhibit a high level of similarity across lineages, geographical regions and time, and have likely been maintained and inherited vertically

Summary

Introduction

Shiga toxin-producing Escherichia coli (STEC) serotype O157:H7 is a zoonotic pathogen that causes gastrointestinal symptoms in humans. Throughout the 1980s, the increasing number of outbreaks of gastrointestinal disease, and HUS. Microbial Genomics 2020 associated with this serotype, stimulated the development of sub-typing methods that provided a higher level of strain discrimination than serotyping. In the late 1980s, a phage typing scheme, developed by the Canadian Public Health Laboratory Service, was adopted by Public Health England (PHE; the Public Health Laboratory Service) [3], and is still used today. In 2015, PHE implemented whole-genome sequencing for routine surveillance of STEC O157:H7 in England [4]

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Conclusion