Comparison of Shiga toxin-encoding bacteriophages in highly pathogenic strains of Shiga toxin-producingEscherichia coliO157:H7 in the UK
Authors: Yara Daniel A , Greig David R , Gally David L , Dallman Timothy J , Jenkins Claire 
Published: November 2019

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Over the last 35 years in the UK the burden of Shiga toxin-producingEscherichia 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 astx2a-encoding bacteriophage by these five sub-lineages appears to have coincided with their respective emergences. Oxford Nanopore Technology (ONT) was used to sequence, characterise and compare thestx-encoding prophage harboured by each sub-lineage to investigate the integration of this key virulence factor. Thestx2a-encoding prophage 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 thestx2a-encoding prophage in sub-lineages I/IIb and IIb revealed similarity to the prophage commonly found to encodestx2c, and the same site of bacteriophage integration (sbcB) asstx2cencoding prophage. These data suggest independent acquisition of previously unobservedstx2a-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, thestx2c-encoding prophage showed a high level of similarity across lineage and time, consistent with the model ofstx2cbeing 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 thestx-encoding bacteriophage contributes to our understanding of the emergence of highly pathogenic strains of STEC O157:H7.

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Impact statement

The application of ONT technology to sequence UK epidemic strains of STEC O157:H7 revealedstx2a-encoding prophage exhibit a high level of diversity. There was little evidence of geographical or temporal patterns of relatedness, or of intra-UK transmission ofstx2a-encoding prophage between indigenous strains. Thestx2a-encoding prophage in the UK lineages associated with severe disease appear to be acquired independently and most likely from different geographical and/or environmental sources. These data provide supporting evidence for the existence of a dynamic environmental reservoir ofstx2a-encoding prophage that pose a threat public health due to their potential for integration into competent, indigenous sub-lineages of STEC O157:H7. We also provide further evidence thatstx2c-encoding prophage exhibit a high level of similarity across lineage, geographical region and time, and have likely been maintained and inherited vertically.

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Data summary

All FASTQ files and assemblies of samples sequenced in this project were submitted to the National Centre for Biotechnology Information (NCBI). All data can be found under BioProject: PRJNA315192 -https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA315192. Strain specific details can be found in the methods section under data deposition.

Publicly available data used in this project can be found via Table 1 and data bibliography.