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

2.AbstractOver 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:H7.3.Impact statementThe 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.4.Data summaryAll 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.