Large chromosomal rearrangements in E. coli O157 strains

While it has been documented that E. coli O157 genomes can exhibit large scale structural variants such as inversions and duplications, the extent and consequence of these in this clonal serogroup has not been characterised. In this study, we demonstrate that these re-arrangements occur in the major lineages of E. coli O157 and focus on sub-lineage 1c strains that have been associated with severe disease in the United Kingdom over the last twenty years. Large-scale chromosomal rearrangements (LCRs) are common in these strains and occurred in culture with evidence of selection during animal colonisation. The majority of previously documented pulsed-field gel electrophoresis variation in sub-clusters of E. coli O157 strains can be accounted for by such intra-chromosomal recombination. LCRs are bounded by specific prophages located towards the terminus region of the genome and large regions of homology within these specific prophages associate with the recombination activity. Lineage I/II had reduced LCR levels and less prophages in this region to drive this activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that specific phenotypes such as Shiga toxin production, type 3 secretion and motility can be affected. Such genome plasticity driving phenotypic sub-populations, yet with the same genetic content, can be considered a form of epigenetic regulation and has important implications for bacterial adaptation and survival.