Genomic rearrangement of the capsule operon in a phylogenetically distinct cluster of the multi-drug resistant Escherichia coli lineage ST131

Escherichia coli ST131 is a dominant cause of multi-drug resistant extra-intestinal infections in humans. The lineage has a three-clade phylogenetic structure of which clade C has gained resistance to multiple classes of antibiotics and is globally disseminated. As well as antimicrobial resistance, a number of virulence factors contribute to the success of ST131 clade C, including the production of capsule. Previous work on a limited number of strains has shown that the capsule operon in ST131 is highly variable. In this study we analysed the capsule genetics of E. coli ST131 by interrogating 3,033 genomes. Our data show a clonal distribution of capsule types and identify a monophyletic group of ST131 clade C strains which are characterised by an atypical capsule operon with highly divergent alleles of the key kpsM and kpsT genes. Our analysis suggests there is ongoing evolution within clade C of ST131 which looks to be driven not by continuing evolution of antimicrobial resistance, but by host-pathogen interactions.