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

ABSTRACT Escherichia coli ST131 is a dominant cause of multi-drug-resistant extraintestinal 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 analyzed 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 that are characterized 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 the continuing evolution of antimicrobial resistance but by host-pathogen interactions. IMPORTANCE Multi-drug-resistant (MDR) Escherichia coli is a problematic cause of invasive disease in humans and animals. Resistance to multiple classes of antibiotics is severely limiting treatment options. ST131-C is a highly successful, MDR clone of E. coli that is a major cause of extraintestinal infections. Capsule is a key virulence factor in contributing to this clone's success, with capsule switching allowing the bacteria flexibility to thrive in different niches. We present evidence that suggests continual evolution of this proliferant clone influenced by host-pathogen interaction. Small genetic changes can define the success of a clone; therefore, it is important to monitor this continual evolution in pathogens.