Extensive diversity inEscherichia coliGroup 3 capsules is driven by recombination and plasmid transfer from multiple species

Abstract

ABSTRACTBacterial capsules provide protection against environmental challenges and host immunity. Historically,Escherichia coliK serotyping scheme, which relies on the hypervariable capsules, has identified around 80 K forms that fall into four distinct groups. Based on recent work by us and others, we predicted thatE. colicapsular diversity is grossly underestimated. We exploited Group 3 capsule gene clusters, the best genetically defined capsule group inE. coli, to analyse publicly availableE. colisequences for overlooked capsular diversity within the species. We report the discovery of seven novel Group 3 clusters that fall into two distinct subgroups (3A and 3B). The majority of the 3B capsule clusters were found on plasmids, contrary to the defining feature of Group 3 capsule genes localising at theserAlocus on theE. colichromosome. Other new Group 3 capsule clusters were derived from ancestral sequences through recombination events between shared genes found within the serotype variable central region 2. Intriguingly, flanking regions 1 and 3, known to be conserved areas among capsule clusters, showed considerable intra-subgroup variation in clusters from the 3B subgroup, containing genes of shared ancestry with other Enterobacteriaceae species. Variation of Group 3kpsclusters within dominantE. colilineages, including multi-drug-resistant pathogenic lineages, further supports thatE. colicapsules are undergoing rigorous change. Given the pivotal role of capsular polysaccharides in phage predation, our findings raise attention to the need of monitoringkpsevolutionary dynamics in pathogenicE. coliin supporting phage therapy.IMPORTANCECapsular polysaccharides protect pathogenic bacteria against environmental challenges, host immunity, and phage predations. The historicalEscherichia coliK typing scheme, which relies on the hypervariable capsular polysaccharide, has identified around 80 different K forms that fall into four distinct groups. Taking advantage of the supposedly compact and genetically well-defined Group 3 gene clusters, we analysed publishedE. colisequences to identify seven new gene clusters and revealed an unexpected capsular diversity. Genetic analysis revealed that Group 3 gene clusters shared closely related serotype-specific region 2 and were diversified through recombination events and plasmid transfer between multiple Enterobacteriaceae species. Overall, capsular polysaccharides inE. coliare undergoing rigorous change. Given the pivotal role capsules play in phage interactions, this work highlighted the need to monitor the evolutionary dynamics of capsules in pathogenicE. colifor effective phage therapy.