Insights into the evolution of Escherichia coli

E. coli is a highly diverse commensal and environmental organism also associated with a broad range of infectious diseases. The work presented in this thesis provides insights into the evolutionary history and genetic diversity of the species through using up-to-date genetically representative sets of genomes. Chapter 3 provides insights into the E. coli pan genome, rates of recombination, the clonal phylogeny, genes associated with major evolutionary diversification events, and identifies a potential new phylogenetic group, tentatively labelled ‘G’. Chapter 4 provides evidence to support the use of a novel 256-gene E. coli core gene multi-locus sequence type (MLST) schema as reliable for assigning clonal and phylogenetic groups to strains in evolutionary studies, and as an alternative to using a core gene phylogeny, other core gene MLST schemas, or 7-15 locus MLST or multiplex schema methods. A novel 7-gene MLST schema and a 10-locus multiplex schema were also developed and presented which are inferred at their current stage of development to provide 100% correct phylogenetic group assignment to E. coli strains. Chapter 5 is an investigation to determine presence and evolutionary insights of genes strongly associated with decreases in ureter contractility observed during the early E. coli colonisation stages of mild to severe urinary tract infections. Contractility decrease phenotypes were found to be significantly linked to strains with genes from a specific set including those encoding two haemolysin operons, nitric oxide stress resistance proteins, and zinc and potassium uptake proteins. The final research chapter reported an analysis of the evolutionary history and genetic diversity of the E. coli type three secretion system 2 locus (ETT2), and the associated eip cluster. Previously unreported ETT2 cluster genes were identified in the genus Citrobacter, the species E. fergusonii, and the E. coli cryptic clades. Widespread truncations and deletions were found in specific lineages, together with multiple horizontal transfer events of ETT2 genes in group C-I strains.