A genetic analysis of Escherichia coli using bioinformatic methods

Escherichia coli is the best-known species of Enterobacteriaceae. The species is genetically diverse and includes both commensal pathogenic strains and plays a significant role in veterinarian, environmental, and medical science. Despite the significance of E. coli, many aspects of the species biology, such as its genetic diversity and the pathogenesis are yet to be truly understood. To understand the diversity of E. coli as a whole, genome data of E. coli derived from variety of sources: humans, animals, and environment are essential. The aims of the research are to take the outstanding opportunity provided by the availability of many new E. coli genomes and to make use of a variety of bioinformatics tools to investigate the genetic diversity and reconstruct the evolutionary history of E. coli based on a genetic analysis and a comparative genomic approach. The thesis includes three main themes. Firstly, "Distribution of extra-intestinal virulence traits among E. coli isolated from native Australian vertebrates with t~ose isolated from humans living in Australia" . The frequency and distribution of extra-intestinal virulence traits in a collection of E. coli isolated from native Australian vertebrates as compared to E. coli isolated from humans living in Australia were reported. The result shows that the freque_ncy and distribution of some traits varies with the source of isolation, human versus animal, and that there are traits typically associated with pathogenicity islands that are absent or very rare in animal isolates. The detected high rates of recombination in phylo-group B2 strains suggest that this is an important evolutionary adaptation for attaining virulence. Secondly, "Investigation of the evolution of conjugative plasmids in E. coli and their changing role in E. coli ecology". Conjugative plasmids: key agents in the adaptation of E. coli populations were investigated. Comparing between Inell and IncF plasmids, Inell plasmids were found to be more homogeneous and genetically conserved than IncF plasmids. These plasmids have changed their role as mediators of intraand interspecies interactions to become associated with E. coli virulence. Lastly, "Genetic and metabolic characteristics of phylo-group F". In this study, phylo-group F: a recently described group of E. coli strains was investigated. Strains belonging to phylo-group F were found to be closely related to phylo-group D strains known to be responsible for extra-intestinal infection. Whilst a high degree of strain-specific genome differences were identified among F strains, some of genes shared by F strains (absent in D, B2, and H299) were also present in other phylo-groups (A, B 1, and E). All together the outcomes of this project lead to significant advances in our understanding presented in E. coli species. iv TABLE OF CONTENTS Page ABSTRACT. 111 FIGURES AND TABLES. Vl CHAPTER 1: General Introduction and Research Significance 1 1.1 General Introduction. 1 1.2 Research Significance. 1 CHAPTER 2: Literature Reviews 3 2.1 Escherichia coli and the genus Escherichia. 3 2.2 Typing methods for E. coli. 3 2.2.1 Phenotypic methods. 3 2.2.2 Multi-locus enzyme electrophoresis (MLEE). 4 2.2.3 DNA-based finger-printing methods. 4 2.2.4 Genome-based methods. 5 2.3 The diversity and phylo-group structure of E. coli. 5 2.3. 1 Genome size and genomic diversity of E. coli. 6 2.3. 2 Ecological niches and life-history characteristics of E. coli 7 2.3. 3 Propensity to cause diseases of E. coli. 7 2.4 Conjugative plasmids in E. coli. 10 2.5 Applications of bioinformatics in the genomic research of E. coli. 11 CHAPTER 3: Distribution of extra-intestinal virulence traits among E. coli isolated from native Australian vertebrates with those isolated from humans living in Australia 13 3 .