Epidemiology and ecology of antibiotic resistance: the story of blaCMY-2 in Escherichia coli

Abstract

Antibiotic resistance in clinically important Enterobacteriaceae, such as Escherichia coli and Klebsiella spp., is frequently mediated by horizontal acquisition of mobile genes. Mobile β-lactamase genes are of particular concern, conferring resistance to agents important in the treatment of severe infections. Hundreds of β-lactamase genes have been reported in these organisms, but only a handful are commonplace in clinical settings. The successful spread of particular genes is dependent on their wider genetic context, that is, the mobile elements, plasmids and host strains responsible for transmission. The dynamics of this spread vary for different genes and between geographical regions, and thus detection of local epidemiological patterns is imperative for understanding and interrupting transmission. This thesis focuses on the epidemiology of blaCMY-2, one of the most common β-lactamase genes worldwide, particularly in E. coli (Chapter 2). Traditional molecular tools and whole genome sequencing were employed to characterise the mobile elements, plasmids and E. coli strains responsible for blaCMY-2 transmission in Sydney, Australia, over the last decade (Chapters 3-5). Two clonal plasmid lineages belonging to the IncI family were identified as the predominant vehicles for transfer and both displayed evidence of adaptive deletions and recombination, important evolutionary mechanisms not yet well-described for IncI plasmids (Chapter 5). Although these plasmids were carried by diverse E. coli subtypes throughout the study period, a specific clonal lineage (ST963) with chromosomally-integrated blaCMY-2 appears to have become important in recent years. The IncI plasmid type IVb pilus, involved in conjugative transfer, was used to explore the strong association of these plasmids with E. coli (Chapter 6). Transcriptional profiling and functional assays offered support for additional roles of this pilus beyond conjugation, such as biofilm formation, an important phenotype in pathogenicity. The importance of appropriate host strains to investigate plasmid-encoded systems was also revealed, as laboratory strains and clinical strains exhibited different behaviours. The epidemiological associations revealed during the course of this doctoral research offer new insights into the spread and stability of blaCMY-2 in E. coli populations, and can be exploited for diagnostic purposes. Monitoring the epidemiology of blaCMY-2 in future would enable detection of increased clinical prevalence or a shift towards chromosomally-located genes, with important implications for clinical medicine, surveillance and infection control. Future work should focus on the determinants of the ecological success of blaCMY-2, as understanding this process is essential if we are to effectively contain the spread of mobile resistance genes.