Understanding the evolution of Enterococcus faecium in the clinical environment

© 2015 Dr. Margaret LamThe presence of Enterococcus faecium is widespread, found as both a human gastrointestinal commensal organism and in healthcare facilities worldwide where isolates serve as a common cause of hospital-acquired infections. Partly due to the lack of high-quality closed E. faecium genomes, knowledge regarding the evolution, ecology and transition from commensalism to opportunistic hospital pathogen has been limited. The research conducted in this thesis explores the variations between the genomic and phenotypic features of strains isolated over a 17-year period at a single healthcare institution to identify key characteristics that have shaped the evolution and help explain the increase of healthcare-associated E. faecium infections. Preliminary genome comparisons, revealing the emergence of a ST203 E. faecium clone and its likely role in causing a prolonged outbreak leading up to 2009, were extended in this thesis by performing detailed whole genome comparisons. Applying several genome closure techniques, the complete genomes were determined for a pre-outbreak strain from 1998 and a ST203 isolate from 2009. Together with three other genomes that have since been determined, the complete E. faecium genomes derived during the course of this PhD address some of the significant gaps in this field of microbiology. Genome comparisons encompassing the complete genomes and a larger collection of E. faecium isolates obtained between 1998 and 2009 revealed the conservation of several genes in the ST203 strains isolated after 2005, with functions relating to metal ion transport, riboflavin metabolism and carbohydrate uptake and transportation. We propose that some of these genes might help explain the phenotypic differences between isolates, with the recently emerged ST203 isolates exhibiting faster growth and the ability to outgrow competing strains, offering a possible ¬explanation for the ST203 outbreak. Increases in E. faecium infections have occurred despite widespread use of alcohol-based hand rubs as an antiseptic agent in hospitals worldwide. A novel alcohol tolerance assay was developed in this thesis to assess survival rates of E. faecium isolates following exposure to alcohol. In the presence of 22.5% v/v isopropanol, recent isolates exhibited a marked improvement in survival (-2.5 log10 reduction) compared to older isolates (-5.7 log10 reduction). The trend of increasing alcohol tolerance over a 17-year period at a single institution coincided with increased usage of alcohol-based hand rubs. Genome comparisons revealed several candidate genes that may explain alcohol tolerance variation, including an alcohol dehydrogenase variant and several phosphotransferase systems. In conclusion, the work outlined in this thesis has revealed several key facets that appear to be driving the evolution and success of E. faecium strains in hospitals. Recent isolates are characterised by their enhanced growth, which coincides with the acquisition of additional metabolic genes, and heightened tolerance to alcohols. These traits confer important advantages that aid in the survival and subsequent spread and transmission of E. faecium. Improvements to our understanding of these features as well as additional differences that may distinguish the more successful strains from others are vital for optimizing therapeutic options and infection control strategies that target E. faecium infections