Using genomics to understand the global spread of Escherichia coli and antimicrobial resistance

Escherichia coli is a Gram-negative opportunistic bacterial pathogen which can develop resistance against many antimicrobials. To combat the increase of resistance in resistant E. coli, it is important to understand how E. coli and its antimicrobial resistance encoding genes spread between reservoirs. Using genomics, this thesis investigated the population structure of E. coli across host species and countries, and which genetic elements are associated with host adaptation and dissemination of ESBL-producing E. coli. Additionally, this thesis investigated resources or methodologies necessary to support genomic analysis of antimicrobial resistant E. coli.
We found that certain E. coli types are able to colonise travellers for extended periods of time and seem well-adapted to colonise the human intestine. These E. coli types are associated with extraintestinal virulence, and are as such often referred to as extraintestinal pathogenic E. coli (ExPEC). It seems ExPEC have not necessarily evolved towards extraintestinal virulence, but rather towards efficient intestinal colonisation.
This thesis also describes research contributing to microbial genomics practices. This includes the designation of a novel species which facilitates better species identification, establishing best practices for software testing and benchmarking phylogenetic methods.