Diversity and Phylogeny of Niche Adapted Escherichia coli

Astorga, Gabriel (2025) Diversity and Phylogeny of Niche Adapted Escherichia coli. Doctoral thesis, University of East Anglia.

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Abstract

Escherichia coli is a diverse bacterial species found in the environment, on food and within the guts of humans and animals. It can be an opportunistic pathogen, cause foodborne illness, and carry antimicrobial resistance (AMR) determinants. However, the majority of E. coli are commensal, therefore it is important to distinguish the different types of E. coli which pose a greater health risk to humans and animals. Furthermore, understanding the environmental and host interfaces is important for investigating the dissemination and transmission of E. coli. Traditional typing approaches for investigating food contamination and between-host transmission offer lower resolution than whole genome sequencing (WGS). The work within this thesis investigated the evolutionary history and diversity of E. coli on retail foods and within hosts co-habiting within the same household using WGS. To identify the optimal phylogenomic method for investigating different E. coli populations, five phylogenomic approaches were applied to a test dataset of 515 genomes. Phylonium was chosen due to computational efficiency and robustness compared to the commonly utilised core gene phylogeny and applied to datasets investigated within this thesis. There were highly diverse E. coli isolated from five different food commodities in terms of sequence types and AMR determinants, including within individual samples. However, there were minimal putative extra-intestinal pathogenic E. coli identified, and more than half of isolates were pansusceptible. A household-based cross-sectional study established that there was limited E. coli co-occurrence between humans and their dogs. This research suggests that while retail foods as well as and co-habiting humans and animals are all potential sources of E. coli and AMR, the impact on human health requires further study. These outcomes were only possible through the high resolution offered by WGS. The results have implications for public health policy, particularly for food safety and One Health surveillance

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Chris White
Date Deposited:	31 Mar 2026 12:57
Last Modified:	31 Mar 2026 12:57
URI:	https://ueaeprints.uea.ac.uk/id/eprint/102671
DOI:

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