The microbial ecology of Escherichia coli in the vertebrate gut.

Foster-Nyarko, Ebenezer (2021) The microbial ecology of Escherichia coli in the vertebrate gut. Doctoral thesis, University of East Anglia.

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Escherichia coli has a rich history as biology's favourite organism, driving advances across many fields. In the wild, E. coli often resides innocuously in the human and animal gut but is also a common pathogen linked to intestinal and extraintestinal infections and antimicrobial resistance. A literature review exposed gaps in our knowledge of the ecology and evolution of this organism in the vertebrate gut. I therefore investigated the genomic diversity and burden of antimicrobial resistance of E. coli in three vertebrate hosts from the Gambia.

First, I explored the population structure of E. coli in non-human primates from the Gambia, where they interact with human communities. Here, I found strains closely related to those causing human extraintestinal infection, together with novel strains specific to the intestinal ecosystems of non-human primates.

Next, I investigated the population structure of E. coli in backyard chickens and guinea fowl, which are commonly reared in Gambian homes as affordable sources of protein. I identified a clade of E. coli sequence type ST155 that includes closely related isolates from poultry and livestock from sub-Saharan Africa, suggesting that poultry and livestock exchange strains of E. coli on this continent. I compared the prevalence of antimicrobial resistance genes in E. coli isolates from Gambian poultry to that seen in poultry isolates from around the world.

Finally, I used genomic analysis to shed light on the relative contributions of immigration and within-host evolution in the generation of diversity among commensal strains of E. coli in the guts of healthy children from rural Gambia.

In closing, I discuss the implications and prospects of these findings.

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
Depositing User: Chris White
Date Deposited: 20 Oct 2022 10:17
Last Modified: 20 Oct 2022 10:17


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