Exploring the human gut microbiota as a reservoir of antibiotic resistance genes

McCallum, Gregory Elliott ORCID: 0000-0002-6795-5579 (2023). Exploring the human gut microbiota as a reservoir of antibiotic resistance genes. University of Birmingham. Ph.D.

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Abstract

The human gut harbours a complex microbial ecosystem, termed the gut microbiome, that includes hundreds of bacterial species. Whilst most bacteria in the human gut have a commensal or mutualistic relationship with their host, the gut microbiome can also act as a reservoir for antimicrobial resistance genes (ARGs). Collectively, these ARGs are known as the gut resistome. Recent decades have seen a rise in multidrug-resistant infections caused by opportunistic pathogens originating from the gut microbiome. There is thus a need to characterise which bacterial species carry and transfer ARGs in the gut. Here, I explored the human gut resistome using chromosome conformation capture (3C) techniques to link ARGs to their bacterial hosts. Metagenomic 3C was implemented on a human faecal sample, and an analysis of my own and published datasets from 3C-based gut microbiome studies revealed that short reads mapping to repetitive elements causes problematic noise during analysis of 3C data. A bioinformatic workflow named H-LARGe (Host-Linkage to Antimicrobial Resistance Genes) was developed to reduce the impact of this noise and successfully link ARGs to their hosts. Next, a derivative of 3C, called Hi-C, was performed on four human faecal samples. Analysis of the data using an updated version of the H-LARGe workflow indicated that ARGs, including clinically important multiresistance genes, were widespread in commensal species from the gut microbiota. Following Hi-C analysis, the hosts of several ARGs were cultured and whole-genome sequenced using both short- and long-read technologies. These data provided genomic context for the ARGs and offered insights into the limitations of using Hi-C to link ARGs to their host in complex metagenomic samples. This highlighted the complementarity of Hi-C and culture-based approaches to fully characterise the gut resistome.

Type of Work:

Thesis (Doctorates > Ph.D.)

Award Type:

Doctorates > Ph.D.

Supervisor(s):