Understanding the evolutionary history and dynamics of the gut bacteria Helicobacter pylori in Cape Verde

Helicobacter pylori is a gut bacteria which has co-evolved with humans since the modern human expansion out of Africa and is associated with an increased risk of gastric diseases, including gastric cancer. The migration of humans around the world has resulted in the bacteria diverging, leading to phylogeographical differentiation. The native human host population of Cape Verde is unique, they have an approximately even admixed African-European ancestry as the result of the Trans-Atlantic slave trade. The Americas were also involved in the Trans-Atlantic slave trade leading to several admixed host populations, as well as admixed Helicobacter pylori subpopulations. I hypothesise that Helicobacter pylori isolated from Cape Verdeans will also have an admixed African-European ancestry. This thesis will focus on the evolutionary history and dynamics of Helicobacter pylori isolated from Cape Verde.

An investigation into the population structure of Helicobacter pylori in Cape Verde confirmed previous findings of four unique subpopulation groups, two of which have recently emerged and are undergoing clonal expansion. The ancestry proportions of Helicobacter pylori from Cape Verde, as well as the Americas, were quantified. Helicobacter pylori in the Americas contained significantly more South African ancestry than Helicobacter pylori from Cape Verde, where one of the Cape Verde subpopulations contained the most West African ancestry.

Differences between the Cape Verde subpopulations of Helicobacter pylori were characterised in terms of genes associated with: virulence, antibiotic resistance, restriction-modification systems and phase variable genes. There were distinct differences in the presence of virulence genes across the subpopulations of Helicobacter pylori. A previously uncharacterised phase variation system, the ArsS family sensor histidine kinase, was identified in all Cape Verde subpopulations of Helicobacter pylori.

Class Caudoviricetes bacteriophages were identified within Helicobacter pylori in Cape Verde; although, the prophages identified in this work were different to the prophages identified in previous studies.