Vibrio cholerae is the aetiological agent of cholera, an acute diarrhoeal disease which is estimated to result in up to 143,000 deaths per annum. Cholera is a considerable public health concern because it can spread rapidly in and explosive pandemics. Current pandemic cholera is caused by a highly-clonal phylogenetic lineage of V. cholerae serogroup O1, which spreads across the globe in periodic ‘waves’. However, V. cholerae is a species rich in diversity, and although much is known about the population structure of the pandemic lineages, the biology and pathogenicity of non-pandemic and non-O1 V. cholerae has been comparatively neglected. In this dissertation, I have studied the biology, genome dynamics, and diversity of non-pandemic V. cholerae, in comparison to the current pandemic lineage. I first present an analysis of the 1992-1998 cholera epidemic in Argentina, a country which had been free of pandemic cholera for nearly 100 years before 1992. I use the genome sequences of 490 V. cholerae from Argentina to study the micro-evolution of the pandemic lineage upon its introduction into a naïve population. I use these data to describe the progression of the Argentinian cholera epidemic using genomic epidemiology approaches, and to contrast this pandemic lineage to the non-epidemic V. cholerae that were present in Argentina at the same time as the pandemic lineage.
I then present a study of important recent and historical V. cholerae isolates, sequenced to completion using long-read technologies. I describe aspects of these genomes that could only be resolved using closed assemblies, and present functional validations of several in silico observations. Having performed this forensic, manual study of a small number of genomes, I then extrapolate those insights into a wider context, by mapping the distribution of key genetic determinants of important V. cholerae phenotypes across a phylogenetic tree of 651 highly-diverse V. cholerae. Finally, I integrate the knowledge gained in this research to make a rational selection of V. cholerae isolates for transcriptomic analysis, based on their phylogenetic position and gene content, to investigate whether differential gene expression might explain the stark differences between pandemic and non-pandemic V. cholerae. The data presented here add substantially to our understanding of the diversity of V. cholerae. They emphasise the stark differences in genome flux and evolution between pandemic and non-pandemic lineages. They also show that many of the genetic and phenotypic markers of epidemic and pandemic lineages are misleading, and do not describe that which they were originally chosen to describe.