Florent Lassalle (WSI) - Genomic epidemiology of cholera [1]: Background & methodology

[English subtitles available]

Speaker: Florent Lassalle (Wellcome Sanger Institute, Parasites & Microbes Programme)
Title: Genomic epidemiology of cholera (part1): Background & methodology

Abstract:
Cholera is caused by the bacteria belonging to the species Vibrio cholerae, an organism native of brackish water environments such as river estuaries. This bacterial species is genomically diverse; however, the pathogen causing cholera is not. Indeed, only strains that carry the CTX toxin genes can cause genuine cholera i.e. the acute watery diarrhoea disease. Toxigenic (CTX+) strains are most often found within those that carry the LPS O-antigen of the serogroup O1. More specifically, the large majority of recent cholera outbreaks were caused by a single lineage that spread worldwide, called 7th pandemic El-Tor (7PET), which has very limited genomic diversity. This clonal pathogen has shown its very high capacity to spread from human to human and to cause epidemics, as well as being transmitted across large geographical distances; it is indeed the single cause of the 7th cholera pandemic, started in 1961. However, other strains from this bacterial species can cause disease, including intestinal disease, even though not genuine cholera. These strains belong to diverse lineages and are often found to be endemic strains living in the environment, from which food or drinking water can sporadically get contaminated and lead to infection, but this rarely leads to an outbreak.
Epidemiological surveillance must therefore account for both these aspects of V. cholerae-associated disease: the epidemic pathogen of lineage 7PET, causing cholera; and the endemic strains belonging to other lineages, causing sporadic disease. Culture-based detection of V. cholerae cannot differentiate between those two categories, and thus may fail to accurately document the start of an outbreak of the epidemic strain. Instead, sequencing the genome of V. cholerae bacterial isolates allows unambiguous typing. In addition, this approach allows to predict the phenotypic properties of the isolate (virulence, antibiotic resistance …) and to track its spread through the phylogenetic reconstruction of clonal relationships of various isolates. In this talk, we describe the background and methodologies for genomic epidemiology of V. cholerae, with a specific approach for each of these two types of V. cholerae.