In 1970, ten years after the beginning of the 7th pandemic (Indonesia, 1961), cholera hit Africa, where it has remained entrenched. Three decades later, the reported incidence of indigenous cholera in sub-Saharan Africa was about 100 times higher than the reported incidence in Asia and >15,000 times higher than the reported incidence in Latin America. The understanding of the transmission routes of cholera to and within Africa is a key factor to get a basic picture of cholera epidemiology and implement efficient control measures. Before the advent of whole-genome sequencing, the tools used were not enough discriminatory to trace this genetically homogeneous bacterium over time and space.
In collaboration with the Bacterial genomics and evolution team at the Wellcome Trust Sanger institute, we are carrying out a large-scale whole-genome sequencing analysis of Vibrio cholerae O1 El Tor strains isolated in Africa between 1970 and 2010, but also of contemporary strains from the Middle East and Asia, in order to better understand the introduction routes to Africa as well as the transmission routes within Africa. This study could be undertaken thanks to the long-lasting expertise and unique collection of strains of the French National Reference Center for Vibrio and Cholera led by Dr Marie-Laure Quilici.
A total of 600 new genomes will be generated during this project. Phylogeographic as well as evolutionary analyses will be carried out on these 600 genomes as well as on 300 already published genomes. A special attention will be given to antimicrobial resistance evolution.