Genomic history of the seventh pandemic of cholera in Africa

Africa was hit by cholera in 1970 and has since become the continent most affected by the seventh pandemic. We use high-resolution population-level genomic data to explain how cholera has spread consistently, and potentially predictably, across Africa between 1970 and 2014. We show that cholera was introduced at least 11 times, at two preferential foci — one in West Africa and the other in Eastern/Southern Africa — causing widespread epidemics lasting from a few years to almost 30 years. We also show that the last five introductions of cholera, all imported from Asia, involved multidrug-resistant Vibrio cholerae O1 lineages, resulting in the disappearance of antibiotic-susceptible isolates in Africa after 2000. The demonstration of the predictable nature of the introduction of a globally important multidrug-resistant infectious disease through stable transmission routes traversing Africa changes the paradigm for the control and prevention of this disease.