Defining epidemiologically relevant units of cholera transmission in sub-Saharan Africa

Abstract Much remains unknown about cholera transmission dynamics in Africa. Applying both traditional phylogeographic techniques and novel methods for combining epidemiologic and genomic data, we identified 3-4 distinct ‘cholera transmission units’ within which cross-border cholera transmission has been more frequent. These units can be grouped into two major transmission clusters, one in Western Africa and bordering countries, and one spanning the Central, Eastern, and Southern regions. Simulation studies show that these clusters can be used to assess the risk of international spread of introduced cholera strains and identify heterogeneities in the speed of international spread based on outbreak location. Our methods further allow us to infer cholera incidence attributable to specific lineages in the absence of sequencing data. This work has clear implications for cholera control.