Microgeographic epidemiology of malaria parasites in an irrigated area of western Kenya by deep amplicon sequencing.

To improve food security, investments in irrigated agriculture are anticipated to increase throughout Africa. However, the extent that environmental changes from water resource development will impact malaria epidemiology remains unclear. This study was designed to both compare the sensitivity of molecular markers used in deep amplicon sequencing for evaluating malaria transmission intensities; and assess malaria transmission intensity at various proximities to an irrigation scheme. Compared to ama1, csp, and msp1 amplicons, cpmp required the smallest sample size to detect differences in infection complexity between transmission risk zones. Transmission intensity was highest within five kilometers of the irrigation scheme by PCR positivity rate, infection complexity, and linkage disequilibrium. The irrigated area provided a source of parasite infections for the surrounding 2-10 km area. This study highlights the suitability of the cpmp amplicon as a measure for transmission intensities and the impact of irrigation on microgeographic epidemiology of malaria parasites.