Direct genome sequencing of Leishmania tropica in tissues of Moroccan patients with cutaneous leishmaniasis reveals micro-focal transmission underlain by (pseudo-)clonal and sexual reproduction modes

Leishmania tropica is causing cutaneous leishmaniasis (CL) from North Africa to India and in Ethiopia and is reported to be transmitted from humans to humans through sand fly bites. While this species is characterized by a high genomic diversity all over the area of endemicity, there is very little information on diversity at micro-epidemiological scale. Here, we zoomed on an epidemic Moroccan focus of CL and studied transmission patterns by comparative genomics of parasites in human patients. We used a culture-independent method of genome sequencing, applied directly on dermal scrapings. We identified 7 groups of nearly identical genotypes, as well as parasites with mixed ancestry. Our results reveal a micro-focal transmission among humans, underlain by (pseudo) clonal and sexual reproductive modes. This study demonstrates the power of direct genome sequencing for evolutionary genetics at a micro-epidemiological scale.