Genome Sequencing of <i>Leishmania tropica</i> in Tissues of Moroccan Patients Reveals Microfocal Transmission Underlain by (Pseudo)Clonal and Sexual Reproduction

Leishmania tropica causes cutaneous leishmaniasis (CL) from North Africa and Ethiopia to India, and is reported to be transmitted from human to human through sand fly bites. While this species is characterized by a high genomic diversity in all the area of endemicity, there is very little information on diversity at a microepidemiological scale. Here, we concentrated 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 microfocal 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 microepidemiological scale.