Direct genome sequencing of Leishmania tropica in tissues of Moroccan patients with cutaneous leishmaniasis reveals micro-focal transmission underlain by 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 genetic 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 - restricted in space and time - and studied transmission patterns by comparative genomics of parasites in human patients. We used a culture-independent method of genome sequencing based on Leishmania genome capture (SureSelect-sequencing, SuSL-seq), applied directly on dermal scrapings. We first compared the genome of paired samples: i.e. parasites in host tissues analyzed by SuSL-seq and derived isolates shortly maintained in culture and analyzed by whole genome sequencing (WGS). Despite the low passage number of isolates, significant differences were observed between karyotypes of 4/7 paired samples, highlighting the clinical and epidemiological relevance of direct genome sequencing. Secondly, we identified 7 groups of nearly identical genotypes, characteristic of clonal propagation as well as parasites with mixed ancestry, a signature of genetic exchange. Our results reveal a micro-focal transmission among humans, underlain by clonal and sexual reproductive modes. This study demonstrates the power of direct genome sequencing for evolutionary genetics at a micro-epidemiological scale.