Expanded genome-wide comparisons give novel insights into population structure and genetic heterogeneity of Leishmania tropica complex

Leishmania tropica is one of the main causative agents of cutaneous leishmaniasis (CL). Population structures of L. tropica appear to be genetically highly diverse. However, the relationship between L. tropica strains genomic diversity, protein coding gene evolution and biogeography are still poorly understood. In this study, we sequenced the genomes of three new clinical L. tropica isolates, two derived from a recent outbreak of CL in camps hosting Syrian refugees in Lebanon and one historical isolate from Azerbaijan to further refine comparative genome analyses. In silico multilocus microsatellite typing (MLMT) was performed to integrate the current diversity of genome sequence data in the wider available MLMT genetic population framework. Single nucleotide polymorphism (SNPs), gene copy number variations (CNVs) and chromosome ploidy were investigated across the available 18 L. tropica genomes with a main focus on protein coding genes. MLMT divided the strains in three populations that broadly correlated with their geographical distribution but not populations defined by SNPs. Unique SNPs profiles divided the 18 strains into five populations based on principal component analysis. Gene ontology enrichment analysis of the protein coding genes with population specific SNPs profiles revealed various biological processes, including iron acquisition, sterols synthesis and drug resistance. This study further highlights the complex links between L. tropica important genomic heterogeneity and the parasite broad geographic distribution. Unique sequence features in protein coding genes identified in distinct populations reveal potential novel markers that could be exploited for the development of more accurate typing schemes to further improve our knowledge of the evolution and epidemiology of the parasite as well as highlighting protein variants of potential functional importance underlying L. tropica specific biology.Author summary: Human cutaneous leishmaniasis (CL) is a parasitic infection transmitted through the bite of an infected sandfly vector. Members of the Leishmania tropica complex are one of the main causative agents of CL in the Old World. Despite having varying phenotypical manifestations and degrees of severity, the genomic differences underlying the observed phenotypic diversity are not well understood. CL outbreaks in Lebanon, Syria and in Azerbaijan and neighbouring countries are evidence that leishmaniasis is still an important public health concern. Here, we explored unique genetic features in L. tropica genomes by comparing the gene variants and gene copy number variations, as well as chromosome ploidy, of two recent isolates collected during a CL outbreak in Lebanon and one historical isolate from Azerbaijan with 16 published L. tropica genomes. In silico MLMT was also performed to integrate the current diversity of genome sequence data in the wider geography-related genetic populations. This study further highlights the distinct population structure and genomic heterogeneity of the L. tropica species complex in the context of the parasite broad geographic distribution. Unique sequence features identified in distinct populations could be exploited for the development of more accurate typing schemes and highlight proteins of potential functional importance to gain new insights into L. tropica specific biology.