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

Abstract

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.

Impact of Genetic Diversity and Genome Plasticity of Leishmania spp. in Treatment and the Search for Novel Chemotherapeutic Targets

“…Variations in the parasite genome can be associated with its geographical distribution and clinical manifestations, which can influence leishmaniasis management. Interestingly, large-scale research involving a large number of samples and wide geographic range has revealed that genetic diversity is significantly higher than that previously reported ( Bussotti et al., 2018 ; Zackay et al., 2018 ; Franssen et al., 2020 ; Imamura et al., 2020 ; Patino et al., 2020 ; Salloum et al., 2020 ; Zheng et al., 2020 ; Patino et al., 2021 ; Schwabl et al., 2021 ). Recently, single-cell sequencing has demonstrated the presence of several distinct karyotypes within the same Leishmania clone ( Imamura et al., 2020 ; Negreira et al., 2020 ), and multiple-genotype infections have been demonstrated to occur even within the same host and tissue ( Cupolillo et al., 2020 ).…”

High genome plasticity and frequent genetic exchange in Leishmania tropica isolates from Afghanistan, Iran and Syria

“…tropica is a heterogeneous species complex with a broad geographical distribution across Africa and Eurasia [3,6,7] that causes mainly CL, though visceral leishmaniases has been reported [8,9]. L. tropica is typically an anthroponotic disease, though zoonotic transmission may be possible as well [10][11][12]. Although the burden of leishmaniasis is decreasing globally, regions with L. tropica have increasing rates due to local conflicts and associated population displacement, migration and relocation [3], which exacerbates incorrect CL diagnoses and inadequate access to appropriate healthcare and treatments.…”

“…L . tropica is typically an anthroponotic disease, though zoonotic transmission may be possible as well [ 10 – 12 ]. Although the burden of leishmaniasis is decreasing globally, regions with L .…”

Molecular-based assay for genotyping Leishmania spp. from clinically suspected cutaneous leishmaniasis lesions in the Garmian area, Kurdistan Region of Iraq

“…Amplification targets are either genomic (nuclear) DNA—such as the small subunit (18S) rRNA gene ( Guillaume et al, 1992 ), the internal transcribed spacer 1 (ITS1), mini-exon regions, the tubulin gene ( Luis et al, 1998 ), and heat shock protein 70 ( Garcia et al, 2004 ) or extrachromosomal DNA, such as repetitive kinetoplast DNA mini-circles and cytochrome b ( Belli et al, 1998 ; Luyo-Acero et al, 2004 ). Up to now, and as far as is known, whole genome sequencing is still as the most advanced and developed technique for the identification of varies species, as it due to the fact that it is with the highest sensitivity and specificity ( Salloum et al, 2020 ).…”