Genomic insights into virulence mechanisms of Leishmania donovani: evidence from an atypical strain

Abstract

BackgroundLeishmaniasis is a neglected tropical disease with diverse clinical phenotypes, determined by parasite, host and vector interactions. Despite the advances in molecular biology and the availability of more Leishmania genome references in recent years, the association between parasite species and distinct clinical phenotypes remains poorly understood. We present a genomic comparison of an atypical variant of Leishmania donovani from a South Asian focus, where it mostly causes cutaneous form of leishmaniasis.ResultsClinical isolates from six cutaneous leishmaniasis patients (CL-SL); 2 of whom were poor responders to antimony (CL-PR), and two visceral leishmaniasis patients (VL-SL) were sequenced on an Illumina MiSeq platform. Chromosome aneuploidy was observed in both groups but was more frequent in CL-SL. 248 genes differed by 2 fold or more in copy number among the two groups. Genes involved in amino acid use (LdBPK_271940) and energy metabolism (LdBPK_271950), predominated the VL-SL group with the same distribution pattern reflected in gene tandem arrays. Genes encoding amastins were present in higher copy numbers in VL-SL and CL-PR as well as being among predicted pseudogenes in CL-SL. Both chromosome and SNP profiles showed CL-SL and VL-SL to form two distinct groups. While expected heterozygosity was much higher in VL-SL, SNP allele frequency patterns did not suggest potential recent recombination breakpoints. The SNP/indel profile obtained using the more recently generated PacBio sequence did not vary markedly from that based on the standard LdBPK282A1 reference. Several genes previously associated with resistance to antimonials were observed in higher copy numbers in the analysis of CL-PR. H-locus amplification was seen in one cutaneous isolate which however did not belong to the CL-PR group.ConclusionsThe data presented suggests that intra species variations at chromosome and gene level are more likely to influence differences in tropism as well as response to treatment, and contributes to greater understanding of parasite molecular mechanisms underpinning these differences. These findings should be substantiated with a larger sample number and expression/functional studies.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5271-z) contains supplementary material, which is available to authorized users.

Evidence that interspeciesLeishmaniahybrids contribute to changes in disease pathology

“…The evidence presented herein for the existence of 4 different populations of L. donovani parasites in Sri Lanka (SL1, SL2A, SL2B and SL3) could help reconciliate differences in lesion morphology 40,41 , spatial distribution 20 and drug susceptibility 26 previously reported across Sri Lanka. Indeed, parasites causing lesions that share features of L major or L. tropica infection 40 or with variable tolerance to sodium stibogluconate 26 could consist of different L. donovani hybrids with varying amount of genes from either L. major or L. tropica as they have different pathological features 42 and drug sensitivity 43 . Further, these co-existing populations supports both theories of recent introduction or prolonged existence of endemic L. donovani parasites in Sri Lanka 20 .…”

“…Indeed, chemoprophylaxis and screening against Malaria upon returning from a mission is routine as part of Sri Lanka personnel deployments in countries such as Sudan 47 . As argued within this and other studies 24–26 , the genetic evidence argues there have been multiple sources of L. donovani entry into Sri Lanka, yet there is no visceral disease and atypical cutaneous leishmaniasis has successfully propagated 20 . Future studies must address why atypical L. donovani parasites would be imported and propagated in Sri Lanka instead of visceral disease-causing L. donovani which are vastly more common in neighboring India and Africa.…”

“…Neighbor Joining based tree of all L. donovani samples analyzed showing clear geographical groupings. 401 Indian Sub Continent samples cluster close to each other and next to the previously sequenced Sri Lankan isolates 26 labeled SL1 (Sri Lanka Group 1) and the Nepalese highland “Yeti” strains. Ethiopian isolates form three separate clusters based on genotype, North, South and hybrid (blue).…”

“…Whole genome sequence analysis of L. donovani causing cutaneous leishmaniasis strains originally isolated from Sri Lanka were however not hybrid parasites and contain 83 gene mutations including altered A2 virulence genes and a polymorphism in the RagC gene from the mTOR signalling pathway 24,25,39 . None of these originally identified 83 genes mutations were present in the more recently sequenced L. donovani strains from Sri Lanka included in this analysis (GenBank ID PRJNA413320) 26 . This argues that there are diverse mechanisms for L. donovani to lose virulence for causing visceral disease in Sri Lanka and become associated with the less virulent cutaneous disease and these include genetic changes within the L. donovani genome 24, 25 and potentially as demonstrated within, propagation of L. donovani hybrid strains with L. major and L. tropica .…”

“…These genetic changes have resulted in biological changes in the conserved mTOR signalling pathway and a reduction in A2 virulence genes that in addition to other unidentified mechanisms, contribute to the atypical cutaneous leishmaniasis phenotype of L. donovani in Sri Lanka 24,25 . More recently, genome sequences from additional L. donovani isolates from Sri Lanka have been reported and deposited in NCBI GenBank 26 . Interestingly, these newer isolates did not contain any of the sequence variations and SNPs that we previously identified in the cutaneous leishmaniasis isolate 24,25 suggesting the presence of multiple co-existing L. donovani strains in Sri Lanka.…”