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Background    Leishmania donovani  is the etiological agent of visceral leishmaniasis (VL) in the Indian subcontinent. However, it is also known to cause cutaneous leishmaniasis (CL) in Sri Lanka. Sri Lankan  L. donovani  differs from other  L. donovani  strains, both at the molecular and biochemical level. To investigate the different species or strain-specific differences of  L. donovani  in Sri Lanka we evaluated sequence variation of the kinetoplastid DNA (kDNA).    Methods  Parasites isolated from skin lesions of 34 CL patients and bone marrow aspirates from 4 VL patients were genotyped using the kDNA minicircle PCR analysis. A total of 301 minicircle sequences that included sequences from Sri Lanka, India, Nepal and six reference species of  Leishmania  were analyzed.    Results  Haplotype diversity of Sri Lankan isolates were high ( H    d   = 0.757) with strong inter-geographical genetic differentiation ( F    ST   > 0.25). In this study,  L. donovani  isolates clustered according to their geographic origin, while Sri Lankan isolates formed a separate cluster and were clearly distinct from other  Leishmania  species. Within the Sri Lankan group, there were three distinct sub-clusters formed, from CL patients who responded to standard antimony therapy, CL patients who responded poorly to antimony therapy and from VL patients. There was no specific clustering of sequences based on geographical origin within Sri Lanka.    Conclusion  This study reveals high levels of haplotype diversity of  L. donovani  in Sri Lanka with a distinct genetic association with clinically relevant phenotypic characteristics. The use of genetic tools to identify clinically relevant features of  Leishmania  parasites has important therapeutic implications for leishmaniasis.    Electronic supplementary material  The online version of this article (10.1186/s12879-017-2883-x) contains supplementary material, which is available to authorized users.

Genetic diversity of Leishmania donovani that causes cutaneous leishmaniasis in Sri Lanka: a cross sectional study with regional comparisons