A novel multilocus sequence typing scheme identifying genetic diversity amongst Leishmania donovani isolates from a genetically homogeneous population in the Indian subcontinent.

•Seven new multi-locus sequence typing (MLST) loci separate Leishmania donovani from Leishmania infantum.•A2P is the most discriminative locus used in the proposed multilocus sequence typing scheme.•Seven genotypes were identified amongst very homogeneous Bangladeshi isolates.•Bangladeshi isolates differ from isolates from India, Nepal, Iraq and Africa.•A new MLST approach detects intra- and inter-species variations in the L. donovani complex.