Phylogenetic position of Leishmania tropica isolates from an old endemic focus in southeastern Iran; relying on atypical cutaneous leishmanisis.

Cutaneous leishmaniasis (CL) is a major health problem in Iran, with a heavy burden on human health and society. There is little knowledge about the molecular epidemiology of the disease, as well as phylogenetic relationship of causative agents in southeastern Iran. The aim of the present study was to investigate the molecular aspects of CL, especially atypical CL in the Bam district, Kerman province, southeastern Iran, as an endemic region of CL in Iran. The smears were collected from lesion samples of 353 patients clinically suspected to CL, who attended local health centers in the Bam district during 2016-2017. Direct smears were examined for Leishmania parasites using the Giemsa staining technique. Amplification of kinetoplast DNA (kDNA) and the ribosomal internal transcribed spacer 1(ITS-1) gene were carried out using polymerase chain reaction (PCR). Then, the ITS1-PCR products were sequenced for phylogenetic analysis.Overall, 278 cases were confirmed as CL by microscopic examination of Giemsa-stained slides. Clinical presentation of the lesions was basically of two types: a) typical lesions, b) atypical including lupoid ulcers, sporotrichoid, nodular, and exudative lesions.The PCR assay on all specimens of skin lesions proved L. tropica as the main pathogenic agent. Phylogenic analysis revealed high similarity among isolates from the Bam district in the southeast with isolates from Birjand in eastern Iran, as well as with isolates from Herat province in western Afghanistan. The study provided valuable information concerning the genetic diversity of the parasite as one of the factors influencing the clinical manifestations in CL in southeastern Iran, which could be the basis for planning future control strategies.