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Background  Leishmaniasis is one of the most important infectious diseases affecting the Colombian National Army due to the high number of reported cases and exposure throughout military operations in endemic areas. The main aim of this study was to estimate the geographical distribution along with the genetic diversity and treatment outcome of  Leishmania  species in Colombian military personnel.    Methods  Skin lesion samples by smear and aspirate were collected in 136 patients having parasitological cutaneous leishmaniasis (CL) diagnosis. DNA was extracted, the nuclear marker heat shock protein 70 ( HSP70 ) was amplified by PCR and sequenced.  Leishmania  species were identified by BLASTn. The geo-spatial distribution of the identified parasites was determined according to the possible site of infection. Gene tree was constructed by maximum likelihood (ML), diversity indices ( π, h ) were estimated and haplotype network was constructed under the Templeton-Crandall-Sing algorithm in order to determine the geographic relationships of the genetic variants of  Leishmania  species circulating in Colombian military population.    Results  The species were identified in 77.94% of the samples, with a predominance of  L. braziliensis  (65.09%), followed by  L. panamensis  (31.13%),  L. naiffi  by the first time reported in Colombia in two patients (1.89%) as well as  L. lindenbergi  in a single patient (0.945%) with possible infection in the municipality of Miraflores, Guaviare and  L. infantum  in a single patient (0.945%) notified with CL in the municipality of Tumaco, Nariño. The phylogenetic analysis was consistent according to bootstrap, showing four strongly differentiated clades.    Conclusions  The geo-spatial distribution suggested that  L. braziliensis  has a greater abundance, while  L. panamensis  has a greater dispersion. The phylogenetic relationships of  Leishmania  species in Colombian military personnel was estimated with the confirmation of two new species circulating without prior report in the country and a species with no background for CL in the Colombian army. A substantial genetic diversity of  Leishmania braziliensis  was defined. This study contributes through the understanding of the molecular epidemiology to the CL transmission in Colombia.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12879-020-05529-y.

Distribution, treatment outcome and genetic diversity of Leishmania species in military personnel from Colombia with cutaneous leishmaniasis