Objectives: Determine the incidence of Histoplasma capsulatum in a population of bats captured in Cuba.

Methods: Detect H. capsulatum from 52 lungs of bats captured in 9 cities of Cuba by nested-PCR using a specific Hcp100 gene fragment. All positives samples were sequenced.

Results: This molecular marker was detected and sequenced in 65.4% (34 of 52) of all bats, showing a similarity of 95.2% (200/210) with reference strains G-217B and NAm1. Using the algorithm maximum likelihood for the gene Hcp100, a high genetic variability was found in all Cuban bat lung samples. Were identified thirteen different molecular patterns, which highlights a pattern found also in Argentina and Mexico from Tadarida brasiliensis migratory bats. The specie Artibeus jamaicensis was the most positive that contributed to the research (14/20, 70%).

Conclusion: The high genetic variability found in this study indicates the great adaptation that has H. capsulatum to different environments at even one island. This study notes that the Cuban bats may serve as potential reservoirs of H. capsulatum, in turn may play an important role in the spread of this fungi in the environment and their respective impact on human health. It also highlights the importance of using new tools for the interpretation of the epidemiology of histoplasmosis, as it demonstrates the high prevalence of H. capsulatum in bats and so contributes to a better understanding of environmental distribution of this pathogen in Cuba.