High genetic diversity of Histoplasma in the Amazon basin, 2006-2017

Genome sequencing has revealed that Histoplasma, the etiological agent of histoplasmosis is composed of several phylogenetic species. Nonetheless, the genetic diversity of the pathogen remains largely unknown, especially in the tropics. We sequenced the genome for 91 Histoplasma isolates from the Amazon basin, and used phylogenomics, and population genetic evidence to measure the genetic variation of the genus in South America. We report a previously unidentified clade of Histoplasma endemic to the Amazon basin. The lineage is widespread across the continent and contains five lineages that are sufficiently differentiated to be considered phylogenetic species. We find that the geographic range of these lineages is largely but not completely overlapping. Finally, we find that the patient median age and sex ratio differs among species suggesting differences in the epidemiology of histoplasmosis caused by each Histoplasma lineage.