Tracing histoplasmosis genomic epidemiology and species occurrence across the USA

Histoplasmosis is an endemic mycosis in North America frequently reported along the Ohio and Mississippi River Valleys, although autochthonous cases occur in non-endemic areas. In the United States, the disease is provoked by two genetically distinct clades of <i>Histoplasma capsulatum sensu lato</i>, <i>Histoplasma mississippiense</i> (Nam1) and <i>H. ohiense</i> (Nam2). To bridge the molecular epidemiological gap, we genotyped 93 <i>Histoplasma</i> isolates (62 novel genomes) including clinical, environmental, and veterinarian samples from a broader geographical range by whole-genome sequencing, followed by evolutionary and species niche modelling analyses. We show that histoplasmosis is caused by two major lineages, <i>H. ohiense</i> and <i>H. mississippiense</i>; with sporadic cases caused by <i>H. suramericanum</i> in California and Texas. While <i>H. ohiense</i> is prevalent in eastern states, <i>H. mississipiense</i> was found to be prevalent in the central and western portions of the United States, but also geographically overlapping in some areas suggesting that these species might co-occur. Species Niche Modelling revealed that <i>H. ohiense</i> thrives in places with warmer and drier conditions, while <i>H. mississippiense</i> is endemic to areas with cooler temperatures and more precipitation. In addition, we predicted multiple areas of secondary contact zones where the two species co-occur, potentially facilitating gene exchange and hybridization. This study provides the most comprehensive understanding of the genomic epidemiology of histoplasmosis in the USA and lays a blueprint for the study of invasive fungal diseases.