Genome Sequences Reveal Cryptic Speciation in the Human Pathogen Histoplasma capsulatum

Abstract

Histoplasma capsulatum is a pathogenic fungus that causes life-threatening lung infections. About 500,000 people are exposed to H. capsulatum each year in the United States, and over 60% of the U.S. population has been exposed to the fungus at some point in their life. We performed genome-wide population genetics and phylogenetic analyses with 30 Histoplasma isolates representing four recognized areas where histoplasmosis is endemic and show that the Histoplasma genus is composed of at least four species that are genetically isolated and rarely interbreed. Therefore, we propose a taxonomic rearrangement of the genus.

Molecular epidemiology of ColombianHistoplasma capsulatumisolates shows their polyphyletic behavior and point out raw chicken manure as one of the infections sources

“…Our work confirming the relatively high diversity of Colombian isolates compared to populations in other geographical regions (32, 33, 35). Although it is not yet certain why there is such a high diversity, it is likely related to Colombia’s ecological and geographical characteristics.…”

“…Since the 1980’s, numerous studies have evaluated the genetic variation of H. capsulatum population using typing techniques such as Restriction Fragment Long Polymorphism (RFLP) (26–30), Variable Number of Tandem Repeats (VNTR) (31), MultiLocus Sequence Typing (MLST) (32) and Whole Genome Sequencing (WGS) (33). These studies have consistently shown a strong association between phylogenetic clusters and geographic origin.…”

Strong population structure in Venezuelan populations ofCoccidioides posadasii

“…Recently, four species of Histoplasma were formally adopted following genomic differentiation. These lineages differ in their genome size, in their ability to cause disease and their geographical distribution (76). Analyses of gene flow show that these species exchange genes rarely but that most introgressions are found at low allele frequency which in turn might indicate the possibility that these exchanged alleles are deleterious, or slightly deleterious.…”

“…For example, Paracoccidioides species show complete mitochondrial capture which is reflected in the discordance between nuclear and mitochondrial gene genealogies (50). Histoplasma ohiense and Histoplasma mississippiense show evidence of admixture in their nuclear genome but such exchanged alleles are at low frequency (76, 82). Cryptococcus species also show evidence of shared genetic variation (91).…”

Identification of Histoplasma causing an unexplained disease cluster in Matthews Ridge, Guyana

“…They can often be isolated from soils containing decaying bat and bird feces, but rarely isolated from fresh feces. Human activities cause the formation of fungal aerosols from surface soil, which can cause infection once inhaled [1][2][3].…”