Worldwide Phylogenetic Distributions and Population Dynamics of the Genus Histoplasma

Abstract

BackgroundHistoplasma capsulatum comprises a worldwide complex of saprobiotic fungi mainly found in nitrogen/phosphate (often bird guano) enriched soils. The microconidia of Histoplasma species may be inhaled by mammalian hosts, and is followed by a rapid conversion to yeast that can persist in host tissues causing histoplasmosis, a deep pulmonary/systemic mycosis. Histoplasma capsulatum sensu lato is a complex of at least eight clades geographically distributed as follows: Australia, Netherlands, Eurasia, North American classes 1 and 2 (NAm 1 and NAm 2), Latin American groups A and B (LAm A and LAm B) and Africa. With the exception of the Eurasian cluster, those clades are considered phylogenetic species.Methodology/Principal FindingsIncreased Histoplasma sampling (n = 234) resulted in the revision of the phylogenetic distribution and population structure using 1,563 aligned nucleotides from four protein-coding regions. The LAm B clade appears to be divided into at least two highly supported clades, which are geographically restricted to either Colombia/Argentina or Brazil respectively. Moreover, a complex population genetic structure was identified within LAm A clade supporting multiple monophylogenetic species, which could be driven by rapid host or environmental adaptation (~0.5 MYA). We found two divergent clades, which include Latin American isolates (newly named as LAm A1 and LAm A2), harboring a cryptic cluster in association with bats.Conclusions/SignificanceAt least six new phylogenetic species are proposed in the Histoplasma species complex supported by different phylogenetic and population genetics methods, comprising LAm A1, LAm A2, LAm B1, LAm B2, RJ and BAC-1 phylogenetic species. The genetic isolation of Histoplasma could be a result of differential dispersion potential of naturally infected bats and other mammals. In addition, the present study guides isolate selection for future population genomics and genome wide association studies in this important pathogen complex.

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

“…The evolutionary model was established as K2+G4. 17 phylogenetic groups were identified with similar distribution as reported by Kasuga, 2003 and Teixeira, 2016 (Figure 2).…”

“…Interestingly, these isolates have shown marked differences among them relative to other H. capsulatum groups. The works by Kasuga et al (1999, 2003), and Teixeira et al (2016) show a high degree of variability among the Colombian isolates by MLST. The Kasuga’s work placed the Colombian isolates in Latin American clades (LAm) LAm A, LAm B and 2 solitary lineages.…”

“…The Kasuga’s work placed the Colombian isolates in Latin American clades (LAm) LAm A, LAm B and 2 solitary lineages. Similarly, the work achieved by Teixeira et al (2016) placed the Colombian isolates in the phylogenetic species LAm B1, LAm A1 and LAm A2. Finally, Sepulveda et al (2017), evaluated two additional Colombian clinical isolates, MV3 and MZ5, which they argue are so divergent that they should be reclassified into two different species: H. capsulatum sensu stricto and H. suramericanum , respectively.…”

“…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.…”

Invasive Everywhere? Phylogeographic Analysis of the Globally Distributed Tree Pathogen Lasiodiplodia theobromae

“…These previous studies have typically revealed phylogeographic structure within species, with multiple cryptic lineages linked to geographic regions, leading to the conclusion that, for fungi, "nothing is generally everywhere" [54,55]. Subsequent studies have shown that lineages in some of these fungi (e.g., Fusarium graminearum and Histoplasma capsulatum) represent cryptic species [56,57]. An exception to this rule is Aspergillus fumigatus, which has very small (2-3 µm), wind-dispersed conidia.…”