Background: Histoplasmosis is a mycosis caused by pathogenic fungi in the genus Histoplasma capsulatum. While Histoplasma capsulatum has been proposed to be sub-divided into cryptic species based on analyses of whole genome sequencing (WGS) data, these designations are not currently considered taxonomically valid and no clinical differences have been observed among cases. We performed a comparative genome-wide phylogenetic analysis of African Histoplasma isolates.
Materials and methods: We analysed 116 sequences for population genomics. We included 79 publicly-available H. capsulatum and 13 outgroup sequence reads for comparison. For mapping and gene annotation, we used the H. capsulatum WU24 strain as a reference. To study the genealogical relationships among H. capsulatum isolates, we built a maximum likelihood (ML) phylogenetic tree. We performed statistical calculations to measure the genetic diversity, population differentiation and gene flow within and between the different monophyletic groups.
Results: Of the 103 Histoplasma, six monophyletic Histoplasma clusters were observed corresponding to North American (Mississippi, Ohio), India, Latin America, Panama and African groups. The 22 African clinical sequences formed their own monophyletic group which was closely related to the Panama group. The two veterinary sequences from South Africa clustered with the Latin American group. Genomic partitions for concordance reflected the proposed species boundaries for India, Mississippi and Ohio groups. Overall, allele sharing between the populations was low.
Conclusions: Genomic analysis and speciation is important to understand the different disease variations observed in histoplasmosis. India, Mississippi, and Ohio can be classified as species as reported by Sepulveda et al. 2017 but we need to understand if there is enough differentiation between Panama group and Africa. Histoplasma has been understudied mostly on the African continent and efforts should be increased to better understand the impact the pathogen has on the continent as a whole.