Genomic Diversity Analysis Reveals a Strong Population Structure in Histoplasma capsulatum LAmA (Histoplasma suramericanum).

Fernando Almeida-Silva,Allan J Guimarães,Rosely M Zancopé-Oliveira,Marcus De Melo Teixeira,Marcela De Faria Ferreira,Daniel R Matute,Rodrigo Almeida-Paes,Bridget M Barker

doi:10.3390/jof7100865

Abstract

Histoplasmosis is a severe mycotic disease affecting thousands of immunocompetent and immunocompromised individuals with high incidence in Latin America, where the disease agents are Histoplasma capsulatum and Histoplasma suramericanum. In this work, we used whole-genome sequencing to infer the species diversity and the population structure of H. suramericanum in South America. We find evidence for strong population structure and little admixture within the species. Genome-level phylogenetic trees indicate the existence of at least three different discrete populations. We recovered the existence of a previously identified population, LAmB, and confirm that it is highly differentiated along the whole genome. We also find that H. suramericanum is composed of two populations, one in Northern South America, and another in the southern portion of the continent. Moreover, one of the lineages from the southern population is endemic to Rio de Janeiro and there was no association with clinical data and species isolated from patients with histoplasmosis. Our results point out the need to characterize the symptomatology of histoplasmosis caused by different species and lineages of Histoplasma spp.

Highlights

Introduction iationsHistoplasmosis is one of the most prevalent endemic fungal diseases and occurs in all continents in tropical and sub-tropical areas of the globe [1]
27_14 lineages share a common ancestor and are limited to the South American continent (Figure 1A). This genome-wide survey revealed that a clade previously identified with Multi Locus Sequencing Typing (MLST) and known as LAm B [14,16] is a monophyletic group
The strains IPEC 11_12 and Infectious Diseases (INI) 03_16 are representative of this lineage (Figures 1A and S1). This clade differs from H. suramericanum, H. capsulatum, Africa clade, and the North American Histoplasma species H. ohiense and H. mississippiense (Figure 1A)

Summary

Introduction

Histoplasmosis is one of the most prevalent endemic fungal diseases and occurs in all continents in tropical and sub-tropical areas of the globe [1]. In Latin America, the disease is responsible for thousands of deaths in immunocompromised patients, primarily due to the high burden of HIV/AIDS disease in this region; it is a neglected disease due to the lack of accurate diagnostic tests and notification [2]. The disease affects immunocompetent hosts, as acute infections acquired from the environment are often associated with mining and speleology activities, fowl roosts, old building demolitions and cleaning of contaminated buildings in urban areas, or disturbing soils containing a high load of the fungus growing on bat guano or bird droppings [3]. Histoplasma is a dimorphic fungus and, under specific environmental conditions or in laboratory cultures at 25 to 30 ◦ C, develops long hyphae that produce

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