Molecular detection and quantification of Coccidioides posadasii and associated fungal communities from soils in endemic areas of coccidioidomycosis in Venezuela

Coccidioides immitis and C. posadasii are fungi distributed throughout arid and semi-arid regions of the American continent, and cause the disease coccidioidomycosis (San Joaquin Valley fever). Genetic analysis suggests that the majority of clinical isolates recovered from South America are C. posadasii; however, little is known about the prevalence, species distribution, and ecological factors that favor the occurrence of this pathogen in those areas. We utilized both qPCR-based approaches and deep ITS2 sequencing in order to detect and quantify the relative abundance Coccidioides spp. in endemic areas of the disease in Venezuela. A highly variable amount of Coccidioides DNA was found depending on the sampled location. Highly positive areas were found in Urumaco, Sucre and Democracia municipalities located in the coastal plains of the Paraguaná peninsula and the depression valleys of Lara and Falcon states of Venezuela. These areas are characterized by warm and dry climates, low altitude, xerophytic vegetation, and sandy soils with high salt concentrations and alkaline pH, which likely favors Coccidioides spp. growth and development. Whole mycobiome analysis of positive soils revealed the presence of two different C. posadasii OTU''s: one phylogenetically related to clinical samples, and a second genotype that clustered apart from C. posadasii clinical strains, which suggests the existence of soil-derived cryptic groups. Finally, we observed an increase in diversity indices as well the enrichment of 7 specific fungal taxa when C. posadasii is abundant, in support of previous findings that Coccidioides inhabits specific environments that select for certain communities of fungal species. Moreover, we discuss the use of a combinatorial approach, using both qPCR and deep sequencing methods to assess and monitor fungal pathogen burden at outbreak sources.