Detection of Coccidioides posadasii from xerophytic environments in Venezuela reveals risk of naturally acquired coccidioidomycosis infections

Abstract

A wide range of mammals are susceptible to infection by the fungal species Coccidioides immitis and C. posadasii. In humans, 60% of infections are asymptomatic; however, certain patients may develop a severe and deep systemic mycosis called coccidioidomycosis. 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. By using a combined quantitative polymerase chain reaction (qPCR)-based approach and mycobiome amplicon sequencing, we provide evidence that at least two genotypes of C. posadasii are found in the xerophytic environment in Venezuela. We detected a 3806-fold range in the amount of Coccidioides DNA when comparing among the sampled locations, which indicates that human exposure risk is variable, and is one critical factor for disease manifestation. We identified fungal communities that are correlated with a higher prevalence of C. posadasii, suggesting that a combination of specific microbes and a xeric microenvironment may favor the growth of Coccidioides in certain locations. 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.

Fig. 1. C. posadasii relative abundance in soil samples from Venezuela.

a Overall relative abundance of C. posadasii comparing three different methods: rarefied to the lowest depth sample (Rarified) or normalized by CSS or DESeq2 transformations. b Site-specific relative abundance of C. posadasii comparing the three matrix normalization methods mentioned above

Fig. 2. Alpha and Beta species diversity index calculated for the fungal communities observed in Lara and Falcon states of Venezuela.

Species diversity indexes were calculated based on the amount of C. posadasii DNA in the soil (a, b), individual sites (c, d), and Venezuelan municipalities (e, f)

Fig. 3. Maximum likelihood (ML) tree of the 300 bp fragment of ITS2 locus of environmental, veterinarian, and clinical samples of Coccidioides immitis and C. posadasii.

Branch lengths are proportional to the number of genetic changes and bootstrap values >70% are displayed next to the branches