Ecology of Coccidioides immitis: Challenges to detecting this fungal pathogen in soil
The dimorphic, soil-dwelling fungal pathogen Coccidioides spp., the causative agent of coccidioidomycosis, is endemic to semi-arid and arid areas in the southwestern U.S., Mexico and South America. Soil disturbance can lead to air-borne arthroconidia of C. immitis and C. posadasii and when inhaled, can lead to disease. The ongoing drought in the southwestern U.S. together with an increase in soil disturbance and a general population increase has resulted in disease incidence of ~400% in some areas compared to the late 1990’s, primarily in the San Joaquin Valley of California, but also in the Phoenix and Tucson area of Arizona. So far, the presence or absence of the pathogen in the soil could not be linked to specific soil parameter or vegetation cover. Areas that belong to the ‘lower Sonoran life zone’ roughly characterize the region where Coccidioides spp. are endemic. But recently, the pathogen has also been detected outside its known range. An expansion of the pathogen to non-endemic areas is also suspected with the predicted warming of the climate in the southwestern U.S.
Polymerase Chain Reaction (PCR) based methods, including real-time PCR and multiplex PCR, have been developed to detect Coccidioidesspp. in patient specimen, as well as in soil and dust samples, but sensitivity and specificity of diagnostic primer pairs vary and false positive and false negative PCRs are frequently observed.
Ongoing research to detect Coccidioides spp. in soil and dust samples using molecular biological tools has led to the detection of the pathogen in areas where it could not be detected before by using traditional cultivation based methods. The analysis of soil samples from Kern County in the Southern San Joaquin Valley of California, Edwards Airforce Base and Lancaster in the western Mojave Desert revealed the presence of the pathogen in up to 17% of the soil samples (confirmed by sequencing). So far, DNA-based studies could not differentiate between ‘dormant sites’ and ‘active sites’, where the pathogen is present in its vegetative form during the rainy season. Recently initiated RNA based studies will allow us to identify active ‘hot-spots’ of Coccidioides spp. Results of our research efforts can be used to develop specific maps that indicate soils that can support the growth of the pathogen under current and future climate scenarios. This information might be helpful to reduce disease incidence and lead to a better understanding of the ecology of Coccidioides spp.