The Powers and Perils of PCR in the Search for the Natural Reservoirs of Coccidioides Species

Valley Fever: Environmental Risk Factors and Exposure Pathways Deduced from Field Measurements in California

Coccidioidomycosis, also known as Valley fever, has been reported among military personnel in Coccidioides-endemic areas of the southwestern United States since World War II. In this study, the prevalence of Coccidioides was confirmed in different soil and dust samples collected near three military bases in California using DNA extraction and Polymerase Chain Reaction (PCR) methods. Analyses of physical and chemical parameters revealed no significant differences between Coccidioides-positive and -negative sites. Soil samples collected in the Mojave Desert (near Twentynine Palms MCAGCC) showed the highest percentage of Coccidioides-positive soil and dust samples. Samples from the San Joaquin Valley (near NAS Lemoore) showed the lowest percentage of positive samples and were restricted to remnants of semi-natural areas between agricultural fields. Our results suggest that soil disturbance around all three military bases investigated poses a potential Coccidioides exposure risk for military personnel and the public. We conclude that once lands have been severely disturbed from their original state, they become less suitable for Coccidioides growth. We propose a conceptual framework for understanding exposure where disturbance of soils that exhibit natural or remnants of native vegetation (Creosote and Salt Bush) generate a high risk of exposure to the pathogen, likely during dry periods. In contrast, Coccidioides-positive sites, when undisturbed, will not pose a high risk of exposure.

Re-drawing the Maps for Endemic Mycoses

Endemic mycoses such as histoplasmosis, coccidioidomycosis, blastomycosis, paracoccidioidomycosis, and talaromycosis are well-known causes of focal and systemic disease within specific geographic areas of known endemicity. However, over the past few decades, there have been increasingly frequent reports of infections due to endemic fungi in areas previously thought to be “non-endemic.” There are numerous potential reasons for this shift such as increased use of immune suppressive medications, improved diagnostic tests, increased disease recognition, and global factors such as migration, increased travel, and climate change. Regardless of the causes, it has become evident that our previous understanding of endemic regions for these fungal diseases needs to evolve. The epidemiology of the newly described Emergomyces is incomplete; our understanding of it continues to evolve. This review will focus on the evidence underlying the established areas of endemicity for these mycoses as well as new data and reports from medical literature that support the re-thinking these geographic boundaries. Updating the endemic fungi maps would inform clinical practice and global surveillance of these diseases.

Direct detection of Coccidioides from Arizona soils using CocciENV, a highly sensitive and specific real-time PCR assay

Coccidioides immitis and Coccidioides posadasii are soil fungi endemic to desert regions of the southwestern United States, and the causative agents of valley fever, or coccidioidomycosis. Studies have shown that the distribution of Coccidioides in soils is sporadic and cannot be explained by soil characteristics alone, suggesting that biotic and other abiotic factors should be examined. However, tools to reliably and robustly screen the large number of soils needed to investigate these potential associations have not been available. Thus, we developed a real-time polymerase chain reaction (PCR) assay for testing environmental samples by modifying CocciDx, an assay validated for testing clinical specimens to facilitate coccidioidomycosis diagnosis. For this study, we collected soil samples from previously established locations of C. posadasii in Arizona and new locations in fall 2013 and spring 2014, and screened the extracted DNA with the new assay known as CocciEnv. To verify the presence of Coccidioides in soil using an alternate method, we employed next generation amplicon sequencing targeting the ITS2 region. Results show our modified assay, CocciEnv, is a rapid and robust method for detecting Coccidioides DNA in complex environmental samples. The ability to test a large number of soils for the presence of Coccidioides is a much-needed tool in the understanding of the ecology of the organism and epidemiology of the disease and will greatly improve our understanding of this human pathogen.

Emergomyces africanus in Soil, South Africa

We detected Emergomyces africanus, a thermally dimorphic fungus that causes an HIV-associated systemic mycosis, by PCR in 18 (30%) of 60 soil samples from a wide range of habitats in South Africa. Direct and indirect culture techniques were unsuccessful. Experimental intraperitoneal inoculation of conidia induced murine disease.