Detection and phylogenetic analysis of Coccidioides posadasii in Arizona soil samples

Reports of coccidioidomycosis are on the rise in the southwestern US. However, the ecology of the pathogen, Coccidioides, remains obscure and there is limited knowledge of the environmental antecedents of disease outbreaks. Detection of the fungus in the environment remains a critical challenge to modeling the source of disease. Using BALB/c mice as a biosensor, 8.9. % of soils analyzed from the Tucson area (Pima County, Arizona) were found to contain the pathogen. The genotypes of 66 Coccidioides strains, recovered from 11 soils, were determined with diagnostic microsatellite loci. Comparison of these genotypes to clinical isolates revealed all were Coccidioides posadasii and they grouped with Arizona isolates. Among sites where multiple strains were recovered, two indicated a clonal population, while others yielded a diversity of genotypes. A secondary goal of this research was to assess applicability of PCR, with its potential for high-throughput screening, as a method for identifying Coccidioides-containing soils.