Breathing can be dangerous: Coccidioides and the diverse community of the lung mycobiome

Coccidioidomycosis, caused by soil-dwelling species of Coccidioides, is endemic to the Southwestern United States. It can present as a mild respiratory illness to lifethreatening disseminated infections. Multi-gene phylogenetics and tracing patient histories revealed the presence of both Coccidioides species in New Mexico, and Native Americans may represent an unrecognized risk group. A PCR method developed distinguishes Coccidioides species by targeting regions of the mitochondrial genome. Recent advancements in molecular genetics solidifies lungs are not sterile. Illumina community data from 199 small mammals from Arizona, California, and New Mexico demonstrated a great diversity of fungi inhabiting lung tissues. One dominant order, Onygenales, contained a high diversity of animal pathogens including Coccidioides and Blastomyces parvus. Coccidioides sequences were detected in 14 species, in relatively low abundance, and the presence of these sequences did not correlate with shifts in the overall mycobiome. Using both clinical and small mammal lung data, we can determine the distribution of Coccidioides in New Mexico and the greater Southwest.