Coccidioidomycosis increases its area of geographic risk: Molecular detection and isolation of Coccidioides immitis in Washington State from soil associated with recent human infection. Coccidioides immitis

Coccidioides immitis is a soil-dwelling fungus which is endemic to the southwestern US. A recent report describes 3 cases of acute coccidioidomycosis in patients from WA (Marsden-Haug, et al.), where epidemiological and clinical data suggested local acquisition of the infection. Coccidioides spp. has never been documented in Washington State (WA). To determine that these infections were indeed acquired in WA, we obtained 22 soil samples to evaluate the presence of Coccidioides spp. from 2 sampling sites collected in locations linked to 2 patients’ infections. Coccidioides DNA was detected in 6 of 22 soil samples using a real-time PCR assay, and C. immitis was recovered in culture from 4 of these samples. When whole genome sequences of 4 representative environmental strains and a clinical patient isolate were compared a total of 10 single nucleotide polymorphisms (SNPs) were detected, with no more than 3 SNPs separating the clinical and any of the environmental strains, confirming near identity of clinical and environmental isolates from WA and linking the patient isolate to the environmental samples. Our data provide molecular and microbiological confirmation of C. immitis in soils linked geographically and genetically with an isolate causing human infection in WA.