CocciEnv qPCR data and accompanying metadata from soil and settled dust in the San Joaquin Valley

Coccidioidomycosis is a typically respiratory fungal disease that, in the
United States, occurs primarily in Arizona and California. In California,
most coccidioidomycosis cases occur in the San Joaquin Valley, a primarily
agricultural region where the disease poses a risk for outdoor workers. We
collected 710 soil samples and 265 settled dust samples from nine sites in
the San Joaquin Valley and examined how Coccidioides detection
varied by month, site, and the presence and abundance of other fungal
species. We detected Coccidioides in 89 of 238 (37.4%) rodent burrow soil
samples at five undeveloped sites and were unable to detect Coccidioides
in any of 472 surface and subsurface soil samples at four agricultural
sites. In what is the largest sampling effort undertaken on agricultural
land, our results provide no evidence that agricultural soils in the San
Joaquin Valley harbor Coccidioides. We found no clear association between
Coccidioides and the greater soil fungal community, but we identified 19
fungal indicator species that were significantly associated with
Coccidioides detection in burrows. We also did not find a seasonal pattern
in Coccidioides detection in the rodent burrow soils we sampled. These
findings suggest both the presence of a spore bank and that
coccidioidomycosis incidence may be more strongly associated with
Coccidioides dispersal than Coccidioides growth. Finally, we were able to
detect Coccidioides in only five of our 265 near-surface settled dust
samples, one from agricultural land, where Coccidioides was undetected in
soils, and four from undeveloped land, where Coccidioides was common in
the rodent burrow soils we sampled. Our ability to detect Coccidioides in
few settled dust samples indicates that improved methods are likely needed
moving forward, though raises questions regarding aerial dispersal in
Coccidioides, whose key transmission event likely occurs over short
distances in rodent burrows from soil to naïve rodent lungs.