Enhanced Detection of Coccidioides spp. Fungi from Environmental Samples Using Droplet Digital PCR

Coccidioidomycosis (Valley fever), caused by Coccidioides spp. fungi, is a reemerging, neglected fungal disease endemic to arid and semiarid regions of the Americas. Environmental detection remains challenging because of spatial heterogeneity, seasonal variability, low DNA abundance, PCR inhibitors, and lack of standardized methods. We conducted environmental surveillance in Baja California, Mexico, an understudied region near the US-Mexico border, by collecting 74 soil samples from active rodent burrows across 5 locations. We evaluated droplet digital PCR (ddPCR) for Coccidioides detection and compared ddPCR with nested PCR targeting the internal transcribed spacer 1 region. ddPCR demonstrated greater sensitivity, detecting Coccidioides spp. DNA at all sampling sites, whereas nested PCR detected Coccidioides spp. DNA from only 1 site. Although additional work is required to rigorously quantify sensitivity and specificity, ddPCR could help identify Coccidioides environmental hotspots, thus enabling public health interventions, such as warning communities of areas that pose higher risk for infection.