A Noninvasive Fecal-DNA Detection Method for Sarcoptic Mange in the San Joaquin Kit Fox (Vulpes macrotis mutica)

Endangered San Joaquin kit foxes (Vulpes macrotis mutica) living in Bakersfield and Taft, California, have declined due to an ongoing sarcoptic mange epizootic. Population monitoring for signs of sarcoptic mange typically involves camera surveillance in these urban populations, but in unmonitored non-urban populations, where camera monitoring is less practical, sarcoptic mange may go undetected. A noninvasive fecal DNA assay would be beneficial in such areas. Because mange mites induce pruritus (itching), they may elicit grooming and ingestion by foxes, enabling the development of a noninvasive fecal-DNA detection method targeting sarcoptic mite DNA in kit fox scats. To evaluate the utility of a fecal-DNA detection method, we tested quantitative (q) PCR and DNA metabarcoding methods aimed at detecting mange mite DNA in fecal samples collected from confirmed and putative infested San Joaquin kit foxes and non-infested foxes. Both methods demonstrated high specificity, estimated at 100% (95% CI: 92-100%), but low sensitivity among all cases (confirmed, putative), specifically 11% (95% CI: 0.04-0.24) for qPCR and 22% (95% CI: 0.11-0.37) for metabarcoding. However, nine of the 11 (82%) confirmed cases tested positive, possibly because most of the putative cases had lower mite burdens or were misdiagnosed. Fecal metabarcoding could represent a useful adjunct to camera traps for sarcoptic mange monitoring in kit fox populations and, pending additional trials, potentially other wildlife as well.