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Background  Fungal skin infections associated with  Ophidiomyces ophiodiicola , a member of the  Chrysosporium  anamorph of  Nannizziopsis vriesii  (CANV) complex, have been linked to an increasing number of cases of snake fungal disease (SFD) in captive snakes around the world and in wild snake populations in eastern North America. The emergence of SFD in both captive and wild situations has led to an increased need for tools to better diagnose and study the disease.    Results  We developed two TaqMan real-time polymerase chain reaction (PCR) assays to rapidly detect  O. ophiodiicola  in clinical samples. One assay targets the internal transcribed spacer region (ITS) of the fungal genome while the other targets the more variable intergenic spacer region (IGS). The PCR assays were qualified using skin samples collected from 50 snakes for which  O. ophiodiicola  had been previously detected by culture, 20 snakes with gross skin lesions suggestive of SFD but which were culture-negative for  O. ophiodiicola , and 16 snakes with no clinical signs of infection. Both assays performed equivalently and proved to be more sensitive than traditional culture methods, detecting  O. ophiodiicola  in 98% of the culture-positive samples and in 40% of the culture-negative snakes that had clinical signs of SFD. In addition, the assays did not cross-react with a panel of 28 fungal species that are closely related to  O. ophiodiicola  or that commonly occur on the skin of snakes. The assays did, however, indicate that some asymptomatic snakes (~6%) may harbor low levels of the fungus, and that PCR should be paired with histology when a definitive diagnosis is required.    Conclusions  These assays represent the first published methods to detect  O. ophiodiicola  by real-time PCR. The ITS assay has great utility for assisting with SFD diagnoses whereas the IGS assay offers a valuable tool for research-based applications.

TaqMan real-time polymerase chain reaction for detection of Ophidiomyces ophiodiicola, the fungus associated with snake fungal disease