A PCR-based assay for screening substrates for Aspergillus fumigatus for application in kiwi hatcheries

Captive facilities across New Zealand strive to mimic natural conditions for captive animals as closely as possible. In the case of the kiwi (Apteryx spp.), captive habitats are augmented with natural stimuli such as soils, leaf litter, bark, plants, logs, and mosses. Interaction with these introduced stimuli has been shown to encourage normal foraging behaviour and is speculated to aid in inoculating young animals with healthy microbial communities. However, introducing non-sterile natural stimuli into the captive environment also carries the risk of exposing kiwi to diseases such as aspergillosis, coccidiosis, and candidiasis. Aspergillosis is of particular concern to rearing facilities - the disease is most commonly attributed to exposure to Aspergillus fumigatus, an opportunistic fungal pathogen. Here we present a PCR-based screen to qualitatively detect the presence and/or absence of A. fumigatus in soils. Soil samples collected from nesting sites of rowi (Okarito brown kiwi, Apteryx rowi) in the Okarito region of the West Coast were screened for A. fumigatus using a species-specific primer set coupled with a basic DNA extraction. Willowbank Wildlife Reserve soil and substrate samples were also screened as a baseline comparison representing captive rearing facilities. Results from the assays showed that the extraction technique was effective at isolating A. fumigatus DNA at detectable levels from a variety of soils, and that Okarito soils did not harbour a higher abundance of A. fumigatus than those found at Willowbank. This preliminary screening method could be used by facilities in New Zealand to quickly and cheaply screen soils and substrates for A. fumigatus before introducing them to captive enclosures.