Batrachochytrium dendrobatidis (Bd) is a pathogenic fungus which causes the disease chytridiomycosis
in amphibians by infecting the animals’ epidermis. The most commonly applied method for the detection
of Bd is the use of a sterile swab, rubbed over the keratinized areas of an amphibian and then processed to yield
DNA for detection by qPCR. This method has been used to infer a threshold of lethal infection in some species;
however, how reliable and reproducible the swabbing method is at detecting the true burden of infection
suffered by individuals is not known. European midwife toads, Alytes obstetricans, are susceptible to chytridiomycosis
and are highly parasitised by Bd across Europe. By quantifying Bd-load throughout the entire skin
and comparing this to swab results taken from the same individual, we determined whether epidermal swabs
provide a quantifiable and accurate indication of the true fungal burden suffered. Further, we examined
whether we could infer a threshold for lethal infection based on comparison of swab data taken from infected
A. obstetricans exhibiting different clinical states. From swab data, we detected significantly higher fungal
burdens from moribund metamorphs compared to visually healthy individuals; however, the ability of these
swab data to provide an accurate indication of the true fungal burden was not reliable. These data suggest that
fungal load dynamics play an important role in disease-induced mortality in A. obstetricans at these sites, but
that using swab data to infer an exact threshold for Bd-associated mortality might be inappropriate and
misleading.