Doherty-Bone, Thomas;
Perkins, Matthew;
Cunningham, Andrew;
(2025)
The challenge of using museum specimens to track the emergence of a pathogen: a case study from amphibian chytrid fungus in Africa.
African Journal of Herpetology
, 74
(1)
pp. 135-148.
10.1080/21564574.2025.2462215.
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Abstract
Archived specimens can provide insights on emerging infectious diseases through the tracking of the progression or occurrence of a pathogen through time. Specimen fixation and preservation may however affect detectability of pathogens, obscuring the signal of emergence. A case study is presented on determining the history of amphibian chytrid fungus (Batrachochytrium dendrobatidis – Bd) in African amphibians using fluid-preserved (such as in ethanol or formalin) specimens. The skin of 860 specimens was sampled and assayed for the pathogen using real-time PCR, yielding negative results only. A retrospective, randomised subsample of 99 DNA extracts were subjected to DNA-clean up and reagents (BSA) that reduce inhibition in the PCR. This resulted in five Bd-positive samples: one each from 1903 and 1933 in Cameroon, one from 1934 and two from 1954 in Uganda, with none from South Africa, despite the latter being renowned for Bd occurrence in the early 20th Century. Concentration of extracted DNA from museum samples was however found to be extremely low (especially following DNA clean-up) compared to samples from live specimens. Without measures to reduce inhibition of PCR and clean up the DNA, it would have been falsely inferred Bd did not infect this sample of preserved frogs, with available specimens originating from small sample sizes at time of collection. Care is needed to interpret historical prevalence and infection intensity when museum specimens are used, especially when preservation method is unknown or likely to inhibit PCR.
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