Development and application of an eDNA method to detect and quantify a pathogenic parasite in aquatic ecosystems

Abstract

Approaches based on organismal DNA found in the environment (eDNA) have become increasingly utilized for ecological studies and biodiversity inventories as an alternative to traditional field survey methods. Such DNA-based techniques have been largely used to establish the presence of free-living organisms, but have much potential for detecting and quantifying infectious agents in the environment, which are necessary to evaluate disease risk. We developed an eDNA method to examine the distribution and abundance of the trematode Ribeiroia ondatrae, a pathogenic parasite known to cause malformations in North American amphibians. In addition to comparing this eDNA approach to classical host necropsy, we examined the detectability of R. ondatrae in water samples subject to different degradation conditions (time and temperature). Our test exhibited high specificity and sensitivity to R. ondatrae, capable of detecting as little as 14 fg of this parasite’s DNA (1/2500th of a single infectious stage) from field water samples. Compared to our results from amphibian host necropsy, quantitative PCR was ∼ 90% concordant with respect to R. ondatrae detection from 15 field sites and was also a significant predictor of host infection abundance. DNA was still detectable in lab samples after 21 days at 25 °C, indicating that our method is robust to field conditions. By comparing the advantages and disadvantages of eDNA versus traditional survey methods for determining pathogen presence and abundance in the field, we found that the lower costs and effort associated with eDNA approaches provide many advantages. The development of alternative tools is critical for disease ecology as wildlife management and conservation efforts require reliable establishment and monitoring of pathogens.

Accuracy, limitations and cost efficiency of eDNA‐based community survey in tropical frogs

“…Although central to deciding on a method for biodiversity surveys, cost comparisons are not straightforward because they need to be based on expert knowledge both in VAES and in eDNA. Cost comparisons were performed for single species eDNA detection (Davy, Kidd, & Wilson, ; Huver, Koprivnikar, Johnson, & Whyard, ; Smart et al, ), but we are not aware of frameworks suitable for eDNA metabarcoding. Here, the VAES cost estimation is informed by over a decade of field and integrative taxonomic work with tropical frogs (Brusquetti et al, ; Pansonato et al, ; Jansen, Álvarez, & Köhler, ; Schulze et al, ), while the eDNA part is only informed by a few years of eDNA biodiversity surveys (Bálint et al, ; Vörös, Márton, Schmidt, Gál, & Jelić, ).…”

The sceptical optimist: challenges and perspectives for the application of environmental DNA in marine fisheries

“…() found a significant correlation ( R 2 = .84) in eDNA concentration between whale shark ( R. typus , Rhincodontidae) and its prey, mackerel tuna spawn ( Euthynnus affinis , Scombridae), illustrating a potential for using eDNA as a tool to study predator‐prey interactions. With a very broad taxonomic approach eDNA analysis can also inform about the general state of the ecosystem and possibly even provide proxies for ecosystem health based on biodiversity indicators (Bienert et al., ; Huver, Koprivnikar, Johnson, & Whyard, ). Further, a number of European Union member states have taken the first actions to implement eDNA in monitoring of indicator and invasive species in concordance with the Marine Strategy Framework Directive (Andersen et al., ; Bourlat et al., ; Walsh & Rhodes, ).…”

Diverse Applications of Environmental DNA Methods in Parasitology

“…Although DNA studies have been developed to identify and genotype many human and veterinary parasites from such samples, the techniques are rarely applied to environmental samples, although this can be equally important [119]. Widespread water or soil surveys specifically for metazoan parasites have been lacking.…”