Résumé
Environmental DNA led to significant advances in the detection of pathogens, including those that are microscopic, endoparasitic, or present at low concentrations, as well as their hosts in aquatic environments. This has enabled the characterisation of community composition, species interactions, and distribution patterns. However, DNAs can persist in ecosystems and do not inform on the physiological status of the targeted organisms (i.e. death or living organism, parasitic life stage). Further investigation is thus required to ascertain the precise nature of the signals detected in water and what they can tell us about host/pathogen interactions. Environmental RNA (eRNA), due to its presumed rapid degradation, could serve as a valuable tool for identifying active organisms, while offering a unique potential for epidemiological monitoring of infectious life stages through the analysis of their specific transcripts. Here we focus on the development of ARNe markers targeting the miracidia and cercariae of Schistosoma mansoni, two infectious stages with distinct epidemiological roles in the complex life cycle of this trematode. We evaluated the specificity, sensitivity and quantification capacity of these markers, first in silico and then experimentally. We quantified ADNe/ARNe ratio and RNAs specific to miracidia and cercariae from water where these two S. mansoni life-stages were present at different ratios (10/90, 50/50, 90/10). We also experimentally studied the dynamics of RNAs and DNAs degradation in aquaria in which the cercariae/miracidia ratio was set to 50/50 after 24h, 48h and 120h. Precise quantification of each of these life-stages would represent a significant step forward in the biomonitoring of complex-cycle pathogens in freshwater, going beyond simple species detection. Furthermore, this study provides new insights on longevity and our ability to quantify eRNAs. It also highlights the usefulness of eRNA in pathogen ecology and epidemiology.