This workshop, taking place in the framework of the EAFP Annual congress, aimed at crossing experiences from research conducted in Europe by VIVALDI project partners with research conducted by other experts in Europe and beyond. About 50 scientists from different countries participated in the workshop. Thanks to a series of flash presentations, different tools and approaches aiming at improving the detection of pathogens were described, discussed and compared.
Presentations on works done in VIVALDI were followed by exchanges between speakers and the people in the room. After the presentations, there was time for further discussion.
The usefulness of passive sensors was debated. Such tools could provide an idea of the microdiversity including information about the presence of pathogens in mollusk production areas. Results obtained in VIVALDI show that detection of viruses (DNA and RNA) using passive sensors is possible. However further works are needed to improve nucleic acid extraction conditions and validate this type of approach. Passives sensors could also be a non-lethal alternative to monitor the presence of pathogen affecting protected species (for example Pinna nobilis)
Then, the limits of eDNA approaches were discussed. Detecting DNA in the environment does not mean that there is a disease. RNA detection could be indicative of the presence of live pathogens whereas DNA detection does not allow concluding about the status (live or inactivated) of the pathogens. When possible, histology remains the best approach to confirm an infection. Detecting listed pathogen DNA in the environment can have questionable regulatory consequences and guidelines are needed at the EU level to advice on the decisions that should be taken in such situations.
An increasing number of studies are carried out to characterize bivalve microbiome during diseases. This has notably been done in oysters showing mortality in VIVALDI. Thanks to data generated by involved partners, it is expected to identify microbiome profile associated with healthy or diseased oysters. Limits of currently used metabarcoding approaches were discussed including the difficulty to reach the species level for bacteria and the difficulty to get rid of the host genome information for eukaryotes. A target enrichment next generation sequencing developed in VIVALDI was presented as an interesting alternative to specifically detect a wide range of known pathogens.