Environmental screening through nanopore native sequencing leads to the detection of Batrachochytrium dendrobatidis in La Mandria Regional Park, Italy

Health surveillance of wildlife is crucial for the early detection of emerging pathogens. The One Health Integrated Wildlife Monitoring approach combines information from the biotic components of the ecosystem such as the abundance and diversity of wildlife with disease surveillance of animals (domestic and wild). Genomics-based detection of pathogens through environmental samples is a promising component of such programs. In this study, we analysed water samples from eight different irrigation channels in the La Mandria Regional Park, Italy, through PCR-free nanopore native sequencing to identify potential pathogens of importance for wildlife populations. Besides the pathogen Fascioloides magna that was previously detected in the park, we found evidence of other candidate pathogens including – for the first time in this area – the detection of the fungal pathogen Batrachochytrium dendrobatidis, and their possible host species. We confirmed the presence of B. dendrobatidis through ddPCR, and could demonstrate the detection of significant wildlife pathogens months before its first case was reported in wild animals of the park. Together with inferences on potential host species, these findings demonstrate the potential of genomics-based environmental monitoring through native nanopore sequencing in the context of One Health.