Investigation of the water environmental DNA/RNA profile for non-invasive biomonitoring of the fish pathogen Aeromonas salmonicida subsp. salmonicida and detection of immune responses in rainbow trout (Oncorhynchus mykiss)

Aquaculture industries face challenges in fish production, primarily due to disease occurrence. Clinical manifestations of these diseases often indicate a considerable advancement in the pathological process. Infected fish often experience morbidity, leading to compromised welfare and substantial economic losses for production facilities. Therefore, prophylaxis and early detection of the pathogens could allow the facility managers to intervene or treat the disease before clinical disease signs occur. For the first time, environmental DNA/RNA (collectively eNA) was used to detect the salmonid pathogen Aeromonas salmonicida subsp. salmonicida in the water hosting rainbow trout (Oncorhynchus mykiss). This took place under controlled experimental conditions, before the occurrence of clinical outcome and mortality. The concentration of bacteria in the water was determined by using a standard curve. To determine the window of possible intervention, bacterial concentration was measured from an early stage of disease and throughout when fish became moribund. Furthermore, the acute phase protein, serum amyloid A produced by rainbow trout, was detected in the water and was found to be up-regulated 4 days post challenge. It was thereby shown that it is possible to detect strong immune responses in the fish in a non-invasive manner. The detection of eNA from the water can be used as a tool to detect pathogens in the early phase of infection before the disease becomes severe. This will facilitate interventions to limit the disease and increase the welfare of the fish, which is becoming a requirement for a more sustainable and ethical animal production.