Hindcasting Farmed Salmon Mortality to Improve Future Health and Production Outcomes

Intracellular, free-floating and biofilm-forming bacterial pathogens have been implicated in summer mortality of farmed Chinook salmon, Oncorhynchus tshawytscha, in New Zealand. A mortality event in 2022 in the Pelorus Sound, Marlborough, was linked to high water temperatures (> 18°C), and bacterial skin disease associated with Piscirickettsia spp. (=Rickettsia-like organisms) and Tenacibaculum species. To understand the progression of infection and potential drivers of the mortality, simulation of the event was conducted using a networked susceptible, infectious and recovered (SIR) model. Parameter exploration shows that reconstruction of observed mortality rates across three affected farm sites was possible. The best SIR simulations identified plausible values for key drivers of disease, which are consistent with previously estimated disease parameter ranges for Piscirickettsia salmonis. Our modelling shows the 2022 Pelorus Sound event likely experienced spread of bacterial pathogens within healthy fish populations at salmon farm sites over a 10-week long incubation period, before elevated mortality was observed. We show evidence that vaccine use at one site likely prevented 10% higher mortality and that an alternative site for the vaccination could have further reduced mortalities. This result highlights the importance of future vaccine developments in aquaculture and the potential to improve vaccine efficacy through considered site selection.