Bacterial and viral pathogens can rapidly spread under intensive aquaculture conditions. Fortunately, fish can be vaccinated against many common or even site-specific (autogenous) pathogens to prevent disease outbreaks from occurring. Fish vaccination can be extremely effective at reducing disease and consequently the use of antibiotics. Norway salmon farmers, who produce over 1 million tonnes of farmed salmon per year, drastically reduced their antibiotic usage through vaccination programs starting about 1994 http://www.who.int/features/2015/antibiotics-norway/en/.
In Maine, we are fortunate to have numerous researchers, veterinarians and private companies with expertise in fish health and vaccine development located here. These include the University of Maine Veterinary Diagnostics Laboratory, Kennebec River Biosciences, and the Fish Vet Group based in Portland. The CCAR has previously vaccinated cod and California yellowtail against bacterial pathogens, using either immersion or injected vaccines.
With immersion, the vaccine is added to the water and the fish basically drink it in. This is commonly done as a first vaccine for very small fish. However, injected vaccine is far more effective, especially if done as a booster shot in fish that were previously vaccinated with immersion. Vaccines can be for a single pathogen, but often they are multivalent, providing protection against two or more pathogens. In the photo below, California yellowtail are injected with a multivalent vaccine developed by Kennebec River Biosciences.