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There are almost twice as many salmon being reared in fish farms today than a decade ago, and aquaculturists lean heavily on vaccines to keep their livestock healthy. Yet for the most part, vaccines are highly specific defenses: each is developed for a single target, such as a species of bacteria or strain of virus. And as a new study shows, when salmon have multiple infections, the efficacy of vaccines declines.

Marine biologist José Gallardo, who works at the Pontifical Catholic University of Valparaíso in Chile, says his study is the first to show that existing vaccines are ineffective at protecting salmon against co-infection by multiple pathogens. “Our research has put this issue in the global public debate on fish health,” Gallardo says.

“Regulations in Chile, Canada, and Norway do not consider this phenomenon,” he adds. “I do not know if fish farmers are aware.”

Gallardo and his team examined how vaccinated Atlantic salmon fared with infections by two agents: the bacteria Piscirickettsia salmonis, which causes a disease known as piscirickettsiosis; and the sea louse Caligus rogercresseyi. The bacteria, and various species of sea lice, are common in salmon farms worldwide. Together, they cause damages in the hundreds of millions of dollars.

Salmon infected by P. salmonis become lethargic, lose their appetites, and develop lesions. For years, Chilean fish farmers relied on antibiotics to control the bacteria, but indiscriminate use led to the emergence of resistant strains. In 2006, Chilean salmon farmers began vaccinating their fish.

The vaccines, however, were less effective on the farm than in laboratory tests. One review even concluded that most P. salmonis vaccines had not improved fish survival in Chilean salmon farms. Now, Gallardo’s work seems to explain why.

In laboratory trials, Gallardo and his team injected a commercially available P. salmonis vaccine into almost 3,000 Atlantic salmon. They then infected the fish with the bacteria. Half of those fish were also infected with sea lice. For comparison, the scientists infected 2,800 unvaccinated fish—some with P. salmonis bacteria and some with both the bacteria and lice. For the next 30 days, they monitored how the fish fared.

The scientists found that, as expected, all of the unvaccinated salmon facing multiple infections died. Of the unvaccinated fish infected with only P. salmonis, 4.7 percent survived.

Meanwhile, 58 percent of the fish vaccinated against and infected with P. salmonis survived. But, for the vaccinated fish that faced both P. salmonis and sea lice, only five percent survived.

Stewart Johnson, who studies fish diseases at Fisheries and Oceans Canada, says the complications of co-infection, as well as other stressors, are fairly well known to vaccine developers. “Chronic exposure to poor environmental conditions definitely limits the effectiveness of vaccines,” he says. “You would likely get the same response if you expose the vaccinated fish to long periods of poor environmental conditions.”

Indeed, past research has shown that by eating away at a salmon’s surface mucus and skin, sea lice rob the fish of its appetite and stunt its growth, and remove its front-line barrier against infection. “Such changes should limit the ability of the fish to fight the bacteria, as we demonstrated in our research,” says Gallardo.

Gallardo does not think that his study negates the need for vaccines. Rather, he suggests that fish farmers ask for vaccines that have been tested against co-infections and in diverse conditions, like those found in fish farms.

“Vaccine efficacy should also be evaluated by laboratories independent to the manufacturers,” says Gallardo.