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The rapid growth of the salmon farming industry in Chile has led to the appearance of various viral, bacterial, parasitic, and fungal pathogens affecting farmed fish. The Chilean salmon industry has suffered several health crises associated with high fish mortalities, such as caused by the infectious salmon anaemia virus (2007) and harmful algal blooms (2016). In addition to these events, marine farms are continuously affected by outbreaks of harmful pathogens, including the bacteria Piscirickettsia salmonis and, most recently, a reappearance of Renibacterium salmoninarum, and the infectious pancreatic necrosis virus. These outbreaks have led to stricter regulations, but the salmon farming industry continues to struggle despite reforms. In addition to the aforementioned pathogens, which are a continuous threat, other apparently under control pathogens have also reappeared in recent years. In this review, we analyse the current state of knowledge on four of the main pathogens affecting salmon farming in Chile. The infectious pancreatic necrosis virus is relevant as it affects freshwater‐stage fish, with survivors then acting as carriers. The infectious salmon anaemia virus currently appears to be under control; however, P. salmonis and R. salmoninarum continue to be the cause for high mortalities in the Chilean aquaculture industry.

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Piscirickettsia salmonis is a fastidious intracellular pathogen responsible for high mortality rates in farmed salmonids, with serious economic consequences for the Chilean aquaculture industry. Oxytetracycline and florfenicol are the most frequently used antibiotics against P. salmonis, but routine use could contribute to drug resistance. This study identified differentiated florfenicol susceptibilities in two P. salmonis strains, LF-89 and AUSTRAL-005. The less susceptible isolate, AUSTRAL-005, also showed a high ethidium bromide efflux rate, indicating a higher activity of general efflux pump genes than LF-89. The P. salmonis genome presented resistance nodulation division (RND) family members, a family containing typical multidrug resistance-related efflux pumps in Gram-negative bacteria. Additionally, efflux pump acrAB genes were overexpressed in AUSTRAL-005 following exposure to the tolerated maximal concentration of florfenicol, in contrast to LF-89. These results indicate that tolerated maximum concentrations of florfenicol can modulate RND gene expression and increase efflux pump activity. We propose that the acrAB efflux pump is essential for P. salmonis survival at critical florfenicol concentrations and for the generation of antibiotic-resistant bacterial strains.