The difference is primarily what the fish eat. Farm-raised fish held in pens are given feed composed of anchovies and other small fish that are caught around the world. These fish tend to be high in PCBs, a carcinogenic toxin banned in the U.S. but still used in some other countries as an industrial lubricant. So anchovies abroad eat the PCBs, our farmed fish eat the anchovies, and we eat the fish. Fish farms also put fish at higher risk of disease and infection due to their close quarters. Wild fish typically get to develop more muscle and have a healthier diet, passing on more beneficial nutrients and fewer PCBs to the diner.
Because of the diseases and infections stefanm mentioned, farmed fish are often given more antibiotics and exposed to more pesticides than wild fish. Farmed salmon are even given more antibiotics by pound than any other form of livestock in North America. While a lot of this is not absorbed by the fish, it still has the ability to create stronger, more resistant strains of bacteria.
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