The primary way they prevent bacteria is to avoid getting bacteria on the fish in the first place. Food safety is very important in sushi kitchens and when handling fish for sushi. And even when you get some bacterial contamination the bacteria is not given the opportunity to multiply. This is why they use whole fish and only prepare the sushi moments before it is consumed. It is also one of the important reasons for flash freezing the fish as any bacteria will hibernate when frozen.
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