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Failing that you need to prevent cross contamination - make sure that the dirt is germ free, make sure that the farmers wash their hands before they harvest the crops, etc.
The most important source of food poisoning germs is toilets/lavatories. Make sure dupes wash their hands after using the bathroom. Dupes won't wait in line to use a sink if it's already occupied when they walk past, so you need 1 sink per toilet, in front of each exit to the room (which means you usually want to have only 1 exit, to cut down on duplicate sinks).
The polluted water coming out of a lavatory will also have germs in it. If you run that through a water sieve, the water sieve will hold onto some germs and the water coming out of it will be infected (seemingly forever). So keep that water separated from your main water supply. You can still use germy water to run lavatories/sinks/showers/carbon skimmers and the germs won't hurt anything, but if you want to use it for crops or have dupes bottle it manually then you should disinfect it first (usually by exposing it to chlorine gas for a full cycle).
Also note that if you make mush bars in a microbe masher, they'll always come out with germs. Best solution there is to stop using mush bars as soon as possible.
Food cooked on an electric grill or gas oven will automatically have germs killed, so cooking your food will cover a multitude of sins as long as dupes don't re-contaminate it after it's cooked.
For germy Water that is not Polluted, the easiest way is to create a sealed room with 3 Liquid Reservoirs chained together, filled with nothing but Chlorine gas. Rig the chain so the final Reservoir can't output until after your bathroom loop is almost filled. This works for 2 reasons. First, while in the Reservoirs, the water will get the "Exposed to Chlorine" effect, doubling the rate at which germs die. The second reason is how Reservoirs average by mass all their contents, both on entering and exiting the Reservoir. Since small quantities of liquid are entering and leaving the Reservoir, it works out in your favor. The large amount of germs on entering will be averaged against the whole volume, then a much smaller amount of germs will be applied on exiting, because it has a much smaller mass than what is in the Reservoir. With 3 chained together, even running at full tilt, the water leaving the 3rd Reservoir will always be free from germs.
If you are doing this with Polluted Water instead of ordinary Water, you need at least a 4th Reservoir, perhaps a 5th, because germs will multiply in Polluted Water, instead of slowly dying in otherwise clean Water.
the ultimate solution, have your fridge in a chlorine filled pit and it'll kill all the germs on food through the day.