That means there's less time to assimilate the food, so feeding a highly-digestible food is important. The more nutrition the dog gets from the food, the stronger the immune system will become. And a strong immune system will allow the dog to tolerate the bacteria. In addition, AFS says the dog has a more acidic pH to its stomach acid to better handle food-borne bacteria. Bacteria thus isn't a big issue for dogs on this diet.
Sanitation is critical for the people involved, though.
It's important to wash and sanitize bowls daily, and to disinfect prep surfaces. Wash your hands carefully for a full 20 seconds after working with this, or any, raw food. E. coli and other bacteria can multiply on counters, bowls, sponges, and your hands, resulting in diarrhea, vomiting, or flu-like symptoms. I now keep a handy spray bottle of disinfectant cleanser like they use in hospitals, and spray and wipe the counters regularly. Despite the stepped-up sanitation, a fact of life with this, and other raw food diets, is that vomiting will occur from time to time.