We live in a world that has a wide diversity of microorganisms, and there are many opportunities for food to become contaminated as it is produced and prepared. Many foodborne microbes are present in healthy animals (usually in their intestines) raised for food. Meat and poultry carcasses can become contaminated during slaughter by contact with small amounts of intestinal contents. Similarly, fresh fruits and vegetables can be contaminated if they are washed or irrigated with water that is contaminated with animal manure or human sewage. Some types of Salmonella can infect a hen's ovary so that the internal contents of a normal-looking egg can be contaminated with Salmonella even before the shell in formed. Oysters and other filter-feeding shellfish can concentrate Vibrio bacteria that are naturally present in seawater, or other microbes that are present in human sewage dumped into the sea.

  Later in food processing, other foodborne microbes can be introduced from the environment of food processing lines. They may also be introduced by infected humans who handle the food, or by cross-contamination from raw products. The unwashed hands of food handlers who are infected can introduce for example, Shigella bacteria, hepatitis A virus and Norwalk virus. In the kitchen, microbes can be transferred from one food to another food by using the same knife, cutting board or other utensil to prepare both without washing the surface or utensil in between. A food that is fully cooked can become recontaminated if it comes into contact with other raw foods or drippings from raw foods that contain pathogens.

  The way that food is handled after it is contaminated can also make a difference in whether or not an outbreak occurs. Many bacteria need to multiply to a larger number before enough are present in food to cause disease. Given warm moist conditions and an ample supply of nutrients, one bacterium that reproduces by dividing itself every half hour can produce 16 billion progeny in 12 hours. As a result, lightly contaminated food left out overnight can be highly infectious by the next day. On the other hand, if the food were refrigerated promptly, the bacteria would not multiply at all. In general, refrigeration or freezing prevents virtually all bacteria from growing but generally preserves them in a state of suspended animation. This general rule has a few surprising exceptions. Two foodborne bacteria, Listeria monocytogenes and Yersinia enterocolitica can actually grow at refrigerator temperatures. High salt, high sugar or high acid levels keep bacteria from growing, which is why salted meats, jam, and pickled vegetables are traditional preserved foods.

  Microbes are killed by heat. If food is heated to an internal temperature above 78°C for even a few seconds, it is sufficient to kill parasites, viruses or bacteria, except for the Bacillus and Clostridium bacteria, which produce a heat-resistant form called a spore. These spores are killed only at temperatures above boiling. This is why canned foods must be cooked to a high temperature under pressure as part of the canning process.

  The toxins produced by bacteria vary in their sensitivity to heat. The staphylococcal toxin, which causes vomiting, is not inactivated even if it is boiled. Fortunately, the potent toxin that causes botulism is completely inactivated by boiling.