The majority of organisms that cause intestinal infections are acquired through contaminated food and water. The major risk factor for gastroenteritis that is caused by food poisoning is improper handling and storage of food. Bacterial or viral food poisoning usually occurs within 16 hours after eating contaminated food.

Some infections are transmitted by person-to-person contact. Fecal-oral transmission is a result of poor hygiene. The viral forms are epidemic viral gastroenteritis and rotavirus gastroenteritis. The epidemic viral form, often called intestinal flu, is transmitted through the fecal-oral route in food and water; the incubation period ranges from 10 to 50 hours. Rotaviruses are transmitted via the fecal-oral or possibly fecal-respiratory routes; the incubation period is 24 to 72 hours.

There are three principal forms of bacterial gastroenteritis: Campylobacter enteritis (traveler's diarrhea), Escherichia coli diarrhea (also known as traveler's diarrhea), and shigellosis (bacillary dysentery). Factors that contribute to the host's susceptibility to the agent are an elevated pH with the use of antacids, decreased production of gastric acid, or excessive intake of high-fat foods, which protect the microbe from gastric acid. Also, slow small bowel motility increases the time the pathogen is in contact with the lumen of the bowel, which aids in the development and duration of symptoms. Normal intestinal flora protect a person from pathogenic organisms.

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