What are intestinal and stomach infections?

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Gastrointestinal (GI) infections are caused by the overgrowth of resident or foreign bacteria, viruses, fungi, or parasites that can lead to vomiting, diarrhea, bloating, fever, and abdominal pain. GI infections occur with a wide range of symptoms, including none, minor or mild, and those requiring hospitalization for treatment; infections can also be fatal. The elderly, the very young, and the immunocompromised are more likely to develop serious complications from a GI infection.
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Gastrointestinal (GI) infections are caused by the overgrowth of resident or foreign bacteria, viruses, fungi, or parasites that can lead to vomiting, diarrhea, bloating, fever, and abdominal pain. GI infections occur with a wide range of symptoms, including none, minor or mild, and those requiring hospitalization for treatment; infections can also be fatal. The elderly, the very young, and the immunocompromised are more likely to develop serious complications from a GI infection.


Certain bacteria, viruses, fungi, and parasites can cause GI infections. In the United States, the most common cause of GI infection is the consumption of food infected with bacteria or food containing toxins released by those organisms (often referred to as food poisoning). Bacteria associated with food poisoning include Campylobacter jejuni, Salmonella, and Shigella species, and enterohemorrhagic Escherichia coli O157:H7.

Botulism is a potentially fatal GI infection caused by consuming food contaminated with a toxin produced by Clostridium botulinum; this infection is often associated with consuming improperly canned or prepared foods. Inflammatory diarrhea (also referred to as bloody diarrhea) can be caused by Shigella or Salmonella spp., C. jejuni, or E. coli. Inflammation of the colon can be life-threatening if it is accompanied by obstruction or rupture of the bowel. Clostridium difficile and Entercoccus fecalis can cause hospital-acquired GI infections.

Causing no symptoms is Helicobacter pylori, a spiral-shaped bacterium. Persons become carriers of the bacteria without knowing they are carriers. In some cases, long-term infection with H. pylori can cause the development of an ulcer.

Cholera is an acute diarrheal illness caused by infection of the intestine with the bacterium Vibrio cholerae. Although rare and easily treated in the United States, cholera can decimate a population in underdeveloped countries. An outbreak began in Haiti in the fall of 2010 among persons living in poor conditions following a deadly earthquake earlier in the year.

Viral gastroenteritis (referred to as a stomach bug or stomach flu) is a GI infection caused by a virus. These infections are common in the United States and can be acquired by consuming improperly prepared food (raw or undercooked) that also contains a virus and by contact with contaminated saliva or feces. Many viruses cause gastroenteritis, including rotaviruses, noroviruses, adenoviruses, enteroviruses, and hepatitis A, with rotaviruses being the most common cause of severe gastroenteritis in infants and young children worldwide.

Generally, GI infections are mild, and most healthy people recover from infection without complications. Noninflammatory diarrhea, which is usually caused by a rotavirus or an adenovirus, is typically self-limiting. Viral gastroenteritis, however, can be life-threatening for those who are unable to drink enough fluids to replace those fluids lost through vomiting and diarrhea. Infants, young children, and immunocompromised, disabled, and elderly persons are at risk for dehydration from the loss of fluids.

Some viruses are seasonal or are found only in certain environments. In the United States, rotavirus and astrovirus infections occur most commonly between October and April, while adenovirus infections can occur anytime during the year. Outbreaks of norovirus infections can occur in schools, child-care facilities, and nursing homes, and they have been associated with outbreaks in banquet halls, on cruise ships, in dormitories, and at campgrounds.

In underdeveloped countries with poor sanitation, parasites are the most common cause of GI infections; however, these infections may also be found in urban areas, depending on the social habits of residents. Parasites that infect humans and cause GI infections include protozoa and helminths.

In the United States, the most common protozoa that infect humans are Giardia intestinalis (also known as G. lamblia) and Cryptosporidium species. These protozoa may be consumed by hikers who drink untreated water from a lake, river, or stream. Protozoa can multiply inside the human body, leading to serious infection. Tapeworms (cestodes) are among the most common helminths that infect people in the United States. Dipylidium is a tapeworm found in cats and dogs. People become infected after accidentally swallowing a flea infected with a tapeworm larvae. Most reported cases involve children. Tapeworms are also found in raw or undercooked pork, beef, and fish. In many cases, the serious health problems that tapeworms cause occur when these parasites pass through the intestines and infect other organs, such as the skin, muscles, eyes, and brain.

Risk Factors

Risk factors for an intestinal or stomach infection include consuming improperly prepared food, such as raw or undercooked beef, pork, chicken, eggs, shellfish, or fish. Another risk factor is drinking water from untreated or contaminated sources or consuming raw food prepared or cleaned with untreated or contaminated water. C. difficile and E. fecalis are associated with recent antibiotic use and long-term hospitalization. GI infections can be very contagious, and pathogens are easily transferred from an infected person to another by touching a contaminated surface such as a door knob, faucet handle, or other common surface. Frequent and proper handwashing reduces the risk of transfer of the bacteria.

Consuming eggs laid by hens infected with Salmonella can cause a GI infection. Hens get infected with Salmonella by consuming contaminated feed. The feed usually acquires Salmonella by contact with flies and rodent feces. Salmonella bacteria may be present on the surface of infected eggs and can also penetrate the shell and infect the egg contents. Therefore, washing the surface of the egg and hands after touching eggs will remove most bacteria. In addition, a hen infected with Salmonella can carry the bacteria in its ovaries. Eggs then become infected with Salmonella as the eggs are forming; bacteria are contained within the shells. The most common site of bacterial contamination is the egg white. Thoroughly cooking the egg until the yolk and egg white are solid will kill the bacteria.

Consuming raw or undercooked contaminated beef can cause bacterial infections with Salmonella and E. coli O157:H7. Risk factors include improper and unsanitary handling of animals at the time of slaughter, of meat products at the time of processing, and of food being prepared at home.

Produce-related outbreaks have become more common in the United States. Cases of E. coli-contaminated spinach and lettuce have led to hospitalizations, death, and the recall of thousands of pounds of produce. It remains unclear exactly how fields of leafy green vegetables, such as spinach and lettuce, become reservoirs for these pathogens, although it is believed that the sources of the pathogens are animal waste and by-products. Also, commercially processed foods that contain contaminated meat or produce, such as frozen pot pies, vegetable snacks, frozen pepperoni pizzas, and canned hot dog chili sauce, have been sources of bacterial GI infections.

Consuming improperly prepared pork or wild game infected with the roundworm Trichinella spiralis can cause GI infections in humans. The incidence of Trichinella infection has declined markedly in the United States since the availability of home freezers and the use of proper food preparation and cooking. Taenia solium is a pork tapeworm that can cause a GI infection if tapeworm eggs are consumed in food or water, are obtained from surfaces contaminated with feces, or are obtained through autoinfection (self-reinfection). After being consumed, the eggs hatch and penetrate the intestine. Once in the bloodstream, the eggs may develop into cysticerci in the muscles, brain, or eyes; they can then cause an infection in these organs known as cysticercosis.

Consuming infected raw or undercooked shellfish or fish may cause an infection with hepatitis A, other hepatitis viruses, several types of bacteria, and cholera. Some soft cheeses and some ready-to-eat foods (such as hot dogs and cold cuts from delicatessen counters) may contain the bacterium Listeria and cause listeriosis in severely immunocompromised persons. To prevent listeriosis, shellfish and fish should be heated until the point of steaming before consumption.

Children in particular may acquire waterborne infections from lakes or pools after swallowing water during recreational activities. Public swimming pools and lakes may be contaminated with pathogens from infected swimmers; exposure to infected feces or soiled diapers can be avoided with proper hygiene, handwashing, and disposal of waste. It is generally recommended, however, that infected persons avoid using public swimming pools and other such recreational sites until the infection has resolved.


Symptoms of GI infections depend on the pathogen and the amount consumed. In general, symptoms can develop quickly (within thirty minutes) or more slowly (within hours) and can worsen over days to weeks. Usually the infection is self-limiting and runs its course within forty-eight hours. GI infections can cause nausea, diarrhea, vomiting, fever, abdominal cramping, bloating, loss of appetite (anorexia), and dysentery (blood or mucus in the stool). If these symptoms continue for many days or if good hydration is not maintained, weight loss and dehydration may occur. Other flulike symptoms include chills, headache, muscle aches, and malaise.

Viral GI infections tend to be self-limited. These symptoms typically begin one to two days after exposure and can last for up to ten days, depending on the type of virus. Self-limited infections are typically noninflammatory; however, inflammatory diarrhea (also referred to as bloody diarrhea) can be life-threatening if obstruction or rupture of the bowel occurs. In some people, E. coli O157:H7 infection can cause a complication called hemolytic uremic syndrome, a life-threatening condition. Prolonged diarrhea can occur when persons are infected with parasites, E. fecalis, or C. difficile.

Each year, rotaviruses cause about one-half million deaths among young children worldwide, with the majority of deaths in developing countries (where access to treatment is limited). Infection with hepatitis A causes a sudden onset of fever, loss of appetite, and malaise, followed by jaundice (yellowing of the eyes and skin). Symptoms of giardiasis (infection with Giardia) normally begin one to two weeks (with an average seven days) after infection and may last two to six weeks in otherwise healthy persons.

Some GI infections may have little or no GI symptoms. Other than passing of eggs and adult tapeworms (which can be quite dramatic), symptoms associated with infection by the pork tapeworm T. solium usually involve the muscles, brain, or eyes (infected with cysticerci or cysts). H. pylori infection often does not cause any symptoms until the person has developed a stomach ulcer.

Screening and Diagnosis

Generally, in the United States, GI infections are diagnosed by a physician after a physical examination and on the basis of symptoms. Stool specimens are collected for the diagnosis of some GI infections. Various laboratory tests can be conducted on stool specimens, including bacterial culture, microscopic analysis, pathogen isolation, serology (to check for antibodies), or antigen detection, which aids in identifying the causative pathogen. Some viruses, such as adenoviruses, may be excreted in the stool for prolonged periods even after resolution of the infection; therefore, presence of the virus does not necessarily indicate active infection. In the case of bacterial infections, antibiotic susceptibility testing may be used to determine microbial resistance to antibiotic therapy.

Treatment and Therapy

Most infections are mild and require only symptomatic treatment and adequate hydration. Dehydration can lead to kidney and other organ failure. Severe dehydration may require hospitalization and treatment with intravenous fluids. To prevent dehydration, one should drink 8 ounces of fluids every two hours until diarrhea and vomiting stop. Oral rehydration fluids are formulated to replace lost electrolytes and nutrients. Drinks containing caffeine or alcohol should be avoided.

Antidiarrheal medications that contain loperamide are generally not recommended for treatment of GI infections because these drugs prevent the body from eliminating the pathogen through the stool, which may make the infection worse. Drugs that reduce symptoms of nausea and vomiting (anti-emetics) but do not reduce bowel movement are helpful and may minimize fluid loss.

Antiparasitic drugs, such as praziquantal or niclosimide, are used to treat tapeworm infections. Antibiotics should not be used to treat most food-borne infections, including those caused by bacteria, because these infections are typically self-limiting. Serious bacterial GI infections, however, which do not respond to hydration and require hospitalization for treatment should receive antibiotic therapy. Bacteria such as E. coli and C. difficile have developed resistance to certain antibiotics, which makes these infections more difficult to treat. No effective antiviral medication is available to treat serious viral illnesses; therefore, only symptomatic treatment is provided for these infections.

Prevention and Outcomes

Most GI infections can be avoided by maintaining frequent and good handwashing technique, by drinking clean water, and by following safe food-storage and food-preparation practices. Two live, oral rotavirus vaccines are available for use in infants in the United States that can prevent rotavirus gastroenteritis.

Good handwashing technique involves wetting hands with clean, warm, running water; applying soap; then rubbing hands together to make a lather and scrubbing for a minimum of twenty seconds. Finally, hands should be rinsed well under running water and dried using a paper towel or air dryer. One should also use a paper towel to turn off the faucet.

Many GI infections can be prevented by drinking only clean, treated water and by using uncontaminated water to wash all food that is to be eaten raw. All raw fruits and vegetables should be washed or peeled (or both) before eating. Persons should avoid consuming uncooked foods when traveling in countries with minimal water treatment and sanitation systems. Persons also should avoid direct contact of the skin with soil or sand (by wearing shoes and protective clothing and using towels on beaches) in areas where fecal contamination of soil is likely, and should wash hands and exposed skin with soap and clean water as soon as possible to avoid oral contact. When camping or backpacking, persons should bring a supply of clean water or should treat water from lakes or streams by boiling (a rolling boil for a minimum of one minute) or by combining disinfection and filtration if the water is to be used for drinking or food preparation. Persons should avoid swimming in water that is likely to be contaminated with human or animal waste and should avoid swallowing water when swimming.

Safe storage and preparation of food means keeping cold food cold and hot food hot. Cold food should be stored in a refrigerator (at 40° Fahrenheit or below) or a freezer (0° F or below). One should cook food to a safe minimum internal temperature. All cuts of pork, ground beef, veal, and lamb should be cooked to a minimum internal temperature of 160° F, while all poultry should be cooked to 165° F. One should maintain hot cooked food at 140° F or above and should reheat cooked food to 165° F. Eggs should be cooked until both the white and the yolk are firm and should be consumed promptly after cooking. One should refrigerate unused or leftover foods promptly, should discard food that is past its expiration date, and should discard cracked or dirty eggs. Raw meat or eggs should not be consumed. After contact with raw meat or eggs, one should wash hands, cooking utensils, and food preparation surfaces with soap and water. The U.S. Centers for Disease Control and Prevention (CDC) has developed the food safety motto, “remember to clean, separate, cook, and chill.”

The two rotavirus vaccines available in the United States differ in composition and schedule of administration. No preference, however, is given to either vaccine by the CDC’s Advisory Committee on Immunization Practices. Additional studies are needed to evaluate the safety and efficacy of rotavirus vaccine administered to infants who are born preterm, who have immune deficiencies, who live in households with immunocompromised persons, who have chronic GI disease, or who start the vaccine series later than recommended.


Centers for Disease Control and Prevention. “Clean Hands Save Lives.” Available at http://www.cdc.gov/cleanhands. Information from the CDC on good hygiene and handwashing technique.

_______. “A Guide to Drinking Water Treatment and Sanitation for Backcountry and Travel Use.” Available at http://www.cdc.gov/healthywater/drinking. Recommendations from the CDC on safe drinking-water practices for outdoor enthusiasts and travelers.

_______. “Prevention of Rotavirus Gastroenteritis Among Infants and Children: Recommendations of the Advisory Committee on Immunization Practices.” Morbidity and Mortality Weekly Report 58 (February 6, 2009): 1-25. Also available at http://www.cdc.gov/mmwr/preview/mmwrhtml/rr5802a1.htm. Recommendations from the CDC on the safety and efficacy of the rotavirus vaccine.

Feldman, Mark, Lawrence S. Friedman, and Lawrence J. Brandt, eds. Sleisenger and Fordtran’s Gastrointestinal and Liver Disease: Pathophysiology, Diagnosis, Management. New ed. 2 vols. Philadelphia: Saunders/Elsevier, 2010. An excellent textbook on gastroenterology, intestinal pathology, and treatment protocols.

Johnson, Leonard R., ed. Gastrointestinal Physiology. 7th ed. Philadelphia: Mosby/Elsevier, 2007. This book contains a variety of specialized topics dealt with by experts on gastrointestinal physiology.

National Center for Immunization and Respiratory Diseases. “Viral Gastroenteritis.” Available at http://www.cdc.gov/ncidod/dvrd/revb/gastro/faq.htm. Information from a center of the CDC on viral gastroenteritis symptoms and management.

U.S. Department of Agriculture. “Foodborne Illness: What Consumers Need to Know.” Available at http://www.fsis.usda.gov/fact_sheets. A fact sheet for consumers about symptoms, pathogens, and prevention of food-borne illnesses.

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