Intestinal Infections

Intestinal infections are caused by such pathogens (PATH-o-jens) as bacteria, viruses, and fungi. Pathogens are microscopic organisms that cause disease. These infections can affect various portions of the gastrointestinal * tract, including the small intestine * and the colon * . Such infections, which often cause diarrhea (dye-uh-REE-uh), are frequently accompanied by gastroenteritis (GAS-tro-en-ter-EYE-tis), an inflammation of the stomach and intestines.

Microorganisms and the Digestive System: What Is Normal?

The inside of the human body is teeming with a wide variety of bacteria, fungi, and other microorganisms. This situation is perfectly normal, and these microorganisms do no harm in most instances. In fact, some of these microorganisms are beneficial. The digestive system is one part of the body with an especially high number of normally occurring microorganisms. Estimates suggest that a single person's digestive system is home to some 100 trillion individual microorganisms from 300 to 500 different species. These normally occurring and either beneficial or typically not harmful microorganisms are collectively known as intestinal microbiota, or sometimes as intestinal flora or gut flora. Certain normally occurring beneficial microbiota have an important part in digestion, and without them the human body would be unable to break down some foods. Studies also suggest that some types of intestinal microbiota may help defend the body against infection or have other roles in maintaining health.

Although many microorganisms are beneficial or exist in the human body without incident, in some cases microorganisms in the digestive system cause intestinal infections, a number of which can be severe and even fatal.

How Do Intestinal Infections Occur?

Intestinal infections can be acquired and spread in many ways. Some people become infected by eating contaminated shellfish, raw or undercooked meat, or unpasteurized * dairy products, or from drinking or swimming in contaminated water. Others get sick by touching something that is contaminated with an infectious organism and then unwittingly transferring that organism to their mouths. This might happen if individuals neglect to wash their hands after touching a surface (such as a kitchen counter or a door handle) or handle anything that might be contaminated with feces (FEE-seez, or bowel movements), such as dirty laundry or a soiled diaper. Outbreaks of intestinal infections sometimes occur when many people eat or drink the same contaminated food or water.

What Bacteria Are Involved?

Campylobacter infection

Diarrhea is usually caused by an infection with Campylobacter (kam-pee-lo-BAK-ter) bacteria, and typically with one particular species known as Campylobacter jejuni (je-JOO-nee). The Centers for Disease Control and Prevention (CDC) estimates that about 8 out of every 1,000 people in the United States experience Campylobacter-caused diarrhea every year. Symptoms, which begin two to five days after infection, include diarrhea that is sometimes bloody, abdominal cramping and pain, and fever. Most people recover on their own within a couple of days to a week.

Campylobacter lives in animals, especially birds. Humans become infected after eating chicken or other poultry that has not been completely cooked or after eating food that has been contaminated by the blood or other juices of uncooked or undercooked poultry. This may happen, for instance, if a person slices a raw chicken on a cutting board and then, without first thoroughly washing the cutting board, uses it again to slice carrots for a raw-vegetable platter. Outbreaks of this type of diarrhea also have occurred after people have drunk contaminated water or unpasteurized milk. In developing countries where clean water is sometimes lacking, Campylobacter infections are particularly common, and sometimes result in death. In addition, travelers to foreign lands often unknowingly drink contaminated tap water.

Clostridium difficile and Clostridium perfringens infection

Clostridium difficile (klos-TRIH-dee-um DIH-fih-seel) bacteria often live in the intestinal tracts of infants and young children without causing disease. In adults, however, especially the elderly, infection with C. difficile can produce fever, watery diarrhea, abdominal pain, and loss of appetite. Risk factors for infection include a hospital stay, gastrointestinal surgery, and having another serious illness. Healthcare workers often spread the bacteria when they touch infected feces or contaminated surfaces then touch patients or give them medicine without first washing their hands. Frequently, infection with C. difficile occurs in people who are taking long courses of antibiotics that fight disease-causing bacteria. These antibiotics limit the growth of the harmless, normal bacteria found in the digestive system, which presents a good environment for C. difficile to multiply, and when they do, to cause an infection.

Escherichia coli infection

Escherichia coli (ESH-ur-ick-ee-uh KOlie) comes in different types, called strains * , and most of these are completely harmless. In fact, it is one of the species of bacteria that normally occurs in the large intestine of the human digestive system, and it plays a part in making vitamin K, which helps blood clot, and in fighting off various infections.

However, a few strains of E. coli are harmful. One of these, known as E. coli 0157:H7, occurs in the digestive system of numerous animals, including cattle. E. coli 0157:H7 produces a toxin that can cause human disease. People come into contact with the bacteria when they eat undercooked beef, such as hamburger, or when they eat other foods contaminated with the bacteria. Such contamination may occur when a farmer uses cow manure as fertilizer on fruit or vegetable crops and a consumer then fails to wash tainted produce before eating it or when a person drinks unpasteurized milk that was contaminated during the milking process. In addition, a person can become infected in other ways, such as by swimming in contaminated water or by being in close contact with an already infected individual. Occasionally, outbreaks of E. coli infections occur when a food-manufacturing plant has a problem with contamination and ships its products over a wide area. Many people may become sick, and some may even die before officials can track down the source of the contamination and issue recalls for the tainted items.

E. coli infections are quite common. The CDC estimates that 73,000 cases of E. coli infection occur in the United States each year, and about 60 result in deaths. The symptoms of E. coli infection include abdominal cramps and bloody diarrhea, which last about five days. Most people do not need treatment, although those with weak immune systems (such as patients undergoing chemotherapy * or people with HIV * or AIDS * ), children, and the elderly require hospitalization if they develop a serious infection.

Helicobacter pylori infection Listeria monocytogenes infection

Listeriosis (lis-teer-e-O-sis) is caused by the Listeria monocytogenes bacterium, which is found in the soil, stream water, food, and sewage. People contract listeriosis from eating vegetables grown in contaminated soil or raw or undercooked meat, drinking contaminated water, or consuming unpasteurized milk or milk products. Listeriosis is rare, affecting only about 20 of every million people.

Symptoms of illness include fever, headache, nausea, and diarrhea. The bacteria also can spread into the bloodstream or nervous system, leading to meningitis * . Pregnant women are at greater risk for the disease, and about 20 times as many pregnant women as other healthy adults develop listeriosis. The disease can cause miscarriage * , stillbirth * , or serious illness in the newborn. Infants, older people, and people with weak immune systems are also at risk.

Salmonella infection

Several different strains of Salmonella (sal-muh-NEH-luh) bacteria can cause illness. The Salmonella typhi (TIE-fee) bacterium causes the most serious illness, typhoid (TIE-foyd) fever, which is frequent in developing countries. The National Center for Infectious Diseases reports an estimated 12.5 million cases of typhoid fever worldwide each year. In the United States, about 400 cases occur each year, mostly in people who have traveled to undeveloped countries. Typhoid fever spreads when people eat or drink food or water contaminated with the bacteria. People who are infected may have a high fever, headache, extreme tiredness or weakness, stomach pain, loss of appetite, and sometimes a flat, red rash. A vaccination * for travelers can help prevent typhoid fever, and antibiotics can help patients who become sick.

The Salmonella bacteria also cause salmonellosis (sal-muh-neh-LOsis), which is more common than typhoid fever. The Centers for Disease Control and Prevention (CDC) reports 40,000 cases in the United States each year and estimates that 20 times that number may go undiagnosed. As many as 1,000 people in the United States die from the disease each year. Eating eggs or meat from contaminated animals can cause salmonellosis. Symptoms start 12 to 72 hours after infection and include nausea (NAW-zee-uh), vomiting, diarrhea, fever, and stomach cramps. The disease usually runs its course in four to seven days. Only infants, young children, the elderly, and people with weakened immune systems typically require treatment. (Antibiotic treatment can actually prolong the time that it takes for Salmonella bacteria to leave the body.)

Shigella * . In addition, infections can spread through contact with contaminated water, by eating contaminated food, or through some forms of sexual activity.

Symptoms of shigellosis include diarrhea (often with blood or mucus * ), fever, vomiting, nausea, and abdominal * cramping. Most people recover without treatment, usually within a week, although doctors may prescribe antibiotics to keep the disease from spreading.


Toxins produced by certain strains of Staphylococcus aureus (staf-ih-lo-KAH-kus AR-ee-us) bacteria can cause food poisoning. When people who are infected with the bacteria handle food such as meat, poultry, egg products, or dishes containing mayonnaise or cream, they may spread the bacteria to the food. The toxins build up when the food sits for a long time at room temperature. When a person becomes infected, symptoms come on quickly, within 2 to 8 hours, and last less than 12 hours. They include severe nausea and vomiting, and sometimes abdominal cramping, diarrhea, and headache.

What Viruses Can Cause Intestinal Infections?

A variety of viruses can cause intestinal infections. Some of the most common are enteroviruses, hepatitis A, noroviruses, and rotaviruses.


Enteroviruses (en-tuh-ro-VY-ruh-sez) are a group of viruses that attack the intestinal tract and cause a wide range of illnesses, including intestinal infections. People who are infected may experience mild diarrhea, vomiting, fever, and abdominal pain. Most get better on their own without treatment from a doctor.

Hepatitis A

The hepatitis (heh-puh-TIE-tis) A virus occurs in water contaminated by sewage, in shellfish taken from tainted water, and in fruits and vegetables grown in contaminated soil. The virus can spread when people eat or drink tainted food or water, or can pass from person to person during sexual intercourse. Infected people who handle or prepare food can transmit the virus if they do not thoroughly wash their hands after going to the bathroom and then go on to prepare food for others.

Some people with hepatitis A infection show no signs of illness, but others may experience fever, extreme tiredness, loss of appetite, nausea, and vomiting. The patient's liver enlarges and the skin may appear yellowish, a condition known as jaundice * . The disease can lead to permanent liver damage, although this is rare. Symptoms appear two to four weeks after infection and may last several weeks to months. A vaccine is available to protect people at high risk of hepatitis A infection. These include people who travel to developing countries or who engage in illegal drug use or sexual relations with others who already have hepatitis A.

Norovirus infections

Infections with noroviruses cause most of the nonbacterial outbreaks of gastroenteritis worldwide. The viruses spread through food or water that is contaminated with feces or through contact with an infected person. Norovirus outbreaks are particularly common on cruise ships, in nursing homes or hospitals, in boarding schools or college dormitories, in prisons, or in other places where people are in long-term and close contact with one another. Symptoms of the infection may include nausea or vomiting, diarrhea, abdominal pain, fever or headache, tiredness, weakness, and general muscle pain. Most people recover within a few days, but infants, elderly people, and people with weakened immune systems may require hospitalization. Norovirus infections are occasionally fatal.


Rotaviruses (RO-tuh-vy-ruh-sez) can infect people of all ages, but infants and young children are infected most often. Outbreaks occur most frequently from November to April in the United States, with about 1 million children affected each year. Of those, between 55,000 and 70,000 require hospitalization. Deaths from the illness are rare in the United States. Worldwide, however, more than 600,000 children die each year from rotavirus infection, according to the World Health Organization.

Rotaviruses spread when people come into contact with infected human feces. The disease is most common in day care centers, hospital pediatric wards, and homes with young children. Symptoms appear about two days after infection. They include fever, vomiting, and abdominal pain, which last for two to three days, and diarrhea, which can linger for up to eight days. Most people do not require treatment.

Medical professionals used a rotavirus vaccine in the United States in the late 1990s, but stopped administering it after it caused bowel problems in some infants. As of 2015, research was underway to develop a replacement vaccine.

Other Causes of Intestinal Infection

Parasites cause many intestinal infections. Some common parasitic infections that lead to intestinal symptoms, such as cramping and diarrhea, include Entamoeba histolytica (en-tuh-ME-ba his-toh-LIH-tih-kuh), which causes amebiasis (ah-mih-BYE-uh-sis); Giardia intestinalis protozoa * , which causes giardiasis (jee-ar-DYE-uh-sis); and Cyclospora cayetanensis (sy-klo-SPORE-uh kye-uh-tuh-NIN-sis).

Certain fungi can also cause intestinal infections. One group in particular is the Candida fungi, which can multiply and lead to an inflammation of the esophagus, a condition called esophagitis. People who are most prone to fungal esophagitis include those who have taken antibiotics over a long time, are undergoing radiation therapy or chemotherapy, have diabetes * , have AIDS, are alcoholics, are suffering from malnutrition, or are elderly. Symptoms include nausea or vomiting, difficulty or an uncomfortable feeling when swallowing, mouth sores, and heartburn. Antifungal drugs usually treat the infection.

Intestinal Infections

Illustration by Frank Forney. © 2016 Cengage Learning®.

How Are Intestinal Infections and Food Poisoning Diagnosed?

Many cases of intestinal infection are so mild that they go unnoticed. Others get better without the patient ever seeing a doctor. The symptoms of gastroenteritis—nausea, vomiting, abdominal pain, diarrhea, and loss of appetite—are common to many intestinal infections and some other diseases as well. When a patient seeks treatment, a doctor often begins with a physical exam and a series of questions about symptoms and food intake. For mild cases, the doctor may not order any laboratory tests and may be satisfied that the patient will recover even though the actual cause of the infection remains unknown. In more severe cases of illness, however, the doctor may need to know the identity of the infecting organism and will collect samples of a bowel movement to examine under the microscope and send to be cultured * , which will help pinpoint the organism involved.

How Are Intestinal Infections Treated?

Most intestinal infections do not require treatment, and patients get better on their own. People with diarrhea and other signs of intestinal infections should talk to their doctors if the symptoms do not clear up in a few days or become severe.

In most cases, patients can remain at home and maintain a relatively normal schedule. To prevent transmission of the infection between young children, parents should consider keeping an infected child at home and out of day care until the illness resolves. All patients should drink plenty of fluids to avoid dehydration * . Doctors also advise that they avoid antidiarrhea medicine because it may keep the infectious agent in the body longer. More severe cases of intestinal infections sometimes require hospitalization so patients can receive intravenous fluids * , antibiotics, or other treatment. In most cases, people should feel better within days to a week, although several more weeks may pass before their gastrointestinal tracts recover completely.

Can Intestinal Infections Cause Other Complications?

In otherwise healthy people, intestinal infections rarely cause complications. Mild dehydration is the most common consequence. Infants and the elderly are most at risk for severe dehydration. For people with weak immune systems, the infectious agent may spread throughout the body, causing widespread disease and even death. In infants and young children, cases of long-lasting illness occasionally lead to malnutrition or a failure to grow properly because the infections interfere with their nourishment.

Preventing Intestinal Infections

Preventing Intestinal Infections
SOURCE: Centers for Disease Control and Prevention. Table by Cenveo Publisher Services. © 2016 Cengage Learning®.

Beyond colitis, Campylobacter, Salmonella, and Shigella infections can lead to Reiter (RYE-ter) syndrome, which is characterized by joint pain, eye inflammation, and difficulty and pain with urination. Campylobacter may spread into the bloodstream and trigger other problems, including a dangerous whole-body inflammation called sepsis or a condition called Guillain-Barré (GEE-yan bah-RAY) syndrome, which is a nerve inflammation that causes muscle weakness or paralysis * . Salmonella infection can result in arthritis * , meningitis, brain abscesses * , and bone infections. In about 3 to 5 percent of cases, E. coli infections can lead to hemolytic uremic syndrome, a disease that can progress to kidney * failure, considerable bleeding, and severe anemia * .

Can Intestinal Infections Be Prevented?

The best way to prevent intestinal infection is by practicing good hygiene, which includes the frequent and thorough washing of hands, especially after changing diapers, after going to the bathroom, and before handling food or eating.

Travelers who plan to visit developing countries must also make sure they have any recommended vaccinations (such as the one for typhoid fever) before they leave. Once there, travelers should drink only bottled water and avoid eating raw fruits and vegetables, food from street vendors, and unpasteurized dairy products. To be safe, travelers should only eat food that is served steaming hot, because high heat kills many disease-causing organisms.

Individuals with weakened immune systems, such as people with AIDS, must take special care to avoid infections, because their bodies are simply unable to wage a strong defense against the intruding bacterium or other pathogen. For this reason, infections can spread very rapidly and lead to serious health problems, including death. A person with a weakened immune system should follow medical advice carefully to avoid an infection and to treat one should it occur.

See also Food Poisoning • Gastroenteritis • Helicobacter pylori Infection • Hepatitis • Inflammatory Bowel Disease • Intestinal Parasites • Shigellosis (Bacillary Dysentery) • Staphylococcal Infections • Travel-Related Infections: Overview


Books and Articles

Blaser, Martin J. Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues. New York: Henry Holt, 2014.

Charisius, Hanno. “When Scientists Experiment on Themselves: H. pylori and Ulcers.” Scientific American. July 5, 2014. (accessed July 20, 2015).

Phillip, Abby. “CDC Warning: Stop Hugging and Kissing Your Pet Chickens.” Washington Post. July 17, 2015. (accessed July 20, 2015).


Centers for Disease Control and Prevention. “Parasites.” . (accessed July 20, 2015).

Digestive Disease Center. “Infections of the Small Bowel.” MUSC Health, Digestive Disease Center. (accessed July 20, 2015).

Enterovirus Foundation. “About EV.” http://www.enterovirusfoundation . org (accessed July 20, 2015).

MedlinePlus. “Infections.” U.S. National Library of Medicine. (accessed July 20, 2015).


Centers for Disease Control and Prevention. 1600 Clifton Rd., Atlanta, GA 30333. Toll-free: 800-311-3435. Website: (accessed July 20, 2015).

Food and Drug Administration, Center for Food Safety and Applied Nutrition. 5100 Paint Branch Pkwy., College Park, MD 20740. Toll-free: 888-SAFE-FOOD. Website: (accessed July 20, 2015).

* gastrointestinal (gas-tro-in-TEStih-nuhl) means having to do with the organs of the digestive system, the system that processes food. It includes the mouth, esophagus, stomach, intestines, colon, and rectum and other organs involved in digestion, including the liver and pancreas.

* small intestine is the part of the intestines—the system of muscular tubes that food passes through during digestion—that directly receives the food when it passes through the stomach.

* colon (KO-lin), also called the large intestine, is a muscular tube through which food passes as it is digested, just before it moves into the rectum and out of the body through the anus.

* unpasteurized (pas-CHUR ized) refers to foods that have not undergone the process of pasteurization (pas-chu-rih-ZAYshun), in which food is heated to a certain temperature over a period of time to kill organisms and help make the food safer to consume.

* strains are various subtypes of organisms, such as viruses or bacteria.

* chemotherapy (KEE-mo-THER-apee) is the treatment of cancer with powerful drugs that kill cancer cells.

* AIDS, or acquired immunodeficiency (ih-myoo-no-dih-FIH-shensee) syndrome, is an infection that severely weakens the immune system; it is caused by the human immunodeficiency virus (HIV).

* HIV, or human immunodeficiency virus (HYOO-mun ih-myoono-dih-FIH-shen-see), is the virus that causes AIDS (acquired immunodeficiency syndrome).

* meningitis (meh-nin-JY-tis) is an inflammation of the meninges, the membranes that surround the brain and the spinal cord. Meningitis is most often caused by infection with a virus or a bacterium.

* miscarriage (MIS-kare-ij) is the end of a pregnancy through the death of the embryo or fetus before birth.

* stillbirth is the birth of a dead fetus.

* vaccination (vak-sih-NAY-shun), also called immunization, is giving, usually by an injection, a preparation of killed or weakened germs, or a part of a germ or product it produces, to prevent or lessen the severity of the disease caused by that germ.

* seizures (SEE-zhurs) are sudden bursts of disorganized electrical activity that interrupt the normal functioning of the brain, often leading to uncontrolled movements in the body and sometimes a temporary change in consciousness.

* abdominal (ab-DAH-mih-nul) refers to the area of the body below the ribs and above the hips that contains the stomach, intestines, and other organs.

* mucus (MYOO-kus) is a thick, slippery substance that lines the insides of many body parts.

* jaundice (JON-dis) is a yellowing of the skin, and sometimes the whites of the eyes, caused by a buildup in the body of bilirubin, a chemical produced in and released by the liver. An increase in bilirubin may indicate disease of the liver or certain blood disorders.

* protozoa (pro-tuh-ZOH-uh) are single-celled microorganisms (tiny organisms), some of which are capable of causing disease in humans.

* diabetes (dye-uh-BEE-teez) is a condition in which the body's pancreas does not produce enough insulin or the body cannot use the insulin it makes effectively, resulting in increased levels of sugar in the blood. This can lead to increased urination, dehydration, weight loss, weakness, and a number of other symptoms and complications related to chemical imbalances within the body.

* cultured (KUL-churd) means subjected to a test in which a sample of fluid or tissue from the body is placed in a dish containing material that supports the growth of certain organisms. Typically, within days the organisms will grow and can be identified.

* dehydration (dee-hi-DRAY-shun) is a condition in which the body is depleted of water, usually caused by excessive and unreplaced loss of body fluids, such as through sweating, vomiting, or diarrhea.

* intravenous fluids (in-tra-VEEnus) are fluids injected directly into a vein.

* paralysis (pah-RAH-luh-sis) is the loss or impairment of the ability to move some part of the body.

* arthritis (ar-THRY-tis) refers to any of several disorders characterized by inflammation of the joints.

* abscesses (AB-seh-sez) are localized or walled-off accumulations of pus caused by infection that can occur anywhere within the body.

* kidney is one of the pair of organs that filter blood and remove waste products and excess water from the body in the form of urine.

* anemia (uh-NEE-me-uh) is a blood condition in which there is a decreased hemoglobin in the blood and, usually, fewer than normal numbers of red blood cells.

Disclaimer:   This information is not a tool for self-diagnosis or a substitute for professional care.

(MLA 8th Edition)