Viruses, Bacteria, and Parasites in the Digestive Tract

What are viruses, bacteria, and parasites?

Viruses, bacteria, and parasites are living organisms that are found all around us. They exist in water and soil, on the surfaces of foods that we eat and on surfaces that we touch, such as countertops in the bathroom or kitchen. Some bacteria live in and on our bodies and do not cause problems. Other kinds of bacteria (as well as parasites and viruses) can make us quite ill if they invade our bodies. Bacteria and viruses can live outside of the human body (for instance, on a countertop) sometimes for many hours or days. Parasites, however, require a living host in order to survive.

Bacteria and parasites can usually be destroyed with antibiotics. On the other hand, antibiotics cannot kill viruses. Children with viral illnesses can be given medications to make them comfortable, but antibiotics are ineffective against treating these infections.

Bacteria, viruses, and parasites can cause a wide variety of illnesses, and can infect any of the organs of the body. Viruses are often responsible for respiratory illnesses (such as the common cold) and digestive illnesses (such as diarrhea). Bacteria can infect any part of the body, but often cause diarrhea when they invade the digestive tract.

What is diarrhea?

Diarrhea can be caused by a variety of bacteria, viruses, and parasites. Children can also have diarrhea without having an infection, such as when diarrhea is caused by food allergies or as a result of taking medications (such as antibiotics). A child is considered to have diarrhea when the child's bowel movements are both more frequent than usual and looser and more watery than usual.

Children with diarrhea may have additional symptoms including nausea, vomiting, stomach aches, headache, or fever.

How does a child usually come in contact with bacteria, viruses, or parasites that cause diarrhea?

  • When touching the stool of an infected person (such as when touching soiled diapers)

  • When touching an object contaminated with the stool of an infected person, and then ingesting the germs--this usually occurs by touching the mouth with a contaminated hand (can occur at day care centers or at home in areas where diapered babies play)

  • By ingesting contaminated food or water

Why is infection with these organisms a concern?

Viruses, bacteria, and parasites that invade the digestive tract usually cause diarrhea. Large amounts of water are lost with the diarrhea, leading to dehydration in children. Children become dehydrated much quicker than adults, and this can lead to serious problems if fluids are not replaced. Infections caused by parasites and a few types of infections caused by bacteria may also need treatment with medications.

Also, children with a severely weakened immune system are at risk for more serious disease. Symptoms may be more severe and could lead to serious illness. Examples of persons with weakened immune systems include those with HIV/AIDS, cancer and transplant patients who are taking certain immunosuppressive drugs, and those with inherited diseases that affect the immune system.

Common bacteria, viruses, and parasites that cause diarrhea



E. coli


Escherichia coli O157:H7 is just one of the hundreds of strains of the bacterium Escherichia coli (E. coli). Most strains of E. coli are harmless and live in the intestines of healthy humans and animals. E. coli, however, produces a powerful toxin that can cause a severe infection. (The combination of letters and numbers in the name of the bacterium refers to the specific markers found on its surface and distinguishes it from other types of E. coli.)

The CDC recognizes E. coli as a foodborne illness. Infection often leads to bloody diarrhea, stomach cramps, vomiting, and fever.


Most E. coli illness has been associated with eating undercooked, contaminated ground beef. E. coli bacteria live in the intestines of healthy cattle and, although the number of organisms required to cause disease is not known, it is suspected to be very small. Meat becomes contaminated during slaughter, and organisms can be thoroughly mixed into beef when it is ground. Contaminated beef looks and smells normal. Other ways to transmit E. coli include:

  • Person-to-person contact in families and in child-care and other institutional-care centers can also be places where the transmission of the bacteria can occur.

  • Bacteria present on a cow's udders, or on equipment, may get into raw milk causing the infection.

  • Infection may also occur after swimming in or drinking sewage-contaminated water.

  • It has been confirmed that unpasteurized juices, such as apple cider, may also cause the infection.

Bacteria in diarrhea stools of infected people can be passed from one person to another if hygiene or handwashing habits are inadequate. This is particularly likely among toddlers who are not toilet trained. Family members and playmates of these children are at high risk of becoming infected.

Young children typically shed the organism in their feces for a week or two after their illness resolves.


CDC recommendations for prevention of the infection include:

  • Cook all ground beef or hamburger thoroughly. Make sure that the cooked meat is gray or brown throughout (not pink), any juices run clear, and the inside is hot.

  • Using a digital instant-read meat thermometer, the temperature of the meat should reach a minimum of 160 degrees F.

  • If you are served an undercooked hamburger in a restaurant, send it back.

  • Consume only pasteurized milk and milk products. Avoid raw milk.

  • Consume only pasteurized juices and ciders.

  • Make sure that infected people, especially children, wash their hands carefully and frequently with soap to reduce the risk of spreading the infection.

  • Drink municipal water that has been treated with adequate levels of chlorine, or other effective disinfectants.

  • Avoid swallowing lake or pool water while swimming.

  • Wash hands thoroughly after using the toilet.

  • People with diarrhea should not:

    • Swim in public pools or lakes

    • Bathe with others

    • Prepare food for others




Salmonella is a bacteria that infects the intestines and causes diarrhea, fever, and abdominal cramps 12 to 72 hours after infection. Over 1 million cases of salmonella infection are reported in the United States each year. The illness usually lasts four to seven days and most people recover without treatment.

However, in some people the diarrhea may be so severe that the patient needs to be hospitalized. In those patients, the salmonella infection may spread from the intestines to the blood stream and then to other body sites and can cause death unless the person is treated promptly with antibiotics. Infants and those with impaired immune systems are more likely to have a severe illness.


Salmonella may be spread by:

  • Eating raw foods contaminated with animal feces.
    Contaminated foods usually look and smell normal. Contaminated foods are often of animal origin, such as beef, poultry, milk, or eggs, but all foods, including some unwashed fruits and vegetables, and peanut butter, may become contaminated. Many raw foods of animal origin are frequently contaminated, but fortunately, thorough cooking kills salmonella.

  • Handling reptiles. Reptiles (such as iguanas and turtles) are particularly likely to harbor Salmonella and people should always wash their hands immediately after handling a reptile, even if the reptile is healthy. Adults should also be careful that children wash their hands after handling a reptile.


Since foods of animal origin pose the greatest threat of salmonella contamination, do not eat raw or undercooked eggs, poultry, or meats. Remember that some sauces and desserts use raw eggs in their preparation, so be cautious of these, particularly in foreign countries. Also, follow these recommendations by the CDC:

  • Make sure poultry and meat, including hamburgers, are well-cooked, not pink in the middle.

  • Do not consume raw or unpasteurized milk or other dairy products.

  • Thoroughly wash produce before eating it.

  • Avoid cross-contamination of foods. Uncooked meats should be kept separate from produce, cooked foods, and ready-to-eat foods.

  • All utensils, including cutting boards, knives, counters, etc., should be thoroughly washed after handling uncooked foods.

  • Thoroughly wash hands before handling foods and between handling different food items.

  • Thoroughly wash hands after contact with feces.

  • Thoroughly wash hands after handling any reptiles, since reptiles are particularly likely to have Salmonella.





Rotavirus is the most common cause of severe diarrhea among children, resulting in the death of over 500,000 children annually worldwide.

In the United States, the disease occurs most often in the winter, with annual epidemics occurring from December to June. The highest rates of illness occur among infants and young children, and most children in the United States are infected by 5 years of age. Adults can also be infected, though disease tends to be mild.

The incubation period for rotavirus disease is approximately two days. The disease is characterized by vomiting and watery diarrhea for three to eight days, and fever and abdominal pain occur frequently. Immunity after infection is incomplete, but repeat infections tend to be less severe than the original infection.


Rotavirus may be spread:

  • Through accidentally swallowing the virus picked up from surfaces contaminated with stool from an infected person, such as toys, bathroom fixtures, changing tables, and diaper pails.

  • Through ingestion of contaminated food, or contaminated water, such as the type of water found in a public swimming pool.


A rotavirus vaccine that was approved by the FDA in 1998 was pulled from the market in 1999 because of an association between the vaccine and an increased risk for intussusception (form of bowel blockage) in infants aged one year or younger. However, no direct link was established to the vaccine as a cause of intussusception.

A new rotavirus vaccine was approved by the FDA in 2006. The risk for intussusception with the new vaccine was evaluated in a large clinical trial of over 30,000 children, and no increased risk was found. The manufacturer of the vaccine will continue to closely monitor the vaccine's safety in additional clinical studies. Some, but not all, studies indicate there may be a very small risk of intussusception, but the benefits outweigh the possible risks and the CDC continues to recommend routine rotovirus vaccination of infants. 

Handwashing is a very important means of preventing the spread of rotavirus. Careful and frequent handwashing can prevent the spread of infection to other people.

The CDC recommends:

  • Adults should wash their hands after using the toilet, after helping a child use the toilet, after diapering a child, and before preparing, serving, or eating food.

  • Children should wash their hands after using the toilet, after having their diapers changed (an adult should wash infant's or small child's hands), and before eating snacks or meals.

  • Toys, bathrooms, and food preparation surfaces are disinfected frequently, especially if a sick child has been in the home.

  • Use diapers with waterproof outer covers that can contain liquid stool or urine, or use plastic pants.

  • Make sure that children wear clothes over diapers.





During the past 15 years, Giardia lamblia has become recognized as one of the most common waterborne diseases in humans in the United States. Giardia is a tiny parasite that lives in the intestines of people and animals. The parasite is passed in the bowel movement of an infected person or animal. It is found in every region of the United States and throughout the world.

Diaper-aged children who attend day care centers, international travelers, hikers, campers, and others who drink untreated water from contaminated sources, are most at risk for developing infection with Giardia. Several community-wide outbreaks of infection have been linked to drinking municipal water contaminated with Giardia.


People become infected after accidentally swallowing the parasite. Giardia may be found in soil, food, water, or on surfaces.

Some of the ways people can become infected with Giardia include:

  • Eating uncooked food contaminated with Giardia.

  • Swallowing water from swimming pools, lakes, rivers, springs, ponds, or streams contaminated with sewage or feces from humans or animals.

  • Accidentally swallowing the parasite picked up from surfaces contaminated with stool from an infected person, such as toys, bathroom fixtures, changing tables, diaper pails.


The CDC recommends:

  • Washing hands with soap and water after using the toilet, changing diapers, and before handling food.

  • Washing and peeling all raw vegetables and fruits before eating.

  • Avoiding drinking water from lakes, rivers, springs, ponds, or streams unless it has been filtered and chemically treated.

  • Boiling drinking water for one minute to kill the Giardia parasite. This will ensure safe drinking water during community-wide outbreaks caused by contaminated drinking water.

  • When camping or traveling in countries where the water supply may be unsafe, avoid drinking unboiled tap water and avoid uncooked foods washed with unboiled tap water. Bottled or canned carbonated beverages, seltzers, pasteurized fruit drinks, and steaming hot coffee and tea, are safe to drink.

If your child has Giardia, avoid swimming in pools for two weeks after the diarrhea or loose stools have cleared. Giardia is fairly chlorine resistant and is passed in the stools of infected people for several weeks after they no longer have symptoms.




Cryptosporidium, often referred to as "crypto," is a tiny parasite that can live in the intestines of humans and animals. The parasite is protected by an outer shell that allows it to survive outside the body for long periods of time and makes it very resistant to chlorine disinfection.


Cryptosporidium may be spread by:

  • Accidentally swallowing anything that has come in contact with the stool of a person or animal

  • Swallowing contaminated water from swimming pools, hot tubs, lakes, rivers, springs, ponds, or streams contaminated with sewage or feces from humans or animals.

  • Eating uncooked contaminated food.

  • Picking cryptosporidium up from surfaces contaminated with stool from an infected person (such as toys, bathroom fixtures, changing tables, and diaper pails).


The CDC recommends:

  • Your child should wash their hands with soap and water after using the toilet, changing diapers, and before eating or helping prepare food.

  • Avoid water or food that may be contaminated.

  • Washing and/or peeling all raw vegetables and fruits before giving them to your child to eat.

  • Avoiding drinking water from lakes, rivers, springs, ponds, or streams unless it has been filtered and chemically treated.

  • Boiling drinking water for one minute to kill the cryptosporidium parasite. This will ensure safe drinking water during community-wide outbreaks caused by contaminated drinking water.

  • When camping or traveling in countries where the water supply may be unsafe, avoid drinking unboiled tap water and avoid uncooked foods washed with unboiled tap water.

  • Avoiding swimming in pools if your child has had cryptosporidium and for at least two weeks after diarrhea stops. Crypto can be passed in the stool and contaminate water for several weeks after your child no longer has symptoms. This has resulted in several outbreaks of cryptosporidium among pool users. Crypto can survive in chlorinated pools for several days.

Can my child get germs from food?

Almost everyone has experienced a foodborne illness at some point in time. Contrary to popular belief, foodborne illnesses can occur when food is prepared at a restaurant or at home. If food is handled and prepared safely, most illnesses can be avoided.

All food may contain some natural bacteria, and improper storage or handling gives the bacteria a chance to grow. Also, food can be contaminated with bacteria from other sources that can make you ill. Contaminated or unclean food can be very dangerous, especially to children. According to the CDC, each year foodborne illnesses kill 3,000 people of all ages. They also cause fever, stomach cramps, vomiting, and diarrhea in an estimated 48 million Americans.

Four major tips recommended by the CDC to prevent contaminating food

  • Use caution when buying food:

    • When at the grocery store, pick up perishable food such as meat, eggs, and milk at the very end of your shopping, so they will stay cool.

    • Take food home right away so that it does not spoil in a hot car.

    • Avoid raw or unpasteurized milk.

    • Because eggs, meat, seafood, and poultry are most likely to contain bacteria, do not allow their juices to drip on other food.

  • Store food properly:

    • Store eggs, raw meat, poultry, and seafood in the refrigerator.

    • A refrigerator should be set between 32 degrees F and 40 degrees F.

    • A freezer should be set at or below 0 degrees F.

    • Regularly clean and disinfect the refrigerator and freezer.

    • Use containers to prevent contaminating other foods or kitchen surfaces. Do not store food uncovered in the refrigerator or freezer.

  • Use special precautions when preparing and cooking food:

    • Wash your hands and clean and disinfect kitchen surfaces before, during, and after handling, cooking, and serving food.

    • Defrost frozen food on a plate either in the refrigerator or in a microwave, but not on the counter.

    • Cook food immediately after defrosting.

    • Use different dishes and utensils for raw foods than you use for cooked foods.

    • Wash raw fruits and vegetables before eating them.

  • Cool and promptly store leftovers after food has been served:

    • Because harmful bacteria grow at room temperature, keep hot food hot and keep cold food cold. This is especially important during picnics and buffets.

    • Do not leave perishable foods out for more than two hours.

    • Promptly refrigerate or freeze leftovers in shallow containers or wrapped tightly in bags.