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 you. They are in water and soil. They are on the surfaces of foods that we eat. They are also on surfaces that you touch, such as countertops in the bathroom or kitchen. Some bacteria live in and on your body and don’t cause problems. Other kinds of bacteria (as well as parasites and viruses) can make you very sick if they get inside your body. Bacteria and viruses can live outside of the human body (such as on a countertop) sometimes for many hours or days. But parasites need a living host to survive.

Bacteria and parasites can often be killed with antibiotics. But these medicines can’t kill viruses. Children sick from a virus can be given medicines to make them feel better. But antibiotics don’t fight viral infections.

Bacteria, viruses, and parasites can cause many illnesses. They can infect any organ in the body. Viruses are often the cause of respiratory illnesses, such as the common cold, and digestive illnesses, such as diarrhea. Bacteria can infect any part of the body. But they often cause diarrhea when they get into the digestive tract.

What is diarrhea?

Diarrhea can be caused by many types of bacteria, viruses, and parasites. Children can also have diarrhea without having an infection. For example, diarrhea can be caused by food allergies or by certain medicines such as antibiotics. A child has diarrhea when bowel movements are loose and watery, and more frequent than normal.

Children with diarrhea may have other symptoms, such as:

  • Nausea

  • Vomiting

  • Stomach aches

  • Headache

  • Fever


How does a child usually come in contact with germs that cause diarrhea?

  • By touching the stool of an infected person, such as when touching dirty diapers

  • By touching an object contaminated with the stool of an infected person, and then eating the germs. This often happens by touching the mouth with the contaminated hand. This can occur at daycare centers or at home in places where diapered babies play.

  • By eating or drinking contaminated food or water

Why is infection with these germs a concern?

Viruses, bacteria, and parasites that get inside the digestive tract often cause diarrhea. Large amounts of water are lost with the diarrhea. This may cause fluid loss (dehydration) in children. Children become dehydrated much quicker than adults. This can cause 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 medicines.

Also, children with a severely weakened immune system are at risk for more serious disease. Symptoms may be worse. They could lead to serious illness. Children with weakened immune systems include those who:

  • Have HIV/AIDS

  • Have cancer or have had a transplant, and are taking certain immunosuppressive medicines

  • Have inherited diseases that affect the immune system

Common bacteria, viruses, and parasites that cause diarrhea


E. coli



There are hundreds of different types, or strains, of the bacteria E. coli (Escherichia coli). Most of these are harmless and live in the intestines of healthy people and animals. But some strains of E. coli make a strong toxin that can cause a severe infection.

The CDC recognizes E. coli as a foodborne illness. This means it is spread by consuming contaminated food or drink. Infection often leads to bloody diarrhea, stomach cramps, vomiting, and fever.


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

  • Person-to-person contact in families and in child-care and other institutional-care centers

  • Bacteria present on a cow's udders, or on equipment, getting into raw milk

  • Infection after swimming in or drinking sewage-contaminated water

  • Drinking unpasteurized juices, such as apple cider

Bacteria in diarrhea stools of infected people can be passed from one person to another if hygiene or handwashing habits are not good. This is very likely among toddlers who are not toilet trained. Family members and playmates of these children are at high risk of getting infected. Young children often pass the organism in their stool for a week or 2 after their illness goes away.


CDC recommends these steps to prevent the infection:

  • 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.

  • Use a digital instant-read meat thermometer. The temperature of the meat should reach a minimum of 160°F.

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

  • Drink only pasteurized milk and milk products. Don't drink raw milk.

  • Drink only pasteurized juices and ciders.

  • Check that infected people, especially children, wash their hands well and often 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.

  • Try not to swallow lake or pool water while swimming.

  • Wash hands well 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. It causes diarrhea, fever, and stomach cramps 12 to 72 hours after infection. Over 1 million cases of salmonella infection occur in the U.S. each year. The illness often lasts 4 to 7 days. Most people get better without treatment.

But in some people, the diarrhea may be so severe that they need to stay in the hospital. In these people, the salmonella infection may spread from the intestines to the bloodstream and then to other body sites. It can cause death unless the person is treated right away with antibiotics. Babies and those with a weakened immune system are more likely to have a severe illness.


Salmonella may be spread by:

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

  • Handling reptiles. Reptiles such as iguanas and turtles are very likely to have Salmonella. People should always wash their hands right away after handling a reptile, even if the reptile is healthy. Adults should also be careful that children wash their hands after handling a reptile.


Don't eat raw or undercooked eggs, poultry, or meats. Remember that some sauces and desserts use raw eggs to make them. So be cautious of these, particularly in foreign countries. Also, follow these tips by the CDC:

  • Check that poultry and meat, including hamburgers, are well-cooked. They should not be pink in the middle.

  • Don't drink or eat raw or unpasteurized milk or other dairy products.

  • Thoroughly wash produce before eating it.

  • Don't cross-contaminate foods. Uncooked meats should be kept separate from produce, cooked foods, and ready-to-eat foods.

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

  • Wash hands well before handling foods and between handling different food items.

  • Wash hands well after contact with feces.

  • Wash hands well after handling any reptiles. Reptiles are very likely to have Salmonella.





Rotavirus is the most common cause of severe diarrhea among children. It results in the death of over 500,000 children each year worldwide.

In the U.S., the disease occurs most often in the winter. Yearly epidemics occur from December to June. The highest rates of illness occur among infants and young children. Most children in the U.S. are infected by 5 years of age. Adults can also be infected. But the disease tends to be mild.

The incubation period for rotavirus disease is about 2 days. The disease causes vomiting and watery diarrhea for 3 to 8 days. Fever and stomach pain occur often. 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.


Two rotavirus vaccines are currently used in babies in the U.S. Both vaccines are given by mouth, not by a shot. Talk with your child’s healthcare provider about which shot is best for your baby.

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.

  • Have children 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 often, especially if a sick child has been in the home.

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

  • Have children wear clothes over diapers.





During the past 15 years, Giardia lamblia has become one of the most common waterborne diseases in humans in the U.S. 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 part of the U.S. and throughout the world.

Diaper-aged children who go to daycare centers, international travelers, hikers, campers, and others who drink untreated water from contaminated sources, are most at risk for getting infected with Giardia. Several community-wide outbreaks of infection have been linked to drinking municipal water tainted 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 get Giardia are:

  • 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, and diaper pails


The CDC advises:

  • 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

  • Not drinking water from lakes, rivers, springs, ponds, or streams unless it has been filtered and chemically treated

  • Boiling drinking water for 1 minute to kill the Giardia parasite. This will ensure safe drinking water during community-wide outbreaks caused by contaminated drinking water

  • Not drinking unboiled tap water and not eating uncooked foods washed with unboiled tap water when camping or traveling in countries where the water supply may be unsafe. Bottled or canned carbonated drinks, seltzers, pasteurized fruit drinks, and steaming hot coffee and tea are safe to drink.

If your child has Giardia, don't swim in pools for 2 weeks after the diarrhea or loose stools have cleared. Giardia is fairly chlorine resistant. It is passed in the stools of infected people for several weeks after they no longer have symptoms.





Cryptosporidium (crypto) is a tiny parasite that can live in the intestines of humans and animals. The parasite is protected by an outer shell that lets it survive outside the body for long periods of time. It is 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 crypto up from surfaces contaminated with stool from an infected person such as toys, bathroom fixtures, changing tables, and diaper pails


The CDC advises:

  • Washing hands with soap and water after using the toilet, changing diapers, and before eating or helping prepare food

  • Staying away from water or food that may be contaminated

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

  • Not drinking water from lakes, rivers, springs, ponds, or streams unless it has been filtered and chemically treated

  • Boiling drinking water for 1 minute to kill the parasite. This will ensure safe drinking water during community-wide outbreaks caused by contaminated drinking water.

  • Not drinking unboiled tap water and not eating uncooked foods washed with unboiled tap water when camping or traveling in countries where the water supply may be unsafe

  • Not swimming in pools if your child has had crypto and for at least 2 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 crypto among pool users. Crypto can survive in chlorinated pools for several days.

Can my child get germs from food?

Almost everyone has had a foodborne illness at one time. These illnesses can happen when food is made at a restaurant or at home. If food is handled and prepared safely, most illnesses can be avoided.

All food may have some natural bacteria. Not storing or handling ir right gives the bacteria a chance to grow. Food can also be contaminated with bacteria from other sources that can make you ill. Contaminated or unclean food can be very unsafe, especially to children. Each year, foodborne illnesses kill 3,000 people of all ages. They also cause fever, stomach cramps, vomiting, and diarrhea in about 48 million Americans.

Tips from the CDC to prevent food contamination

Be careful when buying food

  • When at the grocery store, pick up foods that can go bad (such as meat, eggs, and milk) at the very end of your shopping trip. This helps them stay cool.

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

  • Stay away from raw or unpasteurized milk.

  • Eggs, meat, seafood, and poultry are most likely to have bacteria. Don't let their juices drip on other food.

Store food the right way

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

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

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

  • Regularly clean and disinfect your refrigerator and freezer.

  • Use containers to prevent contaminating other foods or kitchen surfaces. Don't 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 right away 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.

  • Don't leave foods that can go bad out for more than 2 hours.

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

Online Medical Reviewer: Jen Lehrer MD
Online Medical Reviewer: L Renee Watson MSN RN
Online Medical Reviewer: Marianne Fraser MSN RN
Date Last Reviewed: 8/1/2023
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