Viruses, Bacteria and Parasites in the Digestive Tract Symptoms & Causes

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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. 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?

Your child is considered to have diarrhea when her bowel movements are both more frequent and looser and more watery than usual. Your child may have additional symptoms including nausea, vomiting, stomach aches, headache or fever. Some common causes of diarrhea include:

  • a variety of bacteria, viruses and parasites
  • food allergies
  • a result of taking medications (such as antibiotics)

How do you come in contact with bacteria, viruses or parasites that cause diarrhea?

Common ways your child my pick up a bacteria, virus or parasite include:

  • touching the stool of an infected person (such as when touching soiled diapers)
  • touching an object contaminated with the stool of an infected person and then ingesting the germs
  • by ingesting contaminated food or water

Why is diarrhea a concern?

Large amounts of water are lost with the diarrhea, which can cause your child to be dehydrated. Children become dehydrated much quicker than adults, and this can lead to serious problems if fluids are not replaced and the infection treated. If your child has a severely weakened immune system, she is at risk for more serious complications. Examples of children who are high risk include:

  • if your child has HIV/AIDS
  • if your child has cancer or received a transplant and is taking certain immunosuppressive drugs
  • if your child has an inherited disease that affects the immune system

What kinds of bacteria can cause diarrhea?

Two types of bacteria commonly cause diarrhea, including E. coli (a strain of bacteria that produces a powerful toxin that can cause a severe infection) and Salmonella (a bacteria that infects the intestines and causes diarrhea, fever, and abdominal cramps 12 to 72 hours after infection).

E. coli

  • Infection often leads to bloody diarrhea.
  • Illness has been associated with eating undercooked, contaminated ground beef. Meat becomes contaminated during slaughter, and organisms can be thoroughly mixed into beef when it is ground. Contaminated beef looks and smells normal.
  • It can be transmitted person-to-person.
  • The bacteria may get into raw milk causing the infection.
  • Infection may also occur after swimming in or drinking sewage-contaminated water.
  • Unpasteurized juices, such as apple cider, may also cause the infection.
  • Bacteria in diarrhea stools of infected persons can be passed from one person to another if hygiene or handwashing habits are not thorough.

Ways to prevent E. Coli include:

  • Cook all ground beef thoroughly (the temperature of the meat should reach a minimum of 160 F).
  • Consume only pasteurized juices, ciders, milk and milk products; avoid raw milk
  • Wash your child's hands carefully and frequently with soap.
  • Avoid swallowing lake or pool water while swimming.


  • Illness usually lasts four to seven days and most persons recover without treatment
  • In some cases 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 sever illness.
  • Can be caught by eating raw foods (such as beef, poultry, milk, eggs or vegetables) contaminated with animal feces.
  • Thorough cooking kills the bacteria.
  • It can also be caught by handling reptiles (such as iguanas and turtles)

Ways to prevent Salmonella include:

  • Don't eat raw or undercooked eggs, poultry or meats.
  • Don't consume raw or unpasteurized milk or other dairy products.
  • Thoroughly wash produce before eating it.
  • Keep uncooked meats separate from produce, cooked foods and ready-to-eat foods.
  • Thoroughly wash all utensils, including cutting boards, knives, counters 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.

What kinds of viruses cause diarrhea?

The most common cause of severe diarrhea among children is the virus rotavirus. More specific details include:


  • Symptoms include vomiting and watery diarrhea for three to eight days, and fever and abdominal pain occur frequently.
  • It can be caught by accidentally swallowing the virus picked up from surfaces contaminated with stool from an infected person, such as toys, bathroom fixtures, changing tables and diapers.
  • It can be caught by consuming contaminated food, or contaminated water, such as the type of water found in a public swimming pool.

The best ways to prevent rotavirus includes:

  • Proper hygiene, like hand washing and cleaning surfaces (such as toys and door knobs), helps.
  • Two brands of vaccines that can help prevent Rotavirus infections, given when your child is 2 months, 4 months and potentially 6 months old.

What are the most common parasites that cause diarrhea?

The two parasites that usually cause infection include Giardia and Cryptosporidium. More specific details on each include:


  • The parasite is passed in the bowel movement of an infected person or animal.
  • Diaper-aged children who attend day care centers, international travelers, hikers, campers and others who drink untreated water from contaminated sources most at risk.
  • Community-wide outbreaks of infection linked to drinking municipal water contaminated with the parasite.

The best ways to prevent Giardia include:

  • 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
  • when camping or traveling in countries where the water supply may be unsafe,  avoiding drinking unboiled tap water


  • often referred to as "crypto"
  • 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
  • can be caught by accidentally swallowing anything that has come in contact with the stool of a person or animal (such as water from swimming pools, hot tubs, lakes, rivers, springs, ponds, or streams contaminated with sewage or feces from humans or animals)
  • can also be caught by eating uncooked contaminated food and from coming in contact with surfaces contaminated with stool from an infected person (such as toys, bathroom fixtures, changing tables, and diaper pails)

The best ways to prevent Cryptosporidium include:

  • 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
  • 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.

Are bacteria, parasites, and viruses common?

Infections caused by bacteria, parasites, and viruses are relatively common.

What do I do if my child has diarrhea?

If diarrhea is caused by bacteria or parasites, it can usually be treated with antibiotics. Antibiotics cannot kill viruses. Do not use anti-diarrheal medications unless recommended by your child's doctor. No matter what caused the diarrhea, you should make sure your child stays hydrated by drinking plenty of fluids. If your child does have diarrhea, she should not:

  • swim in public pools or lakes
  • bathe with others
  • prepare food for others

Can my child get germs from food?

All food may contain some natural bacteria, and improper storage or handling gives the bacteria a chance to grow. Food can also be contaminated with bacteria from other sources that can make you ill. According to the Centers for Disease Control and Prevention (CDC), each year food-borne illnesses kill up to 9,000 people of all ages. They also cause fever, stomach cramps, vomiting, and diarrhea in almost 80 million Americans, or about one in three people.

To prevent contaminating food, the Centers for Disease Control and Prevention (CDC) recommends:

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.
  • Refrigerator should be set at 40 F or cooler.
  • Freezer should be set at 0 F or cooler.
  • 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 when 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

  • Harmful bacteria grow at room temperature, keep hot food hot at 140 F or higher, and keep cold food cold at 40 F or cooler.
  • Don't leave perishable foods out for more than two hours.
  • Promptly refrigerate or freeze leftovers in shallow containers or wrapped tightly in bags.
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