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Gastrointestinal and Hepatobiliary Infections




Viewed in its simplest form, the gastrointestinal tract is a hollow digestive tube that extends through the center of the body from the mouth to the anus. The walls of the tube are lined with a diverse number of epithelial cells that function well at transmembrane secretion and absorption and maintain the barrier that protects the host from microbial pathogens. The barrier consists of the intact mucosal surface and a population of resident immune cells. The primary function of the gastrointestinal system is digestion and nutrient uptake.

The epithelial cells have a relatively short life, with most cells living between 48 and 72 hours. Because of the constant turnover of cells, it is difficult for pathogens to colonize the gastrointestinal tract. However, the disadvantage of the high rate of cell turnover is that the epithelial cells are more susceptible to mutagenic compounds and tumor formation.

All of the liquid and solid material ingested, along with bacteria, is carried through the tube. Bacteria colonize the areas of the tube that offer a suitable environment for growth. Soon after birth, a microbiota is established in each part of the tube. The oral cavity and the colon are at opposite ends of the tube and are heavily colonized with bacteria. The central part of the tube, the stomach, duodenum, jejunum, and the proximal half of the ileum, are lightly colonized.

Each portion of the gastrointestinal tract has special defense mechanisms that protect it from pathogenic microorganisms. When pathogenic microorganisms or their toxins breach these defense mechanisms, disease can occur.


Defense Mechanisms of the Gastrointestinal Tract


The following are some of the major defense mechanisms in the gastrointestinal tract that serve to prevent infection. There are other defense mechanisms, but they will not be discussed here because they are beyond the scope of these lectures.


Factors that Compromise the Gastrointestinal Tract

The gastrointestinal tract is constantly challenged by pathogenic microorganisms that compromise the gastrointestinal tract.


The Table below is an incomplete list of organisms that cause these diseases.

Table GI-1. Microorganisms that Cause Gastrointestinal Diseases and the Site Most Often Affected

Microbial Agent


Site Affected




Corynebacterium diphtheriae



Streptococcus pyogenes



Streptococcus mutans

Dental caries


Anaerobic bacteria

Gingivitis, periodontal disease, dentoalveolar abscess, periodontal abscess, Ludwig’s angina

Gums for all but Ludwig’s angina

Ludwig’s angina: sublingual and submandibular spaces

Helicobacter pylori

Gastritis, peptic ulcer disease

Stomach and duodenum

Staphylococcus aureus, enterotoxin producing

Nausea and vomiting and diarrhea

Increased serotonin release in intestine stimulates vagal afferent neurons

Bacillus cereus

Type 1 with nausea and vomiting

Type 2 with diarrhea

Type 1 uncouples oxidative phosphorylation in liver mitochondria

Type 2 in small intestine

Campylobacter jejuni

Diarrhea, dysentery, and fever


Enterotoxigenic Escherichia coli, Enteropathogenic E coli, Enteroaggregative E coli



Enterohemorrhagic E coli

Diarrhea followed by bloody diarrhea, hemolytic uremic syndrome

Intestine, kidney

Enteroinvasive E coli

Diarrhea occasionally becoming dysentary


Shigella sonnei, S flexneri

Diarrhea followed by dysentery


Microbial Agent


Site Affected




Salmonella enterica

Diarrhea sometimes followed by dysentery.


Salmonella enterica serovar Typhi

Typhoid fever, enteric fever

Intestine, liver, spleen, blood, bone marrow, gallbladder

Salmonella enterica serovar Paratyphi A, Salmonella enterica serovar Schottmuelleri, Salmonella enterica serovar Hirschfeldii

Paratyphoid fever, enteric fever

Intestine, liver, spleen, blood, bone marrow

Clostridium difficile

Diarrhea, pseudomembranous colitis, toxic megacolon





Epstein-Barr virus

Infectious mononucleosis; pharyngitis


Herpes simplex virus types 1 and 2


Gums, mucosa of mouth, lips, esophagus

Human immunodeficiency virus






Caliciviruses (Noroviruses, Sapovirus, Astroviruses)






Hepatitis A, B, C, D, and E viruses






Candida albicans

Pseudomembranous candidiasis (thrush), esophagitis

Mouth, esophagus




Ascaris lumbricoides

Abdominal tenderness diffuse with partial or complete bowel obstruction

Intestine, appendix, bile duct, liver

Cryptosporidium parvum



Cyclospora cayetanensis



Giardia lamblia



Strongyloides stercoralis

Anorexia, weight loss, nausea, chronic diarrhea or constipation, bloating


Entamoeba histolytica



Enterobius vermicularis

Anal pruritus






Despite all of the defense mechanisms that serve to prevent infection in the gastrointestinal tract, there are numerous diseases associated with the gastrointestinal and hepatobiliary systems.

Areas Affected and Manifestations of Diseases


Gastrointestinal diseases are the second most common reason for a patient to see their physician. Diarrhea is one of the most common gastrointestinal diseases among adults. Approximately 270 million cases of diarrhea in adults result in about 600,000 hospitalizations and 3000 deaths annually in the U.S. An etiologic agent is identified in less than 10% of these cases. Most adults have at least one episode of diarrhea each year, and children have an average of two to three episodes per year. Worldwide, diarrhea kills 2,195 children every day—more than AIDS, malaria, and measles combined. Diarrheal diseases account for 1 in 9 child deaths worldwide, making diarrhea the second leading cause of death among children under the age of 5.

A large number of patients with diarrhea acquire the organism that causes their illness while ingesting contaminated food. The Centers for Disease Control and Prevention estimates that each year roughly 1 in 6 Americans (or 48 million people) get sick, 128,000 are hospitalized, and 3,000 die of foodborne diseases.


The pathology associated with a particular gastrointestinal tract disease depends on the site infected or intoxicated. There are two basic mechanisms that infectious agents utilize in causing disease in these systems. One mechanism involves ingesting a preformed toxin that will cause symptoms such as food poisoning. This is called intoxication. The most common cause of food poisoning in the US is due to an enterotoxin produced by Staphylococcus aureus. Symptoms of intoxication usually occur relatively rapidly, with an incubation period as brief as 30 minutes after ingestion of the toxin.

The other mechanism that infectious agents utilize to cause disease in the gastrointestinal tract involves attachment to or infection of the host cells. Some pathogens only attach to the surface of the epithelial cells and produce toxins while attached to the host cell, which causes cell damage or death. This process often results in a watery diarrhea without inflammatory cells, blood in the stools, or fever. After attaching to the cells, other pathogens enter the cells and damage or kill them. Depending on how deep the infection goes, symptoms can vary from a watery diarrhea (gastroenteritis), to bloody mucus-covered stool (dysentery), to invasion of the bloodstream from the intestine (enteric fever). In cases of dysentery, red blood cells and fecal leukocytes are frequently present in the feces and are a good clinical indicator of an invasive inflammatory gastrointestinal tract infection. Symptoms occur about 24–72 hours after ingestion and if the host mounts a significant immune response, patients may have a fever. Note that the incubation period is usually much longer in this process than when the mechanism for causing a disease is intoxication.


Localizing where pathology is occurring in the gastrointestinal tract is essential to knowing how to treat the patient. Many gastrointestinal tract infections are self-limiting whereas others require treatment to prevent severe complications. In many cases, the manifestations observed in the patient can help the physician determine the specific area of the gastrointestinal tract that is affected (e.g., diarrhea usually indicates a patient has an intestinal disease).

Once the affected area of the gastrointestinal tract is identified, procedures (e.g., endoscopy) can be performed to visualize the pathology associated with the disease and samples (e.g., stools, blood) obtained to determine the cause of the disease.

Treatment and Prevention

The treatment and prevention of a particular infection depends on the site of the infection and the pathogen causing the disease. These topics will be discussed in more detail later.

To prevent many gastrointestinal tract infections, patients should be encouraged to maintain good oral hygiene, properly cook and store all food, drink safe water, take special precautions when traveling to countries outside the U.S. Patients should avoid using illegal intravenous drugs, having multiple sexual partners, and drinking excessive amounts of alcohol.

All travelers to countries where diarrheal diseases are common should only drink water that has been boiled or treated with chlorine or iodine and remember that ice is frequently made with contaminated tap water. Freezing and thawing of ice does not kill many of the organisms and is a source of infection for many travelers. Eat only foods that have been thoroughly cooked and are still hot, or consume fruit that can be peeled just before eating. All vegetables should be cooked; salads should never be eaten because vegetables are washed with tap water. Undercooked or raw fish or shellfish should not be eaten; perishable seafood should not be taken from the restaurant. Foods and beverages should not be purchased from street vendors. A simple rule of thumb to follow when traveling overseas is to boil it, cook it, peel it, or forget it!

This handout is divided into 6 sections;

Send comments and mail to Dr. Neal R. Chamberlain,
Revised 2/4/16
©2016 Neal R. Chamberlain, Ph.D., All rights reserved.

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