Infections of the Gastrointestinal System

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Infections of the Gastrointestinal System



Throughout recorded history diseases such as cholera, dysentery, and typhoid fever have firmly established their place in the annals of human suffering. These fall into a large grouping of diseases known collectively as gastrointestinal/digestive system diseases or diseases of the upper and/or lower alimentary systems. These diseases are caused by a wide range of organisms including bacteria, viruses, fungi, protozoans, and helminths. They can be as mild as an upset stomach or, in extreme cases, cause the victim’s death.

The history of this group of diseases also includes the interesting story of Mary Mallon, a cook living in New York in the early 1900s (see Medical Highlights: Asymptomatic Disease Carriers: Typhoid Mary). Also, during the American Civil War, Willie Lincoln, the beloved son of Abraham and Mary Lincoln, died from typhoid fever, probably contracted from the water supply of the White House, which came untreated from the Potomac River.

The actual mechanisms of pathogenicity are also varied and can be as subtle as a simple case of a parasite robbing the host of nutrients or as complex as the infection pathway of the bacteria Listeria monocytogenes. The diversity of these organisms and their effects on the human digestive system makes them a significant concern in the area of public health.


Whether studying the cholera epidemics that occurred throughout the 1800s here in the United States, which claimed more than 200,000 lives, or a severe diarrhea epidemic that left more than 1500 dead in the Congo in only a 3-week period in 1997, the significant impact of gastrointestinal diseases can easily be demonstrated.

Today, with threats of terrorism in the United States and abroad, the potential of microorganisms as bioweapons is taken seriously. In addition to the widely publicized “anthrax letters” sent to the U.S. Senate starting on September 18 of 2001, in 1984 a cult in Oregon sprayed Salmonella on food at a restaurant salad bar in an attempt to sway a local election by sending the voting residents to hospital beds instead of voting booths. Recent recalls of food products ranging from peanut butter to spinach to beef, which contained pathogens affecting primarily the gastrointestinal system, are further examples of how these microorganisms can impact society. Contaminated products adversely affect public health and also cause serious economic problems in the form of massive recalls and legal actions generated by victims of the pathogen-tainted products.


As long as human beings consume water and naturally grown food, there will be an interaction between microbes and the human digestive system. Most of these will be harmless. Improvements in food processing and handling as well as advances in waste management and attention to personal and public hygiene have gone a long way toward preventing and controlling diseases of the digestive system. Advances such as food irradiation show promise in improving the quality of marketed food products. Recently, products that can improve the body’s defenses against microorganisms that target the gastrointestinal system have appeared on the market. For example, a yogurt product containing a culture of bacteria that is normally present in the intestine has shown some promise in assisting the body’s immune response to potential pathogens.


The gastrointestinal (GI) tract is a common and easily accessible portal of entry for microbes or their toxins, with the ability to cause infection, inflammation, and/or disease. Foodborne diseases are a major concern worldwide. Contaminated food, water, and fomites, if they gain access through the fecal–oral route, all are capable of infecting the gastrointestinal system. Moreover, microbial infections and diseases of the gastrointestinal tract are the second most common cause of illnesses in the United States, with respiratory illnesses being the most common. A summary of organisms causing disease of the digestive system is provided in Table 12.1.

TABLE 12.1

Summary of Disease-causing Organisms in the Digestive System

Organism Source Symptoms Treatment
Oral Cavity: Bacteria
Actinomyces Normal flora Periodontal disease, dental caries Brushing, flossing, fluoride; limit sugars
Fusobacterium nucleatum Normal flora Pulmonary infections/abscesses; trench mouth Brushing, flossing, fluoride; limit sugars; penicillin for infections
Lactobacillus Normal flora Dental caries Brushing, flossing, fluoride; limit sugars

Normal flora Dental caries Brushing, flossing, fluoride; limit sugars Treponema sp. Contaminated food or water; poor oral/dental hygiene Fever, bleeding and painful gums, foul odor (trench mouth) Metronidazole, penicillin, azithromycin Veillonella Normal flora Dental caries Penicillins Oral Cavity: Viruses Paramyxovirus family: Mumps virus Salivary and respiratory secretions Swelling of parotid glands, fever, loss of appetite, headache, damage to reproductive organs in patients past puberty Mumps vaccine for prevention; no antiviral therapy available Herpes simplex virus Direct contact, fomites, contaminated food or water Blisters/lesions of mouth or throat, fever Acyclovir Oral Cavity: Fungi Candida albicans Normal flora of lower GI tract Nausea, vomiting, pustules on tongue or in throat, skin rash, heart valve damage Amphotericin B and fluconazole Gastrointestinal Tract: Bacteria Bacillus cereus Contaminated food Nausea, diarrhea, vomiting No recommended antibiotic treatment; fluid replacement Bacteroides Normal flora Diarrhea, fever Clindamycin Campylobacter jejuni Contaminated food Fever, abdominal pain No recommended antibiotic treatment, erythromycin used in severe cases; fluid replacement Campylobacter fetus Contaminated food Bloody diarrhea No recommended antibiotic treatment; erythromycin used in severe cases; fluid replacement Clostridium perfringens Contaminated food Abdominal pain, diarrhea Electrolyte/fluid replacement Clostridium botulinum Contaminated food Loss of muscle control, slurring of speech, difficulty in swallowing and/or breathing, eventual muscle paralysis Botulism antitoxin, artificial respirator Clostridium difficile Contaminated food Colitis, nausea, vomiting Clindamycin Escherichia coli Contaminated food Nausea, diarrhea; certain strains will cause intestinal bleeding Fluid replacement; gentamicin, polymyxin; fluoroquinolone and bismuth preparations help prevent E. coli gastroenteritis Helicobacter pylori Contaminated food or water Abdominal pain, vomiting, belching, bleeding if ulcers form Combination of two antibiotics (metronidazole, tetracycline, amoxicillin, or clarithromycin) plus medication to reduce or suppress stomach acid Salmonella enteritidis Contaminated food Fever, nausea, cramps, diarrhea No recommended antibiotic treatment unless it invades other tissue or blood; fluid replacement Salmonella typhi Contaminated food Fever, continual headache, nausea, cramps, diarrhea Vaccine available Contaminated food Nausea, cramps, intestinal bleeding (S. dysenteriae only), diarrhea Ampicillin, co-trimoxazole; fluid replacement Staphylococcus aureus Contaminated food, direct contact Nausea, cramps, diarrhea   Vibrio cholerae Contaminated food or water Vomiting, muscle cramps, severe watery diarrhea Preventive vaccine; rapid fluid and electrolyte replacement Gastrointestinal Tract: Viruses Rotaviruses Contaminated food or water Vomiting, slight fever, watery diarrhea No antiviral treatment; fluid replacement Hepatitis A, E Contaminated food or water Nausea, abdominal pain, dark urine, jaundice Vaccine for type A Norwalk virus Contaminated food or water Nausea, vomiting No vaccine, no antiviral treatment Gastrointestinal Tract: Fungi Aspergillus flavus Contaminated food, usually peanuts Liver damage (cirrhosis) Amphotericin B, voriconazole Claviceps purpurea Contaminated food, usually cereal grains or mushrooms Reduced blood flow to extremities, causing gangrene; hallucinations, muscle spasms, and seizures Nifedipine for spasms, seizures—drug detoxification protocol Gastrointestinal Tract: Protozoa Balantidium coli Contaminated food or water Nausea, weakness, weight loss, abdominal pain, diarrhea, vomiting Tetracycline, iodoquinol, metronidazole Cryptosporidium parvum Contaminated food or water, oral–fecal contamination Nausea, weakness, weight loss, abdominal pain, persistent diarrhea, vomiting Spiramycin, nitazoxanide for children from 1 to 11 yr old Entamoeba histolytica Contaminated food or water Nausea, weakness, weight loss, abdominal pain, diarrhea, vomiting, bloody stool Metronidazole plus iodoquinol, paromomycin Giardia lamblia Contaminated water Malaise, nausea, weakness, weight loss, cramps, diarrhea Metronidazole, furazolidone, tinidazole, quinacrine Gastrointestinal Tract: Helminths Taenia saginata (tapeworm) Ingestion of contaminated meat Vague abdominal discomfort, few symptoms if any, anemia Niclosamide (praziquantel, paromomycin, or quinacrine) Echinococcus granulosus Ingestion of eggs of organism found in soil, dust, food, water, clothing, etc. Formation of hydatid cysts Surgical removal of cysts; mebendazole, albendazole Enterobius vermicularis (pinworm) Ingestion of eggs of organism found in soil, dust, food, water, clothing, air, etc. Itching of anal region, restlessness, irritability, poor sleep, nervousness Pyrantel pamoate, mebendazole Necator americanus (hookworm) Contact with contaminated soil Usually no symptoms, sometimes a cough, shortness of breath, diarrhea, nausea, vomiting; anemia can result in mental retardation in children Mebendazole, pyrantel pamoate Ascaris lumbricoides Ingestion of eggs of organism found in soil, dust, food, water, clothing, etc. Usually no symptoms, occasional bouts with fever, trouble breathing, coughing, and wheezing Mebendazole, piperazine Trichinella spiralis Ingestion of contaminated meat Abdominal pain, diarrhea, fever, muscle pain, swelling around the eyes, rash Mebendazole, steroids with thiabendazole Trichuris trichiura (whipworm) Fecal–oral route Small numbers—asymptomatic; large numbers—abdominal pain, weakness, bloody diarrhea, weight loss Mebendazole



The GI tract, also referred to as the digestive tract, is a tubelike structure starting at the oral cavity (mouth); proceeding to the pharynx, esophagus, stomach, small intestine, and large intestine; and terminating at the anus (Box 12.1). Together with its accessory organs, the biological function of the digestive system (Figure 12.1) is to digest and absorb nutrients for all cells of the body, to enable them to function.

The lining of the GI tract is a mucosal lining, and like the skin it acts as the first line of defense against microbes (see Chapter 20, The Immune System). However, it does not have a dead layer of cells as the skin does and therefore it is not as efficient a defense mechanism. On the other hand, it does provide a moist and warm environment, perfect for microbial growth. As with other portals of entry, the GI tract has a normal flora that also helps to protect against pathogens via competition.

Resident Microbial Flora

The GI tract resident (normal) microbial flora is a complex and diverse ecosystem containing a large collection of microorganisms that flourish in the nutrient-rich environment provided by the digestive system. The type and amount of flora vary within the different areas of the GI tract, with increasing numbers as one moves from the upper GI tract areas to the large intestine. The normal flora of the intestine may prevent infection by competing or interfering with pathogens or potentially pathogenic organisms. Treatment with antibiotics that upset the balance of the normal flora may favor infections by exogenous pathogens and also the overgrowth of endogenous pathogens.


The stomach contains few bacteria because of its high acidity, which makes it a relatively hostile environment for bacteria. Bacteria swallowed with food and those dislodged from the mouth will be drastically lowered in number because of this acidity. However, some bacteria do survive this extreme environment and are moved on into the small intestine. It is all about numbers: the more bacteria are ingested with food, the more will survive and be transported into the next part of the GI tract.

One organism that has been discovered to live in the human stomach is Helicobacter pylori, a gram-negative, microaerophilic, spiral-shaped bacterium (Figure 12.2). The organism is highly motile due to its flagella and moves through the stomach lumen until it burrows into the stomach’s mucosa to a depth where the pH is essentially neutral. It is estimated that about 30% to 50% of the earth’s population is colonized by H. pylori. Although colonization of the bacterium in the stomach is not necessarily a problem, H. pylori is the cause of most cases of gastritis and peptic ulcers (see Bacterial Infections later in this chapter).

Small Intestine

The small intestine provides a friendlier environment for microbial survival than does the stomach. However, because of rapid peristalsis and emptying of pancreatic juice and bile into the first portion of the duodenum, it is difficult for bacteria to colonize the small intestine because they get washed out. As a result the bacterial population, especially in the first portions of the small intestine, remains relatively low. Gram-positive bacteria, mainly lactobacilli and Enterococcus faecalis, are inhabitants of this part of the GI tract. The bacterial population increases at the end of the small intestine, and enteric rods and Bacteroides can also colonize this part of the GI tract. Intestinal bacteria are capable of metabolizing some compounds that the human digestive tract cannot, which leads to more efficient utilization of food.

Dental Caries

The oral cavity provides a good environment for a variety of microorganisms to flourish. Teeth, the tongue, and the salivary glands are accessory organs of digestion in this area. Microbial life on teeth was first observed by van Leeuwenhoek (see Chapter 1, Scope of Microbiology), who noticed that even after washing his teeth with vinegar, only microbes on the outer layer were killed, not those in the deeper layers.

The enameled surface of the teeth (Figure 12.3) is hard and does not shed cells, which allows microorganism to attach and form a biofilm known as dental plaque. If not removed on a regular basis it can lead to cavities (caries) or other periodontal problems such as gingivitis (inflammation of the gums). The microorganisms responsible for the formation of dental plaque (Figure 12.4) are almost entirely bacteria, normally present in the oral cavity. Under usual circumstances, these bacteria (e.g., fusobacteria and actinomycetes) do not cause damage; however, failure to remove these biofilms by regular brushing of the teeth will cause the organisms closest to the tooth surface to change to anaerobic respiration. Anaerobic respiration of bacteria converts sucrose and other carbohydrates into lactic acid, which consequently leads to the demineralization of the adjacent tooth surface, resulting in dental caries.

Periodontal Disease

Periodontal diseases include gingivitis and periodontitis, serious infections that if not treated can lead to decay, subsequent tooth loss, and systemic infection. Although the main cause of periodontal disease is dental plaque and an overpopulation of established oral bacteria, other factors also affect the health of the oral cavity. These factors include the following:

If periodontal disease is restricted to the gums, the inflammation is called gingivitis and is characterized by bleeding of the gums, seen predominantly during brushing of the teeth. This condition can progress to a chronic condition and is then referred to as periodontitis. Although this condition usually does not cause much discomfort, with the increase in older people who wish to retain their own teeth, it has become a more common condition of concern. If the health of the gums continues to be untreated, both tissue and bone that support the teeth deteriorate, eventually leading to the loss of teeth. A more serious condition is acute necrotizing ulcerative gingivitis, which causes enough pain to make normal chewing an unpleasant, difficult task.