Introduction

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.

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

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.

Oral Cavity

The normal microbial flora of the oral cavity is complex, with bacteria representing the largest population. More than 700 bacterial species have been detected in the adult oral cavity, but more than 50% of these have not been cultured in the laboratory at this time. At birth the oral cavity is sterile but rapidly becomes colonized by organisms from the environment, especially from the mother during the first breastfeedings. At this time Streptococcus salivarius is dominant, but the complexity of the flora continues to increase with time. Oral bacteria include streptococci, lactobacilli, staphylococci, corynebacteria, aerobes, Bacteroides, various types of spirochetes, and anaerobes.

Stomach

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.

Large Intestine

The flow rate in the large intestine is much slower than in the small intestine and bacteria have time to colonize and reproduce, reaching a high concentration. About 1000 species are present including enteric rods, streptococci, clostridia, and lactobacilli. The predominant species are anaerobic Bacteroides and bifidobacteria, which greatly outnumber Escherichia coli. The colon serves as a holding tank for bacteria that participate in the last stages of food digestion. Intestinal bacteria can metabolize polysaccharides that cannot be broken down by human enzymes (e.g., cellulose) and they also synthesize vitamins K and B, which then can be absorbed by the GI tract. Approximately 20% of the feces of a healthy person consists of bacteria, most of which come from the colon.

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.