Infectious Disorders of the Gastrointestinal Tract

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Chapter 4

Infectious Disorders of the Gastrointestinal Tract

Laura W. Lamps


Gastrointestinal (GI) infections are a major cause of morbidity and mortality worldwide. As the number of transplant patients and those with other immunocompromising conditions increases, and as global urbanization and transcontinental travel become more frequent, the surgical pathologist must be familiar with infectious diseases that were once limited to tropical regions of the world or the realm of esoterica.

The goal of the surgical pathologist in evaluating GI specimens for infectious colitis is twofold. First, acute self-limited processes and infectious processes must be differentiated from chronic idiopathic inflammatory bowel disease (IBD)—ulcerative colitis or Crohn’s disease. Second, dedicated attempts must be made to identify the specific infecting organisms.1 In recent years, the surgical pathologist’s ability to diagnose infectious processes in tissue sections has grown exponentially with the advent of new histochemical stains, immunohistochemistry, and molecular analysis. As these techniques have evolved, our knowledge of the specific histologic patterns of inflammation related to various organisms has also increased.

Most enteric infections are self-limited. Patients who undergo endoscopic biopsies usually have chronic or debilitating diarrhea or systemic symptoms, or they are immu­nocompromised. A discussion with the gastroenterologist regarding symptomatology and colonoscopic findings, as well as knowledge of the patient’s travel history, food intake (e.g., sushi, poorly cooked beef), sexual practices, and immune status can aid immeasurably in the evaluation of biopsies for infectious diseases.

Viral Infections of the GI Tract

The type of viral infection and the manifestations of disease vary with the site of infection and the immune status of the patient.


Clinical Features

Primary cytomegalovirus (CMV) infections in immunocompetent persons are usually asymptomatic. CMV infection may develop anywhere in the GI tract, from mouth to anus, in both immunocompromised and immunocompetent persons. CMV is best known as an opportunistic pathogen in patients with a suppressed immune system, most commonly in those with the acquired immunodeficiency syndrome (AIDS) and in patients who have undergone solid organ or bone marrow transplantation.2 In fact, CMV remains the most common GI pathogen overall in patients with AIDS.

Primary infections in healthy persons are typically asymptomatic. When symptomatic disease does occur, it is usually self-limited and may manifest as a mononucleosis-like syndrome. In most of these cases, GI involvement is subclinical. Symptomatic GI infection has been reported occasionally in immunocompetent patients,3,4 although many of these were elderly or were eventually found to have underlying malignancies or hematologic disorders and therefore may not have had entirely competent immune systems.

Symptoms vary with site of infection. The most common clinical symptoms are diarrhea (either bloody or watery), abdominal pain, fever, and weight loss.2 Patients with esophageal infection often have dysphagia and odynophagia.5 A rare, but important, entity associated with pediatric CMV infection is hypertrophic gastropathy and protein-losing enteropathy resembling Ménétrier disease.6,7

In addition, secondary CMV infection may be superimposed on chronic GI diseases such as ulcerative colitis and Crohn’s disease. In such cases, CMV superinfection is associated with exacerbations of the underlying disease, steroid-refractory disease, toxic megacolon, and a higher mortality rate. Some authorities recommend immunohistochemical evaluation for CMV as part of the routine evaluation of biopsies in patients with steroid-refractory ulcerative colitis.8,9

Pathologic Features

CMV causes a remarkable variety of gross lesions.2,10 Ulceration is the most common; the ulcers may be single or multiple, and superficial or deep. They can be quite large (>10 cm), and often have a well-circumscribed, “punched-out” appearance. Segmental ulcerative lesions and linear ulcers may mimic Crohn’s disease. Other gross lesions include mucosal hemorrhage, pseudomembranes, and inflammatory polyps or masses.11,12

The histologic spectrum of CMV infection is extremely variable, ranging from minimal inflammation to deep ulcers with prominent granulation tissue and necrosis. Frequently observed histologic features include mucosal ulceration, a neutrophil-rich mixed inflammatory infiltrate, and cryptitis of glandular epithelium.2 Crypt abscesses, crypt atrophy and loss, and numerous apoptotic enterocytes may be seen as well.10 CMV may also cause a vasculitis featuring numerous endothelial viral inclusions with associated inflammation, necrosis, and thrombosis of the affected vessel and resultant mucosal ischemia.13

Infected cells show both nuclear and cytoplasmic enlargement (hence the name, “cytomegalovirus”) (Fig. 4.1, A). Characteristic “owl’s-eye” intranuclear viral inclusions and basophilic granular intracytoplasmic inclusions may be seen on routine hematoxylin and eosin (H&E) preparations (see Fig. 4.1, B and C). Inclusions are preferentially found in endothelial cells, stromal cells, and macrophages, and, rarely, in glandular epithelial cells. In contrast to adenovirus or herpes, CMV inclusions are often found deep within ulcer bases rather than at the edges of ulcers or in the superficial mucosa. Adjacent nuclei may be enlarged, appear smudged, or have a “ground-glass” appearance, but they lack typical inclusions. Characteristic inclusions with virtually no associated inflammatory reaction may occur in severely immunocompromised patients.

In biopsy specimens, the diagnosis are easily missed when only rare inclusions are present. Examination of multiple levels and use of immunohistochemistry can be invaluable in detecting the rare cells containing an inclusion. Other diagnostic aids include viral culture, polymerase chain reaction (PCR) assays, in situ hybridization, serologic studies, and antigen tests. Serologic studies often have limited usefulness because of the persistence of latent CMV infection. In addition, isolation of CMV in culture does not imply active infection, because the virus can be excreted for months to years after a primary infection.2

Differential Diagnosis

The differential diagnosis of CMV includes primarily other viral infections (Table 4.1), particularly adenovirus.5 Adenovirus inclusions are usually crescent shaped, located in surface epithelium, and only intranuclear in location. CMV inclusions typically have an owl’s-eye morphology, are typically located in endothelial or stromal cells, and exist in either the nucleus or cytoplasm. The ballooning degeneration phase of adenovirus infection, just before cell lysis, most closely resembles CMV.

The distinction between CMV infection and graft-versus-host disease in bone marrow transplant recipients can be particularly difficult because the clinical and histologic features are similar. Immunohistochemistry or in situ hybridization studies should be used to rule out CMV infection in this setting, because failure to identify CMV infection could result in delay of antiviral therapy.10 Furthermore, these conditions may coexist. Graft-versus-host disease is favored when there is abundant apoptosis associated with crypt necrosis and dropout in the setting of minimal inflammation. The presence of viable nests of endocrine cells favors graft-versus-host disease.


Clinical Features

Herpetic infection can occur throughout the GI tract but is most common in the esophagus and anorectum. Although herpes infection of the gut is often seen in immunocompromised patients and remains one of the most common infections in patients with human immunodeficiency virus (HIV), it is not limited to this group. In immunocompetent patients, infection is often self-limited.14 Immunocompromised patients, however, are at risk for disseminated infection and life-threatening illness.

Patients with herpetic esophagitis are seen with odynophagia, dysphagia, chest pain, nausea, vomiting, fever, and GI bleeding. Many have disseminated herpes infection at the time of diagnosis.15 Herpetic proctitis is the most common cause of nongonococcal proctitis in homosexual men. Patients typically are seen with severe anorectal pain, tenesmus, constipation, discharge, hematochezia, and fever. Concomitant neurologic symptoms (difficulty in urination and paresthesias of the buttocks and upper thighs) are also well described, as is inguinal lymphadenopathy.15

Pathologic Features

Ulcers are the most common gross finding in the esophagus, and these are usually associated with an exudate. The ulcers are often shallow and well-circumscribed. Some patients have vesicles surrounding the ulcers. Many patients have a nonspecific erosive esophagitis without discrete ulcers, however. In herpetic proctitis, the presence of perianal vesicles is common, often in association with pustules or shallow ulcers. Proctoscopic findings include ulceration and mucosal friability. Vesicles may extend into the rectum or anal canal.15,16

Typical histologic findings, regardless of site, include ulceration, neutrophils in the lamina propria, and an inflammatory exudate that often contains sloughed epithelial cells (Fig. 4.2, A). Prominent aggregates of macrophages may also be present.17 In the anorectum, perivascular lymphocytic cuffing and crypt abscesses may be seen as well.

Characteristic viral inclusions and multinucleate giant cells are present in only a minority of biopsy specimens (see Fig. 4.2, B and C).7 The best place to search for viral inclusions is in the squamous epithelium at the edges of ulcers and in sloughed cells in the exudate. Two types of nuclear inclusions may be found: the homogeneous ground-glass inclusions and the acidophilic inclusions with a surrounding clear halo and peripheral chromatin margination (Cowdry type A inclusions). Inclusions may be single or multinucleate. The histologic findings for herpes simplex virus 1 (HSV-1) and HSV-2 are indistinguishable.

Differential Diagnosis

The differential diagnosis predominantly contains other viral infections, including CMV and varicella-zoster, that may infect the GI tract (see Table 4.1).18 Varicella produces histologic findings identical to those of HSV, but patients often have a rash.18 Mixed infections are common in many situations in which herpetic infection is found. Immunohistochemistry and in situ hybridization are very useful, and viral culture is a valuable diagnostic aid as well. Serologic studies may be useful if there is a very high or rising antibody titer, but serologic testing has limited use because latent infections can persist for years.


Adenovirus infection is second only to rotavirus as a cause of childhood diarrhea, and it is associated with a broad spectrum of diseases in both children and adults. It has gained more attention in recent years as a cause of diarrhea in immunocompromised patients, especially those with AIDS and those who have received bone marrow or solid organ transplants.1921 Virtually all patients are seen with diarrhea, sometimes accompanied by fever, weight loss, and abdominal pain. Characteristic inclusions may be seen, especially in immunocompromised patients, in the nuclei of surface epithelial cells (particularly goblet cells); these are often accompanied by apoptotic epithelial cells and epithelial degenerative changes.19,24 Adenovirus is also one of the associated with ileal and cecal intussusception in children.2224 The characteristic nuclear inclusions are known as “smudge cells” because of their enlarged, homogeneous, basophilic characteristics (Fig. 4.3; see Table 4.1). Useful aids to help in the diagnosis of adenovirus infection include immunohistochemistry, stool examination by electron microscopy, molecular studies, and viral culture. This entity is discussed further and illustrated in Chapter 5.

Other Enteric Viruses

Acute viral gastroenteritis is one of the most common causes of illness worldwide. Although most infections are self-limited, viral gastroenteritis can cause severe dehydration (particularly when caused by rotavirus), as well as chronic diarrhea in children with immunodeficiency syndromes such as severe combined immunodeficiency. Enteric viral infections are a significant cause of diarrhea in patients with AIDS. Rotavirus and enterovirus, like adenovirus, are associated with intussusception in children. Many enteric viruses do not cause disease in humans; others seldom cross the stage of the surgical pathologist because they are detected in stool samples rather than biopsy specimens. Common enteric viruses known to cause diarrhea in humans include, but are not limited to, adenovirus, rotavirus, coronavirus, astrovirus, Norwalk virus and other enteric caliciviruses, and echovirus and other enteroviruses.2530 Enteric involvement was documented in the coronavirus-associated severe acute respiratory syndrome (SARS), and diarrhea was a common presenting symptom in that outbreak.25

Small bowel biopsy findings include villous fusion, broadening, and blunting; crypt hypertrophy; and an increased mononuclear cell infiltrate within the lamina propria with variably present neutrophils (Fig. 4.4). There may also be an increase in intraepithelial lymphocytes. Reactive and degenerative epithelial changes are usually present, particularly at the surface, including epithelial cell disarray and loss of nuclear polarity.31,32 Increased apoptosis may be seen in surface and glandular epithelium. In the limited number of human studies available, the severity of the histologic lesion does not appear to correlate with clinical severity of illness. Most human studies of the histopathology associated with enteric viral infection are limited to the duodenum. The rare reports that have evaluated the large bowel have documented histologic findings ranging from normal to focal cryptitis with increased apoptosis. With the exception of adenovirus infection, inclusions are not seen on light microscopy.

Other viruses that affect the GI tract include measles (rubeola),33,34 human herpesvirus 8 (HHV-8; also known as Kaposi sarcomaassociated herpesvirus),35 HHV-6,36,37 and Epstein-Barr virus (EBV), which is associated with a wide variety of lymphoproliferative disorders.

Human Papillomaviruses

Human papillomavirus (HPV) has been implicated in the pathogenesis of esophageal papillomas, esophageal squamous cell carcinomas, anal condylomas, and anal squamous cell carcinomas. These entities are discussed in detail in Chapters 19, 24, and 32.

Human Immunodeficiency Virus

GI disease is an important cause of morbidity and mortality in patients affected by HIV and in those with AIDS. Although opportunistic pathogens are often found in these patients, there is a subgroup in whom no pathogens are found despite extensive clinical and pathologic evaluation. The two major disease entities associated with HIV in the absence of other demonstrable pathogens are chronic idiopathic esophageal ulcers and AIDS enterocolopathy.

Chronic idiopathic esophageal ulcers reportedly cause 40% to 50% of ulcers found in HIV-infected patients.38,39 The ability of HIV to directly cause these ulcers remains controversial, although evidence of HIV within the ulcerative lesions has been demonstrated by molecular analysis, immunohistochemical studies, and enzyme-linked immunosorbent assays (ELISA).40 Patients are seen with severe odynophagia, independent of food intake; chest pain; and weight loss. The middle esophagus is the most common location, followed by the distal esophagus. Endoscopically, the ulcers consist of one or more well-circumscribed lesions of variable depth that can mimic ulcers caused by other infectious agents, particularly viral pathogens. They can be quite large (>3.0 cm in greatest dimension) and deep, with irregular margins and overhanging, edematous edges. Mucosal bridges and sinus tract formation may occur. Histologically, the ulcers contain granulation tissue with a mixed acute and chronic inflammatory infiltrate that often contains eosinophils. By definition, special histochemical stains and immunohistochemical stains for identifiable pathogens must be negative. This finding is especially important because these ulcers are sometimes treated with steroids.41 This entity is also discussed in Chapter 5.

HIV/AIDS enteropathy/colopathy is a somewhat controversial entity that has been loosely defined as the morphologic changes seen in the gut of patients with HIV/AIDS and chronic diarrhea for which no other infectious cause has been identified. The controversy arises because asymptomatic patients may have similar morphologic findings on biopsy and, conversely, severely symptomatic patients may have normal biopsies.42 In addition, there is always the added concern that a causative pathogen simply has been missed. Because patients with HIV/AIDS do have severe impairments of GI function including diarrhea, malabsoprtion, and weight loss, even in the absence of any demonstrable pathogens, many authors support use of the term AIDS enteropathy (or colopathy) to describe the morphologic findings, provided that the bowel has been adequately sampled and all other infectious causes have been excluded.4345 However, other authorities believe that this is a poorly understood term that does not clearly represent a specific disease entity and therefore should be avoided.

Endoscopy and colonoscopy findings are usually normal. In the small bowel, the histologic features include villous blunting and atrophy, crypt hypertrophy, increased intraepithelial lymphocytes, variably increased mononuclear cells in the lamina propria, increased mitoses within glandular epithelial cells, and increased numbers of apoptotic enterocytes at the surface and in the glands. In the colon, inflammatory changes are similar, but the apoptotic epithelial cells in the glandular epithelium are often very prominent (Fig. 4.5). The changes resemble those seen in mild graft-versus-host disease and chemotherapy-related mucosal injury.4345 Other pathogens, particularly other viruses such as CMV and adenovirus that can produce similar histologic features, must be rigorously excluded.

Bacterial Infections of the Gastrointestinal Tract

Bacterial diarrhea is a worldwide health problem. Many bacterial infections of the gut are related to ingestion of contaminated water or food or to foreign travel, especially from an area of good sanitation to one of poor sanitation. Although bacterial pathogens are often recovered by microbial culture, surgical pathologists may play a valuable role in diagnosis. Despite the dizzying array of bacterial infections that may affect the GI tract, many produce a similar spectrum of histologic features and may be generally categorized as follows (Table 4.2):

Acute Self-Limited Colitis

The ASLC pattern is the most common pattern in enteric infections. Typical histologic features include neutrophils in the lamina propria, with or without crypt abscesses and cryptitis; preservation of crypt architecture; and lack of basal plasmacytosis.1,4651 The acute inflammatory component is often most prominent in the middle to upper levels of the crypts. Lack of crypt distortion, Paneth cell metaplasia, and basal lymphoplasmacytosis help to distinguish ASLC from IBD.1,51 The changes may be focal, as in focal active colitis, or diffuse.

Surgical pathologists should be aware of the infections that are most likely to mimic other IBD, particularly Crohn’s disease, ulcerative colitis, and ischemic colitis (see Table 4.2). Because most patients do not present for endoscopy until several weeks after the onset of symptoms, pathologists usually are not exposed to the classic histologic features of acute infectious colitis. This is important because the resolving phase of infectious colitis is more challenging to diagnose. At this stage, only occasional foci of neutrophilic cryptitis and only patchy increases in lamina propria inflammation may be found, and these may, in fact, contain abundant plasma cells and increased intraepithelial lymphocytes, features that are also seen in Crohn’s disease or even lymphocytic colitis. It is important to be aware of the patient’s symptoms (particularly acute versus chronic onset) and, ideally, the culture results, because the exact diagnosis may be difficult to resolve on histologic grounds alone. The pathologic details of specific bacterial infections are discussed in the following sections.

Major Causes of Bacterial Enterocolitis

Vibrio cholerae and Related Species

V. cholerae (specifically the toxigenic O1 strain) is the causative agent of cholera, an important worldwide cause of watery diarrhea and dysentery that may lead to significant dehydration, electrolyte imbalance, and death within hours.52,53 Most infections result from consumption of raw or undercooked seafood, especially shellfish. Other vibrios, including non-O1 strains of V. cholerae, Vibrio hollisae, and Vibrio parahaemolyticus, also can cause severe gastroenteritis.54 Symptoms of cholera include the abrupt onset of diarrhea, usually profusely watery and rarely bloody, accompanied by abdominal pain, vomiting, muscle cramps, and fever. Disseminated infection is a particularly important risk with immunocompromised patients; patients with underlying liver disease, partial or total gastrectomy, and diseases of iron metabolism are also at risk for more serious Vibrio infections.

Despite the severity of the illness, V. cholerae O1 is a noninvasive toxin-producing organism that cause minimal or no histologic change to the intestinal mucosa. Nonspecific findings such as small bowel mucin depletion, degenerative surface epithelial changes, and a mild increase in lamina propria mononuclear cells have been rarely reported.55,56 Non-toxigenic O1 and other non-cholerae Vibrio species may show an erosive enterocolitis with active neutrophilic inflammation and associated hemorrhage. Useful ancillary diagnostic tests include culture, PCR, and serologic studies.57 A history of travel to or emigration from an endemic or epidemic area also can be invaluable.

Aeromonas and Related Species

Initially believed to be nonpathogenic gram-negative bacteria, Aeromonas and related species are increasingly recognized as causes of gastroenteritis in both children and adults.5861 Aeromonas hydrophila and Aeromonas sobria most often cause GI disease in humans. Infection usually is caused by exposure to untreated water but also may result from consumption of contaminated foods such as produce, meat, and dairy products. Infections most frequently occur in the late spring, summer, and early fall, and children are most commonly affected. A mild, self-limited diarrheal illness is most common, sometimes accompanied by nausea, vomiting, and cramping abdominal pain. A more severe, dysentery-like illness occurs in 15% to 25% of patients, featuring bloody or mucoid diarrhea and fecal leukocytes. This variant is most likely to mimic chronic idiopathic IBD endoscopically.

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