Inflammatory Disorders of the Small Intestine

Epidemiology and Clinical Features

Celiac disease (also known as gluten-sensitive enteropathy) is an autoimmune disorder that results in damage to the small intestinal mucosa and leads to malabsorption of nutrients. Although this disease was described more than a century ago, ^, it is only since 1950 that the role of dietary gluten in its pathogenesis has been recognized. Celiac disease has a worldwide distribution, but is most common in countries with populations of European descent (Europe, North and South America, and Australia), where the prevalence rate is approximately 1%. ^, Although historically less common in Asia and Africa, the incidence of celiac disease is rising in these countries due to increased wheat consumption. ^{, ,} A recent change in the gluten reaction landscape is the emergence of nonceliac gluten sensitivity as a separate, poorly understood and possibly immune-mediated (not autoimmune) condition, that along with wheat allergy and celiac disease, form a spectrum of gluten-related disorders. ^, This discussion is limited to celiac disease.

Celiac disease may appear at any time in life, from early childhood to late adulthood. Factors governing the timing of clinical disease in genetically at-risk patients are complex and appear to relate to a combination of environmental triggers, including age and amount of gluten in the initial gluten exposure years, usual viral infection exposures, and microbiome alterations. Because of the tremendous variability in clinical presentation, patients, especially adults, often have a greater than 10-year lag between symptom onset and diagnosis. Classic symptoms include abdominal discomfort, diarrhea, and steatorrhea. ^, However, some patients have no gastrointestinal (GI) manifestations, and instead exhibit other signs and symptoms, including short stature, infertility, neurological disorders, recurrent aphthous stomatitis, or dermatitis herpetiformis. ^{, ,} In some adults with occult celiac disease, complaints of fatigue often uncover the presence of iron-deficiency anemia, which ultimately leads to the correct diagnosis. ^, Further, some patients are entirely asymptomatic and present initially only with histological changes on biopsy analysis. The term latent celiac disease has been used to describe patients with this presentation (see later). ^, Factors governing the type of clinical presentation and the expression of symptoms are poorly understood. While it was once thought that the development and severity of symptoms were related to the length of intestine involved rather than the severity of mucosal pathology in a single biopsy specimen, additional studies appear to refute that theory. ^, At the time of this writing, attention is focused on the action of interleukin (IL)-15 as a promoter of gluten-sensitized T lymphocytes that increase mucosal cytokine levels as a determiner of clinical symptoms, regardless of severity or length of mucosa showing villous blunting.

Pathogenesis

Celiac disease is an immunological disorder that occurs in genetically susceptible hosts. Environmental influences are important as well. The familial nature of the disease was originally established in a study of 17 probands, and their families, who underwent small bowel biopsies. This study found an increased incidence of celiac disease in first-degree relatives of symptomatic patients. Studies have documented that 10% to 20% of asymptomatic first-degree relatives have mild histological changes, such as increased intraepithelial lymphocytes without villous blunting, or have mild villous blunting. ^{, ,} In the asymptomatic setting, the decision to institute a gluten-free diet depends on a variety of factors. When symptomatic first-degree relatives are assessed, up to 44% of patients have villous blunting and tissue transglutaminase antibody titers in the diagnostic range.

Genetic studies have established a strong association with major histocompatibility complex (MHC) class II HLA-DQ2 (majority) and DQ8 , with up to 95% of patients carrying one of these two genes. However, these genetic phenotypes do not explain the pathogenesis entirely, because 30% of the normal population carry the DQ2 haplotype without disease, and not all patients with celiac disease carry this specific phenotype. ^, Genome-wide association studies have identified more than 100 non-HLA genes associated with an increased risk of celiac disease, including CCR3 and IL2-IL21 . ^{, ,} Some of the identified genes are also common in type 1 diabetes, and rheumatoid arthritis, suggesting that they impart a generalized increased risk of autoimmunity. ^, Further, evidence linking transcription factors operating across multiple disease loci related to Epstein-Barr virus proteins suggest mechanisms that may be important in numerous autoimmune diseases. The reader is referred to several reviews on the genetics of celiac disease. ^{, , ,}

In the proper genetic environment, exposure to gliadins, or the prolamin fraction of gluten found in wheat, rye, and barley, results in both a local and systemic immune response. ^{, , ,} Additional environmental components may be related to previous infections, for example, with adenovirus 12, reovirus, enterovirus, and perhaps other microbes. ^{, ,} The E1b protein of adenovirus has been shown to contain amino acid sequence homology with α-gliadin antibodies, and T cells that recognize these viral proteins cross-react with gliadin.

In 1997, the crucial role of intestinal tissue transglutaminase (tTG), a ubiquitous enzyme in human tissues, in the pathogenesis of celiac disease was uncovered. This enzyme catalyzes cross-link formation between glutamine and lysine residues in substrate proteins. tTG is believed to stabilize extracellular matrix molecules in the setting of mucosal injury and granulation tissue. In their landmark description, Dieterich et al. demonstrated that dietary gliadin, rich in the amino acid glutamine, serves as a substrate for tTG. It is thought that the resulting cross-linked molecules (gliadin–gliadin or gliadin–tTG) become antigenic epitopes for a subsequent immune response. Of the more than 50 T-cell–stimulating epitopes in gluten proteins, a 33-mer peptide that may be the primary initiator of the inflammatory response in celiac disease has been identified, although it is likely other epitopes also play a role. Gliadin can also cause an immediate, transient increase in tight junction permeability, affecting the barrier function of the gut. ^, Investigations into the role of tTG in celiac disease have led to improved diagnostic tests, described further later.

The immune response to dietary gluten involves both the innate and adaptive immune systems in a complex interplay of cytokines, T and B lymphocytes, dendritic cells, and transglutaminase 2. Antibody-induced injury may occur via antigen–antibody complex deposition with complement activation and also by the induction of cell-mediated cytotoxicity. Activated mucosal T cells have been shown to cause epithelial injury through the release of cytokines, including interleukin 15. ^{, , ,}

The clinical diagnosis of celiac disease depends on detecting the appropriate combination of symptoms, laboratory evidence of malabsorption, the presence of serum autoantibodies, and mucosal injury in duodenal biopsies. It is important that pathologists are aware that new algorithms in children allow for the correct diagnosis of celiac disease to be made without endoscopy and biopsy.

Highly accurate serological tests have been added to the “diagnostic tool kit” for celiac disease ( Box 16.2 ). These include the enzyme-linked immunosorbent assay for IgA anti-tTG antibodies, which has a high degree of sensitivity and specificity (77% to 100% and 91% to 100%, respectively). tTG antibody determination has become the serological test of choice for celiac disease and has replaced the antiendomysial antibody test as a first-line approach. The antiendomysial antibody (EMA) test remains as sensitive and specific as the anti-tTG test using human recombinant protein, but the immunofluorescence-dependent EMA test is labor intensive and relies on a more subjective interpretation than anti-tTG determinations. Today, EMA antibody testing is often used as a confirmatory test when tTG testing or clinical/biopsy findings are ambiguous. The older anti-gliadin antibody test no longer has a place in celiac disease diagnosis because of its lack of specificity. However, a new generation of antigliadin antibodies, deamidated gliadin peptides (DGPs), are a widely used IgG-based test, with high concordance with both tTG and EMA antibody tests, and possibly greater sensitivity in children and in early disease. ^{, ,} This test also has the advantage of detecting celiac disease in IgA-deficient patients. HLA testing to detect susceptible HLA phenotypes (DQ2 and DQ8) is frequently used as a confirmatory test in ambiguous settings or in order to avoid biopsy in children. The absence of DQ2 or DQ8 virtually excludes the diagnosis. ^, Finally, transglutaminase-specific IgA deposits can be found in frozen sections of small intestine mucosal biopsies by immunofluorescence in patients with celiac disease, even those with normal to near normal histology. However, it is unlikely this technique will become widely used as a diagnostic test. For a more detailed discussion of the current approach to clinical diagnosis and management of celiac disease, several excellent reviews and guidelines are available. ^{, , , ,}

Pathological Features

Background

In Western countries before 1990, celiac disease was a diagnosis that was made with ease and confidence on small bowel biopsies. The pathological diagnosis required severe villous blunting (flat mucosa), usually accompanied by increased intraepithelial lymphocytes (IELs) and lamina propria inflammation in duodenal biopsies obtained distal to the duodenal bulb. A diagnosis of untreated celiac disease was not normally considered when a biopsy did not show significant loss of villous architecture.

Since the early 1990s, several changes in our understanding of celiac disease have altered the diagnostic algorithm for this disease and have eliminated the gold standard status of small bowel biopsies. ^{, , ,} These changes include (1) recognition that latent or occult (minimally symptomatic) celiac disease in adults represents a large, previously unappreciated disease population ^{, , ,} ; (2) revision of histological criteria to include minimal inflammatory changes with intact, or only mildly abnormal architecture as a part of the histological spectrum of celiac disease ^{, , ,} ; and (3) the discovery that tTG is the target autoantigen of antibodies in patients with celiac disease, and the subsequent development of a highly accurate diagnostic test for anti-tTG antibodies that can now be used in combination with the tests described in the previous section. ^{, , ,}

These developments have had a great impact on pathologists, who can now correlate minimal histological findings with objective clinical and serological evidence of celiac disease. They have also decreased the need for reliance on small bowel biopsy findings, which can be subject to interpretive challenges due to orientation and nonspecificity of changes. At the time of this writing, the sophisticated pathologist and clinician must understand that evaluating patients for celiac disease may or may not include the need for mucosal biopsy, especially in children ( Fig. 16.1 ). ^, In children, small intestinal mucosal biopsies can be obtained to help fulfill diagnostic criteria, or may be reserved for patients in whom serological laboratory results are inconclusive, the caveat being that histological findings in the latter category of patients may also be inconclusive ( Box 16.3 ). Notwithstanding these considerations in children, there is still general consensus worldwide that adults being considered for a diagnosis of celiac disease should undergo small bowel biopsy as part of the diagnostic workup ( Box 16.4 ).

BOX 16.3

Diagnostic Criteria for Celiac Disease ∗

∗ At least four of the five criteria must be met (or three of four if the HLA genotype is not performed).

Modified from Catassi C, Fasano A. Celiac disease diagnosis: simple rules are better than complicated algorithms . Am J Med. 2010;123:691-693.

HLA , Human leukocyte antigen; IgA , immunoglobulin A.

• Typical symptoms of celiac disease

• Positivity of serum celiac disease IgA class autoantibodies at high titer

• HLADQ2 or HLA-DQ8 genotype

• Celiac enteropathy at the small intestinal biopsy

• Response to the gluten-free diet

BOX 16.4

Whom to Test for Celiac Disease and Method

Modified from Al-Toma A, Volta U, Auricchio A. European Society for the Study of Coeliac Disease (ESsCD) guideline for coeliac disease and other gluten-related disorders. United European Gastroenterol J , 2019:5:583-613.

CD , Celiac disease; GI , gastrointestinal.

Duodenal biopsy even if CD serology is negative

• Chronic nonbloody diarrhea

• Diarrhea with features of malabsorption (e.g., weight loss)

• Iron-deficiency anemia in absence of other causes

• GI symptoms with a family history of CD

• GI symptoms with autoimmune disease or IgA deficiency

• Failure to thrive in children

• Skin biopsy proven dermatitis herpetiformis

• Video capsule findings suggestive of villous atrophy

CD serology is indicated: Biopsy needed only when serology is positive

• Irritable bowel syndrome

• Elevated otherwise unexplained liver transaminases

• Chronic GI symptoms without a family history of CD

• Chronic GI symptoms with a personal history of autoimmune disease

• Microscopic colitis

• Hashimoto’s thyroiditis and Graves’ disease

• Osteopenia/osteoporosis

• Unexplained ataxia or peripheral neuropathy

• Recurrent aphthous ulcerations/dental enamel defects

• Infertility, recurrent miscarriage, later menarche, early menopause

• Chronic fatigue syndrome

• Acute or chronic pancreatitis after excluding other causes

• Epilepsy; headaches; mood disorders; or attention deficit disorders

• Hyposplenism or functional asplenia

• Psoriasis or skin lesions other than dermatitis herpetiformis

• Pulmonary hemosiderosis

• IgA nephropathy

Gross Pathology

In a landmark study, Rubin et al. described the appearance of normal duodenal mucosa on biopsy samples with the use of a hand lens and showed that the mucosa is characterized by numerous slender villi with a delicate capillary network that floats in formalin like “the tentacles of a sea anemone.” ^, In contrast, biopsies from patients with celiac disease have a barren, stubby surface, without normal villi, and contain widely spaced irregular capillaries ( Fig. 16.2 ).

Endoscopic findings in patients with celiac disease are subtle and often unreliable. ^, A flat, scalloped appearance of the duodenal mucosa, most likely reflecting loss of villi, may be seen. ^, One endoscopic study found that a reduction of folds, scalloping, mosaic pattern, and nodular mucosa were sensitive, but not specific, endoscopic findings in celiac disease, as they were also noted in some dyspeptic patients without celiac disease. Likewise, a meta-analysis of studies testing the diagnostic sensitivity and specificity of video capsule endoscopy in celiac disease reports that the images seen can correctly diagnose the condition. However, there are insufficient data on the performance of this instrument in mild histological forms that are recognized today. Of note, at least one capsule endoscopy study reports endoscopic abnormalities (reduction of Kerckring folds, scalloping, and mosaic pattern) limited to the jejunum with normal duodenal appearances in some celiac disease patients, although no confirmatory biopsies were taken. Endoscopic diagnosis appears to be far less reliable in children than in adults. ^, Advanced techniques, such as confocal laser microscopy, narrow-band imaging, and immersion technique, may improve diagnostic accuracy, but are as yet not widely tested in clinical practice.

Histology of Untreated Disease

Normal small bowel mucosa exhibits a villous height-to-crypt depth ratio of from 3:1 in the proximal duodenum to 5:1 in more distal locations ( Fig. 16.3 ). Epithelial cells lining the villi contain basally located nuclei with abundant mature cytoplasm and a preponderance of absorptive cells admixed with goblet cells. A faint density, representing the microvillous brush border, can be appreciated on hematoxylin and eosin (H&E)-stained tissue sections. Studies have confirmed that there are approximately 20 lymphocytes per 100 epithelial cells in health, with minor variations. In health, IELs are most numerous in the base of villi and taper from the base to the villous tip, where they are less numerous. This is in stark contrast to the distribution in untreated celiac disease, in which villous tip IELs are markedly increased. The lamina propria normally contains a mixture of plasma cells, lymphocytes, and occasional eosinophils. Each of the three mucosal components (architecture, epithelium, and lamina propria) should be carefully examined in cases of suspected celiac disease, and, indeed, in the assessment of all small bowel biopsies.

In the following paragraphs, the pathology of celiac disease is described in conjunction with a grading scheme that can be used in pathology reports ( Table 16.1 ). At the time of this writing the Marsh-Oberhuber classification is used regularly in Europe but is far less widely used in the United States in routine pathology reports. Including the Marsh-Oberhuber subtype requires prior knowledge (e.g., by serology) of the patient’s having celiac disease, information often not provided in biopsy requisition forms. ^, In addition, differences among types 0, 1, and 2 in the Marsh scheme are subtle, so that a high degree of observer variability between pathologists exists. To avoid these issues, it is reasonable to discuss abnormalities in villous architecture with a descriptive modifier (e.g., mild, moderate, or severe; or partial vs. complete), as detailed later, to reflect the degree of villous blunting, adding classification designations as agreed upon by pathologists and clinicians.

TABLE 16.1

Diagnostic Terminology for Pathology Reports

Histology	Pathology Report ∗
	A, Duodenal mucosa with normal villous architecture and a patchy/diffuse increase in intraepithelial lymphocytes. Note: Increased intraepithelial lymphocytes in the setting of normal villous architecture can be seen in patients with symptomatic or asymptomatic celiac disease. Other associations include Helicobacter pylori gastritis, medications (especially NSAIDs and olmesartan and related angiotensin II receptor blockers), infections, and immune-mediated disorders. Correlation with celiac disease–associated serological and/or genetic tests may be considered.
	B, Duodenal mucosa with mild villous blunting and increased intraepithelial lymphocytes. Note: The findings suggest celiac disease in the appropriate clinical setting. Other associated conditions include medication injury (especially olmesartan and related angiotensin II receptor blockers), infections, and immune-mediated disorders. Correlation with celiac disease–associated serological and/or genetic studies is suggested.
	C, Duodenal mucosa with moderate villous blunting and increased intraepithelial lymphocytes. Note: The findings suggest celiac disease in the appropriate clinical setting. Other associated conditions include medication injury (especially olmesartan and related angiotensin II receptor blockers), infections, and immune-mediated disorders. Correlation with celiac disease–associated serological and/or genetic studies is suggested.
	D, Duodenal mucosa with severe villous blunting and increased intraepithelial lymphocytes. Note: The findings suggest celiac disease in the appropriate clinical setting. Other associated conditions include medication injury (especially olmesartan and related angiotensin II receptor blockers), infections, and immune-mediated disorders. Correlation with celiac disease–associated serological and/or genetic studies is suggested.

∗ The content of the note will depend on the clinical information provided and findings in gastric and other biopsies. Whenever possible, tailor the report to fit the clinical situation. (Modified from Robert ME, Crowe SE, Burgart L, et al. Statement on best practices in the use of pathology as a diagnostic tool for celiac disease: a guide for clinicians and pathologists. Am J Surg Pathol . 2018;42:e44-e58.)

Even if not utilized in reports, it is important from both a research and clinical perspective to be aware of the Marsh-Oberhuber classification scheme ( Table 16.2 ). ^, This system describes five histological lesions associated with celiac disease, termed preinfiltrative (grade 0), infiltrative (type 1), infiltrative-hyperplastic (grade 2), flat-destructive (grade 3), and atrophic-hypoplastic (grade 4). Two modifications to this scheme have been proposed in an attempt to simplify the diagnosis for pathologists and clinicians. ^, Neither has been universally accepted, but both are included for the sake of completeness in Table 16.3 .

Biopsies Without Villous Blunting

Preinfiltrative lesions (Marsh-Oberhuber grade 0) refer to normal mucosa seen predominantly in patients with dermatitis herpetiformis but without evidence of malabsorption.

Infiltrative lesions (Marsh-Oberhuber grade 1) refer to finding increases in IELs with preserved villous architecture, whereas infiltrative-hyperplastic lesions (grade 2) show the additional feature of elongated crypts. Both of these patterns of injury are seen in patients with celiac disease (with or without symptoms) as well as in first-degree relatives of patients with celiac disease and in patients with dermatitis herpetiformis. Phenotypic analyses have shown that the increase in IELs is the result of increased numbers of γ/δ T cells. Biopsies with these subtle changes are challenging to interpret and require clinical correlation with serology in order to confirm a diagnosis of celiac disease, as similar histology is seen in other conditions. By definition, the villous height and the villous-to-crypt ratio is normal or near normal ( Fig. 16.4 ). The diagnosis relies on the detection of increased IELs, the assessment of which is now a routine part of small bowel biopsy interpretation (see later). The proportion of patients with these minimal histological changes who eventually develop severe histological lesions and symptoms is unknown. ^{, ,} One small study suggested that 4 of 12 people (33%) with mild changes (Marsh-Oberhuber 1–2) on duodenal biopsies progress to celiac disease with flat mucosa, at follow-up, and a second study found that 3 of 5 (60%) patients with positive tTG antibodies and initial Marsh-Oberhuber 1 lesions progressed to Marsh-Oberhuber 3c at follow-up. ^, However, in a larger study with 8 to 25 years of follow-up, only 5 of 236 patients (2.1%) with biopsies showing increased IELs, or a slight reduction in villous-to-crypt ratio, eventually developed celiac disease. These data are complicated by the newer knowledge that patchy histological findings are more common in celiac disease than once appreciated. Sampling error in the above studies cannot be excluded.

Counting Intraepithelial Lymphocytes in Biopsies Without Villous Blunting

Numerous studies have shed light on appropriate methods to count IELs ( Table 16.4 ). Reassessment of the normal range of IELs in the second portion of the duodenum has been performed by several investigators, using H&E-stained sections and sections stained for CD3 antigen, establishing an upper limit of 20 lymphocytes per 100 epithelial cells in normal mucosa in the duodenum. ^, Careful analysis using CD3 and γ or δ T-cell stains have shown that IEL counts of greater than 25 per 100 epithelial cells (or a ratio of greater than 1:4) merit suspicion for potential celiac disease, whereas counts greater than 29 per 100 epithelial cells provide sound diagnostic evidence for active celiac disease, in serologically positive patients. ^{, , ,} However, it is entirely impractical to count IELs per 100 enterocytes in busy clinical practices.

TABLE 16.4

Methods of Counting IELs in Architecturally Normal Duodenal Biopsies ∗

Interpretation	Counts	Stain
Diagnosis by Counting IELs per 100 Enterocytes (300-500 Cells Counted)
Upper limit of normal	20/100 25/100	H&E CD3
Borderline increased	25-29/100	H&E or CD3
Definitely increased	>29/100	H&E or CD3
Diagnosis by Villous Tip Method (5 Villi, 20 Enterocytes per Villous Tip, Mean Count)
Upper limit of normal	5/20	H&E or CD3
Definitely increased	≥6/20	H&E or CD3

H&E , Hematoxylin and eosin; IELs , intraepithelial lymphocytes. See text for references.

∗ Avoid all lymphoglandular complexes. Average the sum of at least five villi.

A more practical approach, the villous tip counting method, has been validated in at least four studies. ^{, , ,} Averaging IELs per 20 epithelial cells in five well-oriented villous tips was found to result in a rapid and accurate assessment of IEL counts in either H&E- or CD3-stained sections. Using this approach, lymphocyte counts of 6 to 12 IELs per 20 epithelial cells in the tips of villi in architecturally normal mucosa are found in patients with serological or other evidence of celiac disease. The IEL counts are lower than in untreated flat celiac disease biopsies, and higher than in normal controls. Although CD3 stains were used for cell counting in one study, equivalent results were obtained using H&E stains in the other two. ^, The counts obtained using the villous tip method correlate well with previously cited studies counting IELs in 100 consecutive enterocytes that found that greater than 29 IELs per 100 epithelial cells is abnormal. A slightly different counting approach was taken in a landmark prospective study comparing IEL counts with serology in a random adult population. IELs were counted in a total of 50 enterocytes (in groups of 10) along the sides and tops of villi. In this study, counts of >25 IEL/100 detected celiac disease, while higher cutoffs missed 50% of cases. Importantly, this study found equally elevated IELs in 3.8% of nonceliac controls, most of whom had Helicobacter pylori gastritis. The terms “lymphocytic enteropathy” and “duodenal lymphocytosis” have emerged to describe the spectrum of patients with increased IELs and normal villous architecture. The term “lymphocytic duodenosis” has been proposed to refer to the subset of this group that is proven serologically to not have celiac disease.

Numerous conditions other than celiac disease are associated with increased IELs in architecturally normal duodenal biopsies ( Table 16.5 ). These include H. pylori gastritis ( Fig. 16.5 ), viral gastroenteritis ( Fig. 16.6 ), tropical sprue, cow milk protein sensitivity, bacterial overgrowth, some immune conditions, and an ever-expanding list of medications. ^, Further, the reliability of IEL assessments to detect celiac disease is entirely dependent on active gluten consumption by the patient at the time of endoscopy. Duodenal biopsies from patients already on low- or no-gluten diets will have fewer IELs and less villous blunting.

TABLE 16.5

Disorders Showing Histological Overlap with Gluten-Sensitive Enteropathy

Conditions Associated with Increased Intraepithelial Lymphocytes ∗	Conditions Associated with Villous Blunting
Helicobacter pylori gastritis Viral gastroenteritis Autoimmune enteropathy Tropical sprue Refractory sprue Protein intolerance Bacterial overgrowth NSAID injury Immune checkpoint inhibitors	Common variable immunodeficiency Microvillous inclusion disease Autoimmune enteropathy Tropical sprue Refractory sprue Protein intolerance Bacterial overgrowth Radiation or chemotherapy Nutritional deficiencies Eosinophilic gastroenteritis Crohn’s disease Immune checkpoint inhibitors ARB injury (Olmesartan and others) Idelalisib

∗ Not all conditions associated with increased intraepithelial lymphocytes also show villous blunting. ARB , Angiotensin II receptor blocker; NSAID , nonsteroidal antiinflammatory drug.

In summary, the following approach is recommended for biopsies in patients with normal or near-normal villous architecture and a perceived increase in IELs, or with the clinical potential for a diagnosis of celiac disease (i.e., positive tTG serology). First, perform a low- to medium-magnification scan of villi and villous tips, looking for either a diffuse or patchy increase in IELs. Avoid areas of lymphoglandular complexes, as they lead to falsely elevated IEL counts. If a striking increase in IELs is detected, there is no need to perform an IEL cell count. Evaluation of the number of IELs can be performed with the villous tip method for subtle cases, if desired, without the need for CD3 or γ/δ T-cell immunostains. ^{, ,} If a CD3 stain is employed, care must be taken to not include lymphocytes just beneath the epithelial basement membrane, a region often challenging to distinguish on immunohistochemical stains.

Because correlation with serology is required in all cases, use of excessive time or expense counting IELs in the diagnostic setting is not recommended. Further, reporting exact numbers of IELs in pathology reports is not a standard practice outside of research settings, and is not recommended as a rule. Qualitative comparisons to prior biopsies are useful and should be performed when possible, as this provides important follow-up information to clinicians and patients. Pathology reports should contain a descriptive diagnosis, such as “duodenal mucosa with normal villous architecture and increased intraepithelial lymphocytes,” with a note listing the differential diagnosis and a recommendation to correlate with serological evidence of celiac disease (see Table 16.5 Table 16.6 ). Further, an indication that the IEL increase is patchy or diffuse is appropriate to report. A partial list of causes of increased IELs in the small intestine is provided in Table 16.7 . ^,

TABLE 16.6

Differential Diagnosis of Celiac Disease: Distinguishing Clinicopathology

Modified from Robert ME, Crowe SE, Burgart L, et al. Statement on best practices in the use of pathology as a diagnostic tool for celiac disease: a guide for clinicians and pathologists. Am J Surg Pathol . 2018;42:e44-e58.

Disease	Increased IEL’s	Villous Blunting	Distinguishing Pathological Features	Distinguishing Clinical Features
Helicobacter pylori gastritis	Yes	Rare, if present mild	Fewer IELs than in CD. Blunting almost never present.	May need to do serology to exclude CD
Peptic duodenitis	No	Yes, variable	Neutrophils, erosions, changes usually confined to bulb; gastric surface metaplasia common, but may be physiological	No specific clinical symptoms in peptic duodenitis
NSAID injury	Yes	Patchy	Patchy involvement, erosions, neutrophils	History of NSAID use; lack of typical celiac symptoms/serology
Tropical sprue	Yes	Yes, moderate	Changes extend to ileum. Usually not severe blunting	Patient demographics, and travel history
Bacterial overgrowth	Yes	Sometimes	Most biopsies normal in this setting, but no distinguishing features when abnormal	Condition predisposing to intestinal stasis.
Soy and cow’s milk protein intolerance	Sometimes	Yes	Colitis and enteritis, including ileum, prominent eosinophils	Usually children with feeding intolerance
Crohn’s disease	Sometimes	If present, not usually diffuse	Patchy involvement, erosions, ulcers, crypt branching, granulomas (rare)	Usually occurring in setting of known Crohn’s disease with distal intestine involvement
UC-associated duodenitis	Not usually	Sometimes	Diffuse lamina propria expansion with basal plasmacytosis, IELs not usually increased	Usually discovered in setting of known UC
ARB injury (olmesartan and others)	Yes	Yes	No distinguishing features, may show collagenous sprue	History of ARB use; must have high index of suspicion
Immune modulatory drugs (including checkpoint inhibitors)	Rarely	Yes	Mixed inflammation, with neutrophils, apoptosis, and occasionally crypt branching. Involves upper and lower GI tract	Usually easily distinguished by clinical setting
CVID	Yes	Sometimes	Absence of mucosal plasma cells, giardiasis, BNLH	History of chronic infections.
Autoimmune enteropathy	Not usually	Yes, variable	Neutrophils, crypt apoptosis, decreased goblet and Paneth cells, involves entire small bowel, stomach and colon, usually no increase in IELs	Often infants, syndromic, gut epithelial autoantibodies
Refractory celiac disease	Often	Yes	Thin mucosa, basal plasmacytosis, collagenous sprue; histology may be indistinguishable from untreated responsive celiac disease. In some patients, loss of CD8 and surface CD3 antigens in IELs on IHC.	Refractory clinical course after initial response to GFD or never responded to GFD

ARB , Angiotensin II receptor blocker; BNLH , benign nodular lymphoid hyperplasia; CD , celiac disease; CVID , common variable immunodeficiency; GFD , gluten-free diet; IEL , intraepithelial lymphocytes; IHC , immunohistochemistry; NSAID , nonsteroidal antiinflammatory drugs; UC , ulcerative colitis.

TABLE 16.7

Criteria for Refractory Celiac Disease Types I and II

Modified from Rubio-Tapia A, Murray, JA. Classification and management of refractory coeliac disease. Gut . 2010;59:547-557.

Criteria Pathological/Clinical	RCD Category
	RCD I	RCD II
Abnormal intraepithelial lymphocyte phenotype by IHC or flow cytometry	No	Yes
Monoclonal γ or δ T-cell receptor gene rearrangement	No	Yes
Clinical response to incremental therapies	No	Variable
Risk of EATL	Rare	Frequent

EATL , Enteropathy associated T-cell lymphoma; IHC , immunohistochemistry; RCD , refractory celiac disease.

Biopsies with Blunted Villi

The flat-destructive pattern (Marsh type 3) is the classic mucosal lesion associated with symptomatic, untreated celiac disease. Duodenal biopsies showing type 3 changes reveal loss of normal small intestinal architecture resulting from a decrease in the height of villi (villous blunting) accompanied by crypt hyperplasia. Type 3 has been further subdivided by Oberhuber into types 3a (mild blunting), 3b (moderate blunting), and 3c (severe blunting). Interobserver variability among pathologists in assessing the degree of villous blunting is recognized, such that a proposed scheme of normal villi, partial blunting, and flat mucosa may be more reproducible than a four-tiered approach. ^, This is especially worthy of consideration because studies show a lack of correlation between Marsh score and clinical disease severity. ^{, ,}

In assessing villous architecture in duodenal mucosal biopsies, several well-oriented villi must be visualized, away from lymphoid aggregates, gastric heterotopia, and extensive mucosal Brunner glands. The liberal use of level sections to achieve well-oriented regions should be considered the routine standard of care, not an exceptional practice. The histology of celiac disease with villous blunting is characteristic but variable. Biopsies from the duodenum reveal loss of normal architecture caused by a decrease in the height of villi. In many cases, the mucosa appears completely flat. In others, the villi may be broad and only mildly to moderately shortened, or they may show irregularity. In clinical practice, histological overlap between mild, moderate, and severe blunting is often observed in a single biopsy series ^, ( Fig. 16.7 ). Loss of villous height is usually matched by crypt elongation or hyperplasia, such that the overall width of the mucosa usually remains unchanged. The degree of injury observed in surface and crypt epithelia can vary widely and does not always reflect the degree of villous blunting or the severity of symptoms. When the condition is histologically severe, the surface epithelium shows loss of columnar shape, mucin depletion, vacuolization, and enlargement of cell nuclei (see Fig. 16.7A ). Cells may show loss of polarity, with stratification, pyknosis, and fragmentation of nuclei. IELs are increased, especially in the tips of villi. Surprisingly, the epithelium situated along the sides of blunted villi may appear entirely normal, despite the proximity to severely affected cells at the surface. The cells at the base of hyperplastic crypts often show nuclear enlargement and increased mitoses, reflecting an increase in proliferative activity. ^,

The lamina propria in celiac disease typically shows a variable increase in plasma cells. Neutrophils, crypt abscesses, and increased eosinophils are not classic findings but are present in a substantial minority of patients at diagnosis. ^{, ,} However, the finding of diffuse or marked acute inflammation should prompt consideration of other diagnoses, such as drug reactions, “peptic duodenitis,” Crohn’s disease, and refractory sprue.

It is suggested that pathology reports be accompanied by a note, the content of which depends on the degree of clinical information available at the time of sign-out (see Table 16.1 ). This is especially needed when clinical information is not provided. If a prior history of celiac disease is known or positive tTG antibodies have been identified, the note could read, “The histological findings support a clinical diagnosis of celiac disease.” Comparison to prior biopsies should be included if at all possible. In some specialized celiac centers, synoptic templates are utilized.

Atrophic-hypoplastic lesions (type 4) are rare and are similar to the lesions described in biopsies from patients with refractory, or unclassified, sprue (see later). The finding of atrophic mucosa may correlate with a lack of response to a gluten-free diet.

Histology of Treated Disease (Response to a Gluten-Free Diet)

Patients who respond clinically to a gluten-free diet are not routinely subjected to repeat biopsy. Studies have shown that mucosal injury, including persistently increased IELs and villous blunting, may persist for up to 1 year after following a strict gluten-free diet. ^, However, in many patients, biopsies show a return to normal or near normal within a year or less if diet adherence is achieved (see Fig. 16.7C ). Some patients show persistence of moderate or even severe lesions despite marked clinical improvement. Repeat biopsies are indicated when the clinical response is poor and when other disorders, such as refractory sprue, lymphoma, or infection are under consideration.

Refractory Celiac Disease

Approximately 10% of patients with celiac disease have persistent symptoms despite good faith attempts to adhere to a gluten-free diet, so-called nonresponsive celiac disease. Only 10% of those, or approximately 1% of all celiac patients, develop refractory celiac disease (RCD) with a female-to-male ratio of 2:1. RCD is defined as an absent or incomplete clinical response to a strict gluten-free diet, usually in a patient with prior serological or genetic evidence of celiac disease, and is further subdivided into RCD I and RCD II based on clinicopathological criteria (see later). When considering reasons for nonresponsive celiac disease, inadvertent gluten ingestion should be ruled out, in addition to other potential causes of diarrhea or malabsorption, such as pancreatic insufficiency, concomitant collagenous colitis, lymphoma, or other rare entities, such as adult-onset autoimmune enteropathy ( Fig. 16.8 ). These entities leading to “apparent refractoriness” must be excluded carefully by clinicians before considering the serious and potentially life-threatening condition of RCD. Expert reviews and multicenter studies of this rare condition highlight the salient features of RCD. The prevalence is unknown, with approximately 900 unique patients reported from referral centers as of 2018 ^, ; precise definitions vary between centers; the pathogenesis is poorly understood; and therapies are based on anecdotal practices and opinion. ^, The following information appears to be supported by numerous studies.

RCD is categorized into two types based on the immunophenotype and clonality of IELs in duodenal tissue, and also based on responses to incremental therapies (see Table 16.7 ). Patients with RCD I have normal intraepithelial T-cell phenotype by flow cytometry or immunohistochemical analysis (CD3+, CD8+), do not show clonal rearrangements of the TCR gene, often respond to generic immunosuppression regimens, have a low risk of progression to enteropathy-associated T-cell lymphoma, and have a normal life expectancy. ^, By definition, patients with RCD II have abnormal intraepithelial T cells (CD3 cytoplasmic +/surface−, CD8−), often have monoclonal TCR gene rearrangements, are usually refractory to immunosuppression, and are at increased risk of progression to lymphoma and death. ^, These findings have led to the theory that a significant proportion of refractory sprue cases represent a form of in situ, or cryptic, T-cell lymphoma. There is no agreement on appropriate therapy, but numerous chemotherapeutic and immunomodulatory regimens have been used. ^{, , ,} Specific regimens that have been attempted include cladribine, recombinant IL-10, alemtuzumab (an anti-CD52 monoclonal antibody), and most recently, anti-IL-15 antibodies. ^, A seven-center study of 232 RCD patients found that an algorithm combining age, albumen levels, and detection of abnormal lymphocyte populations or presence of clonal populations accurately predicted 5-year survival in RCD.

The pathologist’s role in considering a diagnosis of RCD is pivotal. While much of the RCD literature states that TCR clonality studies and immunostains for CD3 and CD8 are useful in confirming a diagnosis of RCD and in distinguishing RCD1 from RCD II, ^{, , , ,} newer data have shown monoclonality established using polymerase chain reaction (PCR) in formalin-fixed, paraffin-embedded tissue to be unreliable and nonspecific, especially if common causes of persistent symptoms have not been excluded. Monoclonal TCR gene rearrangements are present in new-onset celiac disease, in patients not adhering to a gluten-free diet, in Helicobacter pylori –associated duodenitis, and in RCD I. Likewise, by immunohistochemistry, RCD II should be considered only when CD8+ IELs are almost nonexistent, since they comprise only a subset of CD3+ IELs in inflammatory states. Although these tests can be informative in the truly refractory patient, it is important that pathologists avoid embarking on tests for RCD until the extensive clinical workup to detect other causes is complete. In that setting, fresh tissue for flow cytometry may be a useful adjunct to findings in formalin fixed tissues.

From a histological (not causative) point of view, small bowel biopsies in refractory sprue usually reveal moderate to severe villous flattening despite adherence to a gluten-free diet ( Box 16.6 ). The lesions are typically patchy and variable in distribution, although diffuse flattening of the entire small intestine may occasionally occur. In a longitudinal study of 10 patients with refractory sprue, several histological features were strongly associated with a refractory course. In that study, collagenous sprue developed in five patients. In addition, basal plasmacytosis and mucosal thinning (corresponding to Marsh type 4) were found almost exclusively in biopsies from refractory patients.

Collagenous sprue has since been reported in several series as a pattern of injury seen in the setting of RCD or unclassified sprue. ^{, ,} Like its counterpart in the colon, collagenous sprue is a female-predominate injury pattern characterized by increased deposition of collagen beneath the surface epithelium basement membrane. Rigorous diagnostic criteria, including entrapment of small capillaries and fibroblasts in the collagen layer, should be applied to establish this diagnosis ( Fig. 16.9 ). A trichrome stain to highlight collagen is often helpful. Collagen deposition may be patchy and often appears late in the course of illness. Associated collagenous gastritis and collagenous colitis may occur. Clonal T-cell populations are sometimes found by PCR analysis of fixed tissue, but this may be a prognostically insignificant finding. While early reports suggested dismal clinical outcomes, ^, more current literature provides evidence that collagenous sprue represents a histological pattern with a heterogenous clinical outcome. Some patients respond to a gluten-free diet and steroids, others require total parenteral nutrition and chemotherapy, and some die of intractable disease. ^{, ,} In summary, collagenous sprue is a histological injury pattern that usually is seen in patients who fulfill criteria for RCD. Its presence cannot, by itself, be used to discriminate between RCD I and RCD II.

Malignancy in Celiac Disease

An association between celiac disease and an increased incidence of lymphoma and carcinoma has been reported. While some studies suggest a relative risk of approximately 30-fold, recent population-based studies suggest that the increased risk may be lower. In two large population-based studies of patients with latent celiac disease, defined as positive serology with normal biopsy, there was no increase in mortality or lymphoma risk on follow-up. ^, The role of adherence to a gluten-free diet in decreasing the risk of malignancy in patients with celiac disease is controversial. ^{, ,} A number of studies have confirmed that strict dietary compliance, especially beginning in childhood, probably confers protection from malignant complications.

Intestinal lymphoma in celiac disease, first documented in 1937, occurs in 5% to 10% of patients in some series. Lymphomas that arise in this setting were originally classified as reticulum cell sarcomas or malignant histiocytosis. In some reports, the term ulcerative jejunitis (now understood to be synonymous with lymphoma) was used to describe tumors that develop in the setting of malabsorption. The term enteropathy-associated T-cell lymphoma is the current terminology in use, based on their characterization in 1985 by Isaacson et al. ^, However, rarely, B-cell lymphomas may develop in association with refractory sprue as well.

Lymphoma may present as solitary or multiple tumors and may involve any portion of the small bowel, either with or without involvement of the mesenteric lymph nodes. Clinically, the onset of lymphoma is frequently associated with relapse of malabsorption in previously gluten-free diet–responsive patients.

Studies of the risk of carcinoma in celiac disease patients are inconclusive. While older studies cite an increased frequency of carcinomas, especially those arising in the GI tract, in patients with celiac disease, ^, recent population studies in Sweden and the United Kingdom suggest no increase in solid tumor incidence in celiac disease, but confirm an increase in lymphoproliferative disorders. In a meta-analysis of cancer risk, an increase in overall and small intestinal carcinomas was found, which may decrease on diet adherence. Interestingly, the molecular pathogenesis of celiac disease–associated small bowel carcinoma may differ from that occurring in patients with Crohn’s disease.

Other Complications in Celiac Disease

A variety of intestinal and extraintestinal pathological conditions occur in patients with celiac disease. These include lymphocytic gastritis, collagenous gastritis, lymphocytic colitis, collagenous colitis, ^{, ,} dermatitis herpetiformis, ^, nonspecific intestinal ulceration, ^, and a variety of other associations. ^,

Differential Diagnosis

As with mild infiltrative lesions, the villous blunting of type 3 lesions is not specific for celiac disease (see Tables 16.5 and 16.6 ). ^, Flattening of small intestinal villi can be seen in several conditions, such as tropical sprue, bacterial overgrowth, ^, unclassified sprue, specific food allergies, common variable hypogammaglobulinemia, and an ever-increasing list of medications (see Box 16.7 and the section Drug Injury of the Small Bowel). Villous blunting is also noted in infants and young children with viral gastroenteritis or cow’s milk protein intolerance. Small bowel Crohn’s disease and eosinophilic gastroenteritis may rarely result in villous blunting. ^, Distinction of these entities from celiac disease rests primarily on clinical, not pathological, data. However, in the rare instance of a flat mucosal biopsy in common variable hypogammaglobulinemia, the lack of lamina propria plasma cells and concurrent infection with Giardia are clues to the correct diagnosis. Biopsies in tropical sprue are only rarely completely flat, and a history of residence in tropical climates allows distinction from celiac disease, although this may be a less reliable indicator since the incidence of celiac disease is rising around the world. Above all, serum antibody tests, a careful medication history, and a response to a gluten-free diet are of paramount importance in distinguishing celiac disease from other conditions.

Epidemiology and Clinical Features

Tropical sprue is a chronic malabsorptive syndrome, often associated with folate and vitamin B ₁₂ deficiency, that occurs in residents of, or visitors to, the Indian subcontinent and parts of Southeast Asia, Central America, and the Caribbean. Notable exceptions are Jamaica and sub-Saharan Africa. In tropical populations, adults are more severely affected than children. The disease occurs in both endemic and epidemic forms. Patients present with chronic nonbloody diarrhea, weight loss, bloating, and abdominal cramps. In severe cases, secondary vitamin deficiencies can lead to complications of nutritional deficiencies (such as subacute combined degeneration of the spinal cord due to vitamin B ₁₂ deficiency).

The cause of tropical sprue remains unknown, although the preponderance of evidence supports an infectious origin. ^, The illness probably begins with an acute infection of the small or large intestine that may be bacterial, viral, or parasitic in origin. Subsequently, a chronic infection, with colonization of the small bowel by aerobic enterotoxigenic bacteria, is believed to occur, which probably results in ongoing injury to enterocytes. Bacteria isolated from patients with tropical sprue include Klebsiella pneumoniae , Escherichia coli, and Enterobacter cloacae. However, a consistent and specific causal agent has not been identified. An environment conducive to bacterial overgrowth may result from the release of enteroglucagon, a potent inhibitor of peristalsis, during the acute infectious phase of the disease. A study from India documented contamination of the small bowel with aerobic bacteria, and prolonged orocecal transit time in patients with tropical sprue, with both abnormalities reversing after prolonged antibiotic treatment. The theory of bacterial overgrowth is strongly supported by the response of some patients to broad-spectrum antibiotics, such as tetracycline, along with folic acid. In addition, studies have shown an increased frequency of HLA antigens Aw19 and Aw13 in some patients with tropical sprue. However, the role of HLA antigens in the pathogenesis of this disease remains poorly understood.

The entire small bowel is usually affected in tropical sprue, including the ileum, ^, leading to vitamin B ₁₂ and folate deficiency in most symptomatic patients. Vitamin deficiencies may lead to proliferative injury (e.g., megaloblastic change) to the intestinal crypts and other epithelia. Megaloblastic change, or macrocytosis, refers to the nuclear and cytoplasmic enlargement of epithelial cells that occurs in the setting of interrupted DNA synthesis and cell division (see Chapter 7 ).

Pathological Features

Asymptomatic native populations susceptible to tropical sprue often harbor pathological changes that include villous shortening and increased inflammation. The degree of abnormality in asymptomatic people is generally minor but is occasionally pronounced. ^, Evidence of malabsorption is also frequently found in asymptomatic native residents.

As stated above, the entire small bowel, including the ileum, is usually affected in tropical sprue. ^, This is in contrast to celiac disease, in which pathological lesions are present in the duodenum and jejunum and only rarely extend into the ileum. The patterns of distribution of these two diseases are consistent with their pathogenesis. Tropical sprue is caused by colonization of the bowel by bacteria, whereas celiac disease is a response to a dietary antigen that is present in highest concentrations in the proximal gut.

Microscopic Pathology

There is significant overlap in the histological features of tropical sprue and celiac disease. Small bowel biopsies in tropical sprue reveal varying degrees of villous blunting, crypt hyperplasia, and increased mitotic activity ( Fig. 16.10 ). ^{, ,} An increase in lamina propria lymphocytes, plasma cells, and eosinophils, as well as IELs, is also seen. In tropical sprue, IELs are more numerous in the crypts than in the surface cells, unlike celiac disease, in which the reverse situation occurs. In severe cases, decreased mitotic activity is combined with a lack of surface epithelial cell maturation. The cells acquire a cuboidal shape, become mucin depleted, and accumulate cytoplasmic fat droplets. ^{, , ,} As previously mentioned, concomitant folate and vitamin B ₁₂ deficiency may lead to mucosal atrophy, manifested by crypts lined by cells with markedly enlarged (megaloblastic) nuclei. Completely flat mucosa, common in celiac disease, is almost never seen in tropical sprue.

Electron microscopic studies of small bowel biopsies in tropical sprue have revealed irregularities of microvilli, increased lysosomes, accumulation of fat in surface epithelium, and the presence of dense material beneath the basal lamina.

Differential Diagnosis

The histological changes in tropical sprue are nonspecific and can be seen in a variety of conditions (see Fig. 16.8 ). Thus a clinical history of residence in, or prolonged visits to, endemic areas is critical in establishing a correct diagnosis. Parasitic and other specific infections must be excluded before a diagnosis of tropical sprue can be made confidently. Biopsies that show completely flat mucosa should arouse suspicion for other diseases such as celiac disease and drug reactions. However, mild to moderate mucosal lesions can be seen in both celiac disease and tropical sprue. Clinical improvement after treatment with broad-spectrum antibiotics further supports a diagnosis of tropical sprue.

Pathogenesis

Bacterial overgrowth by coliform bacteria in the small intestine occurs in a variety of conditions, all of which predispose the individual to decreased motility and stasis. ^{, ,} These include motor and neural disorders such as scleroderma, diabetes mellitus, pseudo-obstruction, and amyloidosis; structural defects such as diverticulosis and strictures; genetic conditions such as pancreatic deficiency due to cystic fibrosis; and surgical manipulations that lead to isolated bowel segments, such as Billroth II gastrojejunal anastomosis or short bowel syndrome. Immune deficiency states, such as AIDS and common variable immune deficiency, may also result in bacterial overgrowth and may contribute to the diarrheal illness that frequently occurs in these conditions. ^, Clinically significant bacterial overgrowth also occurs in older adult patients without any other predisposing features, especially among those with disabilities. ^, Several studies have documented bacterial overgrowth in patients with irritable bowel syndrome. Small intestinal bacterial overgrowth has become a subject of renewed study as the role of the microbiome in general health has come to light.

Clinical Features

Regardless of the underlying cause, this syndrome is characterized by overgrowth of anaerobic bacteria, normally confined to the colon, within the small intestine. ^{, ,} Patients with this condition typically have abdominal pain, bloating, diarrhea, and steatorrhea, although malabsorption of vitamin B ₁₂ , carbohydrates, and other nutrients can occur as well. Proposed theories of pathogenesis include deconjugation of bile salts by anaerobic bacteria, which leads to fat malabsorption. In addition, certain nutrients, such as vitamin B ₁₂ , may be depleted by luminal bacteria. Ultrastructural studies of this condition have revealed evidence of damage to surface epithelium and the brush border, with some evidence of defective fat transport and absorption.

Several methods of diagnosis have been used to detect bacterial overgrowth. The traditional gold standard is small intestinal aspirate culture showing growth of at least 10 ⁵ colony-forming units of bacteria per milliliter of small bowel fluid (normal small bowel has fewer than 10 ⁴ colonies per milliliter). Typically, multiple organisms are identified and include species of Bacteroides , Enterococcus , and Lactobacillus . Other diagnostic tests include the ¹⁴ C- d -xylose or hydrogen breath tests. When bacterial overgrowth is suspected or proven, antibiotic therapy may result in marked improvement. ^,

Pathological Features

Small bowel biopsies from patients with bacterial overgrowth may be histologically normal despite clinical evidence of malabsorption. When abnormal, biopsies typically reveal mild to moderate villous blunting with increased chronic inflammation in the lamina propria and epithelium, as well as crypt hyperplasia ( Fig. 16.11 ). ^{, ,} Vacuolated epithelial cells, probably containing lipid, may also be seen. One study found that villous blunting, defined as a villous-to-crypt ratio less than 3:1, was the most common abnormality present in small bowel biopsies of patients with bacterial overgrowth versus controls. However, in the same study, more than half of the biopsies from patients with bacterial overgrowth were scored as histologically unremarkable. In contrast to celiac disease, IELs may not be increased in bacterial overgrowth. When present, histological abnormalities tend to be patchy and vary from segment to segment, so that biopsies taken during the same procedure from different sites may show variable changes. This pattern of involvement helps distinguish bacterial overgrowth from celiac disease.

As in other conditions characterized by villous blunting, the histological features are entirely nonspecific and do not correlate with severity of clinical symptoms.