Inflammatory Bowel Disease - IBD

Inflammatory bowel disease (IBD) includes a spectrum of chronic disorders that affect the gastrointestinal (GI) tract and is believed to develop as a result of immunologic, environmental, and genetic influences.   Crohn disease (CD) and ulcerative colitis (UC) are the primary subtypes of IBD; a third subtype that cannot be categorized as either CD or UC based on features at diagnosis is referred to as IBD, unclassified (IBD-U) (sometimes referred to as “indeterminate colitis”).   IBD can vary in severity; a higher inflammatory burden and greater anatomic extent of disease characterize more severe IBD.  Early diagnosis is important for disease management,  but distinguishing between the IBD subtypes can present a diagnostic challenge, particularly because CD and UC can manifest as atypical phenotypes.  A combination of clinical tools, including laboratory tests, clinical examination and patient history, and endoscopic and radiologic findings, is used to establish diagnosis and to determine the extent and severity of disease.  Laboratory testing is also used for disease management and for therapeutic drug monitoring, which is particularly important in IBD to optimize clinical outcomes.  Laboratory tests for IBD include serum and fecal inflammatory marker and stool culture tests to rule out enteric infections.   Due to their limited sensitivities, serologic tests may only be useful as adjunct diagnostic tools for IBD diagnosis and/or risk stratification.

Quick Answers for Clinicians

How are the two main forms of inflammatory bowel disease, Crohn disease and ulcerative colitis, differentiated?

Differentiating between Crohn disease (CD) and ulcerative colitis (UC) can be challenging, but features such as rectal bleeding and anemia are more common in UC than CD, whereas perianal involvement, stenosis, abscesses, and fistulas are more common in CD than UC.  Distinguishing the two diseases generally requires endoscopic evaluation and/or imaging.  Serologic testing may help to differentiate between inflammatory bowel disease (IBD) subtypes (eg, antiglycan antibodies are more frequently seen in CD than in UC), but this testing is not highly sensitive, which limits its usefulness.  Serologic antibody testing is not currently recommended by the American College of Gastroenterology (ACG) for IBD diagnosis.   The ACG also discourages the use of serologic testing to predict disease course or severity in UC.  However, serologic response to certain microbial antigens is a recognized risk factor for progression in CD; therefore, serologic testing may aid in the risk stratification of patients with CD.  See Serologic Markers.

How is genetic testing used in inflammatory bowel disease?

Although some genetic variants are associated with specific inflammatory bowel disease (IBD) phenotypes, genetic testing has not been found to be of significant benefit for IBD diagnosis or prognosis.   Genetic testing is primarily used for therapeutic decision-making in IBD because variants in TPMT and NUDT15 genes can affect how patients metabolize thiopurine drugs used for IBD treatment. See Thiopurine Therapy-Related Testing.

What factors affect diagnosis of inflammatory bowel disease in pediatric patients?

Diagnosis of inflammatory bowel disease (IBD) in pediatric patients is complicated by the fact that studies in recent years have reported atypical phenotypes of all three subtypes of IBD in children and adolescents, which points to a need to more accurately define the subtypes.  A new subtype of ulcerative colitis (UC) in pediatric patients is referred to as atypical UC.  Diagnosis is more challenging when disease onset occurs in infancy and when the disease primarily affects only the colon; it is more difficult to distinguish between Crohn disease (CD), UC, and IBD, unclassified (IBD-U) in these cases.  A greater percentage of IBD cases (up to 33%) are diagnosed as IBD-U in patients younger than 2 years.  As these patients become older, a more definitive diagnosis of CD or UC is often made. 

Indications for Testing

Laboratory testing for IBD is appropriate to:

  • Diagnose individuals who present with abdominal pain, diarrhea or bloody stool, frequent/urgent bowel movements, tenesmus, fatigue, weight loss, anemia, fever, fistulas, and/or growth failure (in children)
  • Guide treatment decisions in patients with an established diagnosis
  • Monitor disease activity and therapeutic response

Laboratory Testing


Initial Testing

Most laboratory tests used for IBD diagnosis are nonspecific; however, the following tests can help to identify inflammation associated with IBD. Definitive diagnosis of IBD typically involves imaging and endoscopic evaluation. 

Complete Blood Count

The American College of Gastroenterology (ACG), European Society for Pediatric Gastroenterology, Hepatology, and Nutrition (ESPGHAN), and North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition (NASPGHAN) recommend that initial laboratory testing for IBD include a CBC. CBC results may reveal anemia and increased platelet counts in patients with IBD. 

Inflammatory Markers

The ACG recommends tests for inflammatory markers, such as C-reactive protein (CRP) or erythrocyte sedimentation rate (ESR), in the initial workup for IBD.  Serum CRP and ESR concentrations will be increased in some patients with IBD  ; however, both CRP and ESR are nonspecific markers of inflammation.  CRP is the more sensitive and specific marker for detecting acute phase inflammation. 

ESPGHAN and NASPGHAN recommend that initial testing for IBD in pediatric patients include at least two tests for inflammatory markers such as albumin, transaminases (aspartate or alanine aminotransferase), and gamma-glutamyl transferase (yGT).  Albumin concentrations may be decreased in patients with IBD. Transaminases and yGT concentrations may be increased, and measurement of these markers is recommended to evaluate patients for extraintestinal disease.  However, increased levels may be associated with causes other than extraintestinal illness. 

Measurement of fecal calprotectin, a calcium-binding protein, is useful to screen for intestinal inflammation associated with disease activity (eg, at initial presentation or relapse).    Fecal calprotectin testing is a noninvasive substitute for endoscopy if the procedure is unavailable or unfeasible.  Fecal calprotectin is considered among the most useful of the inflammatory markers for IBD. Concentrations of fecal calprotectin have been found to correlate well with the level of mucosal inflammation,  and a normal fecal calprotectin result has a high negative predictive value for IBD.  Fecal calprotectin measurement can also be used as a screening test to help distinguish between IBD and irritable bowel syndrome (IBS). 

Fecal lactoferrin, an iron-binding protein, is another useful marker of intestinal inflammation in IBD ; however, more evidence is available for fecal calprotectin.  One potential caveat is that fecal biomarkers may have high variability between different sample collections from a single patient. 

A negative fecal calprotectin result and a low pretest probability of disease may be sufficient to rule out a diagnosis of IBD. 

Fecal Pathogens

The ACG, ESPGHAN/NASPGHAN, and the British Society of Gastroenterology (BSG) recommend testing to identify fecal pathogens and Clostridium difficile in cases of clinical suspicion for IBD.     However, an enteric infection may not rule out a diagnosis of IBD because such an infection may initiate IBD.  The ACG recommends stool culture testing for Salmonella, Shigella, Yersinia, Campylobacter, and C. difficile, as well as testing for Giardia lamblia if exposure is suspected. 

Serologic Markers

Serologic marker testing is not currently recommended by the ACG for IBD diagnosis or prognosis due to its limited sensitivity and usefulness in differentiating between IBD subtypes.   Some specific markers, such as anti-Saccharomyces cerevisiae antibodies (ASCAs) and perinuclear antineutrophil cytoplasmic antibodies (pANCAs), have been associated with IBD. ASCAs are more common in CD and less common in UC, whereas pANCAs are more common in UC cases and less common in CD.  Patients with IBD-U are often negative for both antibody types.  Other serologic markers associated with IBD include laminaribioside carbohydrate (immunoglobulin G [IgG]), mannobioside carbohydrate (IgG), and chitobioside carbohydrate (IgA) antibodies.

Although serologic marker testing is not considered useful to predict disease course or severity in UC, serologic response to certain antigens is a recognized risk factor for progression in CD.   Therefore, serologic testing may aid in risk stratification of patients with CD. 

Genetic Testing

Although some genetic variants are associated with specific IBD phenotypes, genetic testing is not currently recommended for IBD diagnosis.   No one genetic variant has a high enough frequency in CD to be considered helpful for diagnosis.  Genetic markers in UC have been only modestly helpful in determining the course or severity of disease.   However, genetic testing has a role in guiding IBD treatment (see Thiopurine Therapy-Related Testing).

Other Testing

A workup for IBD relies on a variety of diagnostic tools, such as endoscopic, radiographic, pathologic, and histologic findings, in addition to laboratory tests.  Endoscopic examination, in conjunction with histologic confirmation, helps determine the extent of disease and provides baseline data for later assessment of therapeutic response. 

Tests Before Treatment Initiation

In addition to the tests used for diagnosis, some specific tests are recommended before treatment initiation. The European Crohn’s and Colitis Organisation (ECCO) recommends that pretreatment laboratory testing include electrolyte, renal function, iron level, immunization status, and vitamin D tests.  See Monitoring for tests used to monitor treatment.

Anti-JC Virus Antibodies

Testing for antibodies to JC virus is recommended in patients with CD; natalizumab should be used for CD treatment only in patients negative for anti-JC virus antibodies. 

Thiopurine Therapy-Related Testing

Pharmacogenetic testing before treatment initiation may be helpful to guide therapeutic decisions, particularly because treatment failure due to individual differences in medication response is not uncommon in IBD.  Thiopurine drugs are commonly used in treating IBD.

The American Gastroenterological Association (AGA) recommends either phenotype or genotype testing in adults beginning thiopurine therapy.  TPMT and NUDT15 gene variants (detected by genotype testing) as well as reduced TPMT enzyme activity (determined by phenotype testing) are associated with a greater risk of myelosuppression in response to treatment with thiopurines due to accumulation of active thiopurines.  Phenotype testing should not be performed in patients already receiving treatment with thiopurines because results will be falsely low. In addition, the current TPMT phenotype may not reflect the future phenotype, particularly in patients who received blood transfusions within 30-60 days of testing.

Guidelines for thiopurine dosing are published by the Clinical Pharmacogenetics Implementation Consortium  and can help avert myelosuppression. In patients with TPMT and/or NUDT15 variants or patients with demonstrated TPMT enzyme activity deficiency, a significant reduction in dose may be needed.  Pharmacogenetic testing does not replace the need for clinical monitoring of patients treated with thiopurine drugs.

Monoclonal Antibody Therapy-Related Testing

Before treatment with monoclonal antibodies such as antitumor necrosis factor (anti-TNF) agents, the ACG recommends testing for inactive opportunistic infections such as tuberculosis (TB).  Evaluation for viral hepatitis is also recommended before anti-TNF treatment is introduced.  See Monitoring for information about testing during treatment with monoclonal antibodies.


Tests to Monitor Disease

Patients with IBD should be monitored for complications, relapse, and anxiety and depressive disorders associated with IBD.  Long-term IBD is associated with an increased risk of colorectal cancer and dysplasia, most likely due to long-term inflammation, and patients must be monitored for the development of these conditions as well. 

Laboratory tests for monitoring in IBD include fecal and serum marker testing (in conjunction with imaging and endoscopic evaluation) to evaluate inflammatory responses.  Quantitative fecal calprotectin and fecal lactoferrin tests are sensitive markers that can be used to gauge IBD activity, recurrence, and relapse,  although they may be more useful tools in UC than in CD.  Serum CRP is not specific for inflammation in IBD but may aid in monitoring the activity of disease and therapeutic response. 

Tests to Monitor Treatment

CBCs should be monitored during treatment.  Additional tests may be indicated for specific types of treatment. For example, repeat testing for anti-JC virus antibodies is recommended at least every 6 months in patients receiving natalizumab for CD because of the risk of progressive multifocal leukoencephalopathy caused by the JC virus.  Liver and renal function monitoring are recommended during treatment with drugs such as sulfasalazine or mesalamine for UC.  Testing for cytomegalovirus colitis using sigmoidoscopy is recommended by the International Consortium for Health Outcomes Measurement (ICHOM) in adult patients with colitis that is unresponsive to treatment with corticosteroids; however, this testing is not recommended in children. 

Monoclonal Antibodies

Patients who do not respond initially (primary response failure) or who stop responding to treatment (secondary response failure) should be evaluated using therapeutic drug monitoring to determine the cause of response failure and to guide clinical decisions.  Some patients develop neutralizing antidrug antibodies (ADAs) that affect response to treatment, whereas others will manifest immunogenicity to anti-TNF-alpha (anti-TNF-α) antagonist drugs (eg, adalimumab, infliximab). See the following table for clinical interpretation of tests used to monitor treatment with adalimumab and infliximab.

Therapeutic drug monitoring is not indicated for patients who are receiving maintenance regimens but are in remission. 

Clinical Interpretation of Adalimumab/Infliximab and Antibody Testing Resultsa
Adalimumab/Infliximab Activity Neutralizing Antibody Titer Clinical Interpretation
Not detected   Not detected

Subtherapeutic dose (nonimmune-mediated failure)

Consider higher dosage of adalimumab/infliximab or shortening the dosing interval

Not detected   Detected

Neutralizing antibodies may be responsible for failure (immune-mediated failure)

Consider alternate anti-TNF-α drug

Detected Above targetb Not detected

Likely a mechanistic failure

Consider alternate therapy (non-anti-TNF-α drug)

Detected Below target Not detected

Subtherapeutic dose (nonimmune-mediated failure)

Consider intensification of therapy

Detected   Detected Future retesting suggested to rule out decreasing activity and/or increasing neutralizing antibodies

aARUP Laboratories offers combined tests and reflex tests for both adalimumab and infliximab: Adalimumab Activity and Neutralizing Antibody (2011248), Adalimumab Activity with Reflex to Antibody (2013605), Infliximab or Biosimilar Activity and Neutralizing Antibody (2008320), Infliximab or Biosimilar Activity with Reflex to Antibody (2013612).

bSuggested target trough concentrations for reactive monitoring of patients with active IBD on maintenance therapy is ≥5 µg/mL for infliximab and ≥7.5 µg/mL for adalimumab. 

The AGA makes no recommendation regarding the use of routine, proactive therapeutic drug monitoring in adults with quiescent IBD treated with anti-TNF-α agents. In the presence of sufficient trough concentrations, results of antibody testing should not guide treatment decisions.

ARUP Laboratory Tests

Inflammatory Marker Tests

Preferred test to detect acute phase inflammation

May be a useful marker of inflammation

Aids in differentiation of IBD from IBS and other functional disorders of the GI system

Aids in monitoring IBD and predicting relapse

Do not use to diagnose IBD or IBS; may be useful for monitoring IBD activity

Fecal Pathogen/Stool Culture Tests

Recommended rapid, stand-alone diagnostic test for C. difficile-associated diarrhea

Do not order for patients with diarrhea developed during prolonged hospitalization

Use as a sensitive alternative to traditional, insensitive ova and parasite examinations of stool specimens for the evaluation of GI infections

Detects Cryptosporidium hominis and parvum, Cyclospora cayetanensis, Dientamoeba fragilis, Entamoeba histolytica, Giardia lamblia/intestinalis/

Use to diagnose Vibrio-associated diarrhea in patients with appropriate exposure history or risk factors

Use to diagnose Yersinia-associated diarrhea in patients with appropriate exposure history or risk factors

Use to identify presence of Campylobacter species in stool as potential cause of diarrhea with appropriate exposure history or risk factors

Serologic Marker Tests

May be useful to aid in differentiating UC and CD in some patients with suspected IBD

Components: ASCA, IgG; ASCA, IgA; antineutrophil cytoplasmic antibody (ANCA), IgG

Aids in the diagnosis and prognostication of CD

Positive results may indicate aggressive disease

A negative result does not rule out CD

Components: ASCA, IgG; antilaminaribioside carbohydrate antibody (ALCA), IgG; antimannobioside carbohydrate antibody (AMCA), IgG; and antichitobioside carbohy-drate antibody (ACCA), IgA

May be useful for the diagnosis of CD

Test by itself is not diagnostic and should be used in conjunction with other parameters to confirm disease

Inflammatory Bowel Disease Differentiation Panel is the preferred test

Recommended adjunct diagnostic tool to differentiate UC from CD in IBD

Tests to Guide and Monitor Treatment

Phenotype test to assess risk for severe myelosuppression with standard dosing of thiopurine drugs

Testing should be performed before initiation of thiopurine therapy

For therapy optimization or toxicity evaluation, order Thiopurine Metabolites by LC-MS/MS

Genotype test to assess risk, due to genetics, for severe myelosuppression with standard dosing of thiopurine drugs

Use for individuals being considered for thiopurine therapy or who have had an adverse reaction to thiopurine therapy

Preferred test for patients with recent heterologous blood transfusion

Can be performed irrespective of thiopurine therapy

Use to evaluate response failure to infliximab or biosimilar therapy

Use to determine and adjust dosage or identify the need to change to another anti-TNF-α inhibitor

Use to evaluate response failure to adalimumab therapy

Use to determine and adjust dosage or identify the need to change to another anti-TNF-α inhibitor

Use to evaluate response failure to ustekinumab therapy

Use to adjust dosage

Use to evaluate response failure to vedolizumab therapy

Use to adjust dosage


Additional Resources

Medical Experts



Gwendolyn A. McMillin, PhD
Professor of Pathology (Clinical), University of Utah
Scientific Director, Mass Spectrometry Platform; Medical Director, Clinical Toxicology and Pharmacogenomics, ARUP Laboratories