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Helicobacter pylori Infection: Test Utilization Strategies for Diagnosis

November 2013


Approximately one-half of the world’s population is estimated to be infected with Helicobacter pylori, a gram-negative, curved bacterial rod, which has been associated with symptoms ranging from peptic ulcer disease and dyspepsia to gastric adenocarcinoma and mucosa-associated lymphoid tissue (MALT) lymphoma. Due to the potentially severe consequences of infection, accurate diagnosis and prompt initiation of therapy are important for successful disease resolution. Multiple different testing methodologies are available commercially to detect H pylori infection. Serologic evaluation for the presence of antibodies to H pylori is the most commonly ordered assay. However, according to recently published guidelines by the American Gastroenterology Association (AGA), the American College of Gastroenterologists (ACG), and the Infectious Diseases Society of America (IDSA)/the American Society for Microbiology (ASM), serologic testing should not be used by providers to diagnose active H pylori infection since the presence of antibodies may simply reflect prior exposure to the organism rather than current infection.1 This article reviews the current AGA and ACG recommendations, comments on current practices at Mayo Clinic, and provides clinicians with alternative testing strategies to identify active H pylori infection.

Helicobacter pylori

Available Diagnostic Assays

The currently available diagnostic assays for detection of H pylori can be classified as either invasive, requiring gastric endoscopy and tissue biopsy, or noninvasive, requiring readily available specimen types (ie, serum, breath, and stool samples). The specific indications for endoscopy will not be discussed in this article, although, in general, clinicians may wish to rule out malignancies or other noninfectious causes of the patient’s symptoms. When symptoms are considered typical of H pylori disease, noninvasive testing for that infection will be initially performed. The advantages and limitations of the various testing methodologies will be reviewed within this article.

Invasive Tests

Following recovery of 1 or more gastric tissue biopsies, evaluation for the presence of H pylori can be accomplished by 1 of 4 methods—culture, rapid urease tests, histopathology, or molecular testing (Table).


Isolation of H pylori by culture of a biopsy specimen is definitive evidence of active infection and isolates can subsequently be tested for susceptibility to various antimicrobial agents (Figure 1). However, the sensitivity of this method is limited by a number of factors, including 1) the site of biopsy and the quantity of viable organisms, 2) ability to maintain viability of this fastidious bacterium during transport to the laboratory (<3 hours from collection to culture), and 3) unique culture conditions that are not routinely available in all clinical laboratories. Due to the rigorous transport conditions, Mayo Medical Laboratories will currently only perform antimicrobial susceptibility testing on specimens submitted as H pylori isolates.

A. Gram stain of H pylori B. H pylori culture on sheep blood agar
C. H pylori culture on selective HP agar

Rapid Urease Tests

Rapid urease tests (RUTs) are based on a pH color indicator system and are designed to detect the presence of urease, an enzyme produced by H pylori that metabolizes urea to ammonia and carbon dioxide. For this assay, biopsy samples are submerged into the RUT solution, and if ammonia is produced, the pH will increase, leading to a color change that indirectly indicates the presence of H pylori. While these assays perform well (>90% sensitivity and specificity for active infection), the sensitivity decreases by approximately 25% among patients using bismuth-containing compounds, proton pump inhibitors (PPIs), or antibiotics.2 Similar to culture, these assays are limited by the site of biopsy and the ability to maintain viability during specimen transport prior to RUT testing. Additionally, other urease-producing organisms have been identified in the gastric mucosa which may lead to nonspecific RUT results.3


Similar to culture, the detection of H pylori in gastric biopsies by histopathologic evaluation is considered diagnostic for active infection (Figure 2). However, the sensitivity of this method is likewise limited by the site of biopsy and a lack of specificity as other nonpathogenic, curved bacteria may reside in the gastric mucosa. Immunohistochemical stains have been developed to improve specificity, though cross-reactivity has been seen with other Helicobacter species (ie, Helicobacter heilmannii).

Figure 2. Detection of Helicobacter pylori in Gastric Biopsy Tissue Using Specific Immunostains

Real-Time Polymerase Chain Reaction

Finally, molecular evaluation of biopsy specimens for the presence of H pylori DNA by real-time polymerase chain reaction (RT-PCR) is promising and numerous studies have found increased sensitivity and specificity of this method compared to culture, RUTs, and histopathology. However, RT-PCR is not widely available in the clinical setting and is currently restricted to research laboratories.

Noninvasive Tests

Currently, 3 noninvasive assays are available to detect H pylori infection. Of the 3 assays, the urea breath test (UBT) and the stool antigen test (SAT) are preferred over serologic evaluation to identify active disease. (Table)

TABLE. Advantages and Limitations of Invasive and Noninvasive Assays for Diagnosis of Helicobacter pylori Infection

Urea Breath Test

Similar to the RUT, the principle behind the urea breath test (UBT) is based on production of urease by H pylori and a positive result is indicative of active infection. For the UBT, the patient is asked to ingest a preparation containing 13C-labeled urea—a nonradioactive carbon isotope. If H pylori urease is present in the stomach, the urea is degraded to ammonia and labeled carbon dioxide (13CO2). The labeled 13CO2 is exhaled through normal respiration and collected in a specialized bag. The sample is subsequently analyzed on a spectrophotometer, which determines the level of 13CO2 present. This value is compared to a breath sample taken prior to ingestion of the labeled urea and a final result of positive or negative is determined (Figure 3).

Figure 3. Urea Breath Test Instrumentation

The clinical sensitivity and specificity of the UBT to detect active H pylori infection exceeds 93% in most studies, though a few reports indicate potential cross-reactivity with other gastric urease-producing organisms.3-6 A distinct advantage of this assay is that it can also be used to determine treatment efficacy. Current AGA and AGC guidelines recommend that providers wait at least 4 weeks following cessation of therapy to test for eradication of H pylori by the UBT.7

Despite the excellent performance characteristics, the utility of the UBT is limited by a number of factors. Most notable is the decreased sensitivity of this assay in patients who have taken proton pump inhibitors (PPIs), bismuth-containing products, or antibiotics within 14 days prior to testing. Therefore, it is recommended that these compounds be withheld for 7 to 14 days prior to performing the UBT, if possible.8 Additionally, the UBT assay currently offered through Mayo Medical Laboratories is not approved for use in patients <18 years of age. For individuals <18 years, Mayo Medical Laboratories recommends that the stool antigen test (SAT) be offered instead. Finally, the performance of this assay requires prolonged patient preparation (approximately 1 hour) and careful sample collection, which may be challenging if the collecting laboratory is unfamiliar with this test.

Stool Antigen Test

The stool antigen test (SAT) is an enzyme immunoassay (EIA) designed to detect H pylori in fecal specimens by measuring H pylori antigen released from organisms lining the stomach wall (Figure 4). As antigen is only detected if H pylori is present, the SAT can be used as an accurate tool to diagnose active H pylori infection and to establish eradication of the organism following treatment8,9 However, similar to the UBT, current guidelines recommend performing confirmatory testing for clearance of infection at least 4 weeks following cessation of therapy since, in the interim, residual antigen may continue to be shed from nonviable organisms and lead to false-positive results. Though numerous SATs are commercially available, those using monoclonal antibodies to the H pylori antigen (including the assay used at Mayo Medical Laboratories), show high clinical sensitivity and specificity, typically greater than 90%.8.9 Unlike the UBT, specimen collection (ie, stool) is much simpler for SATs and this assay is approved by  the US Food and Drug Administration (FDA) for use in pediatric patients.

Figure 4. Helicobacter pylori Stool Antigen Test

Similar to the UBT, the sensitivity of the H pylori antigen test is decreased if the patient has taken PPIs, bismuth-containing compounds, or antibiotics up to 14 days prior  to specimen collection. Therefore, if possible, these treatments should be withheld for at least 2 weeks prior to SAT testing. Additionally, while specimen collection is simpler compared to the UBT, patients may be uncomfortable with the process and may need to return  to the clinic for specimen submission.


Currently, detection of antibodies (ie, IgM, IgA, IgG) to H pylori remains the most commonly selected test by most providers to diagnose H pylori infection, due to the ease of specimen collection and single time-point testing. Additionally, unlike other noninvasive methods (ie, UBT and SAT), serologic profiles are not affected by prior use of PPIs, bismuth-containing compounds, or antibiotics, making serology an increasingly attractive method for immediate patient evaluation.

Despite these advantages, serologic testing for antibodies to H pylori should be ordered and results should be considered with significant caution. The greatest concern regarding this testing method is the poor positive predictive value (PPV) for many of these assays, particularly in regions of low H pylori endemicity (ie, 20%-30%), which represents the majority of the United States.8,10 Therefore, while a negative serologic result suggests the absence of prior exposure to H pylori, a positive result cannot be used to predict the presence of active disease. Additionally, the performance characteristics of these assays are poor, with clinical sensitivity and specificity parameters ranging from 76% to 85% and 79% to 90%, respectively.8,11 Finally, as antibodies to H pylori often remain for years following resolution of infection, serologic testing cannot be used to distinguish active from past infection or to document eradication of the organism following successful treatment. From a regulatory standpoint, while the UBT, SAT, and some H pylori IgG assays are FDA approved for use in most patient populations, there are currently no FDA-approved assays to detect H pylori IgM or IgA.

Based on these limitations, both the AGA and the AGC guidelines indicate that serologic methods should not be used to establish a diagnosis of active H pylori infection.  To minimize improper diagnosis and unnecessary treatment regimens, providers are strongly encouraged to amend their testing strategies by replacing serologic evaluation of patients with suspected H pylori infection, with either the UBT or the SAT assay. An exception to this universal recommendation is that in patients with bleeding ulcers, gastric atrophy, mucosa- associated lymphoid tissue (MALT) lymphoma and in those where other noninvasive tests may be falsely negative (due to use of PPIs, bismuth compounds, or antibiotics), positive serologic results  may support the diagnosis of active H pylori infection.9  In many of these patients, invasive testing results will  also be available.

The Experience at Mayo Clinic

To conform to current H pylori testing guidelines and to improve patient management, leadership from Mayo Clinic’s divisions of Clinical Microbiology and Gastroenterology worked together to update our algorithm to detect H pylori infection. As a result of this meeting, Mayo Clinic providers will now order either the UBT or the SAT for patients with suspected H pylori infection. Serologic evaluation is now considered a third-line testing option. This algorithm is available to all providers on the Mayo Medical Laboratories website (www.mayomedicallaboratories.com) and is included in this article.

Helicobacter pylori Diagnostic Algorithm


In conclusion, this article outlines the advantages and limitations of the available invasive and noninvasive testing methods to diagnose H pylori infection. By working collaboratively with our Mayo Clinic gastroenterology colleagues, the Clinical Microbiology Laboratory has successfully improved ordering practices, replacing serologic testing with either the SAT or the UBT to  evaluate patients with suspected H pylori infection. Implementation of this practice change will lead to more accurate diagnosis of active H pylori infection and is expected to decrease the number of prescriptions for unnecessary antimicrobial agents.

Authored by Elitza S Theel, PhD

Helicobacter pylori tests available from Mayo Medical Laboratories


  1. Baron EJ, Miller JM, Weinstein MP: A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2013 Recommendations by the Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM). Clin Infect Dis 2013 Aug;57(4):e22-e121
  2. Midolo P, Marshall BJ: Accurate diagnosis of Helicobacter pylori. Urease tests. Gastroenterol Clin North Am 2000;29:871-878
  3. Brandi G, Biavati B, Calabrese C, et al: Urease-positive bacteria other than Helicobacter pylori in human gastric juice and mucosa. Am J Gastroenterol 2006;101:1756-1761
  4. Gisbert JP, Pajares JM: Review article: 13C-urea breath test in the diagnosis of Helicobacter pylori infection -- a critical review. Aliment Pharmacol Ther 2004;20:1001-1017
  5. Chey WD: Accurate diagnosis of Helicobacter pylori. 14C-urea breath test. Gastroenterol Clin North Am 2000;29:895-902
  6. Solnick JV: Clinical significance of Helicobacter species other than Helicobacter pylori. Clin Infect Dis 2003;36:349-354
  7. Chey WD, Metz DC, Shaw S, et al: Appropriate timing of the 14C-urea breath test to establish eradication of Helicobacter pylori infection. Am J Gastroenterol 2000;95:1171-1174
  8. Chey WD, Wong BC: American College of Gastroenterology guideline on the management of Helicobacter pylori infection. Am J Gastroenterol 2007;102:1808-1825
  9. Malfertheiner P, Megraud F, O’Morain C, et al: Current concepts in the management of Helicobacter pylori infection: the Maastricht III Consensus Report. Gut 2007;56:772-781
  10. Go MF: Review article: natural history and epidemiology of Helicobacter pylori infection. Aliment Pharmacol Ther 2002;16 Suppl 1:3-15
  11. Loy CT, Irwig LM, Katelaris PH, Talley NJ: Do commercial serological kits for Helicobacter pylori infection differ in accuracy? A meta-analysis. Am J Gastroenterol 1996;91:1138-1144


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