Test Catalog

Test ID: HPFRP    
Helicobacter pylori with Clarithromycin Resistance Prediction, Molecular Detection, PCR, Feces

Useful For Suggests clinical disorders or settings where the test may be helpful

Aiding in the diagnosis of Helicobacter pylori infection and prediction of clarithromycin resistance or susceptibility directly from stool

Testing Algorithm Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

See Helicobacter pylori Diagnostic Algorithm in Special Instructions.

Clinical Information Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Helicobacter pylori is the main cause of peptic ulcer disease and, when left untreated, a risk factor for gastric cancer. Traditionally, H pylori diagnosis has included non-invasive tests (eg, urea breath test, fecal antigen test) or invasive tests (eg, gastric biopsy). Antimicrobial resistance in H pylori is poorly studied but is rising, challenging it's treatment; in 2012, an international clinical consortium study group recommended monitoring of clarithromycin resistance rates and ceasing its use at a threshold range of 15% to 20%.(1) Local monitoring has been practically impossible as not all patients undergo invasive testing, which yields a culture isolate that can be subjected to susceptibility testing. Even if invasive testing is performed, the organism can be difficult to isolate in culture and is highly fastidious once isolated, oftentimes not being amenable to phenotypic susceptibility testing. Further, there are only a handful of specialized microbiology laboratories that perform H pylori susceptibility testing. In an internal study of local and referred isolates published in 2016, clarithromycin resistance was observed to be most commonly due to A2143G (70/88 isolates, 79.6%), followed by A2142G (12/88 isolates, 13.6%) and A2142C (3/88 isolates, 3.4%) alterations in the 23S ribosomal RNA gene.(2) Overall, one of these alterations was found in 97% of clarithromycin resistant H pylori isolates studied.

Reference Values Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

Not applicable

Interpretation Provides information to assist in interpretation of the test results

A detected result indicates the presence of Helicobacter pylori 23S ribosomal RNA gene; also indicated is whether or not one the 3 most common 23S ribosomal RNA gene single nucleotide variations (A2143G, A2142G, and A2142C) associated with clarithromycin resistance is detected.


A not detected result for H pylori indicates the absence of detectable H pylori DNA, but does not negate the presence of the organism and may occur due to inhibition of the polymerase chain reaction (PCR), sequence variability underlying primers or probes, or the presence of H pylori DNA in quantities less than the limit of detection of the assay.

Cautions Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

Avoidance of bismuth compounds, antibiotics, and acid suppressive drugs (histamine H2preceptor antagonists and proton pump inhibitors) should occur for at least 2 weeks before the test, as these medications may lead to a false-negative test result due to potential activity against Helicobacter pylori.


Test results should be used as an aid in the diagnosis. The single assay should not be used as the only criterion to form a treatment decision; results of this test should be correlated with clinical presentation and results of other laboratory tests. A negative result does not negate the presence of the organism or active disease.


Potential cross-reactivity may occur with the following nonpylori Helicobacter species: Helicobacter acinonychis, Helicobacter cetorum, and Helicobacter mustalae (not been reported to cause disease in humans) and Helicobacter canis, Helicobacter cinaedi, Helicobacter bizzozeronii, and Helicobacter heilmannii (infrequently found in humans).


This assay examines the three most common 23S ribosomal RNA single point variants associated with clarithromycin resistance. Other mechanisms of clarithromycin resistance are not assessed, nor are mechanisms of resistance to non-clarithromycin antimicrobial agents.

Supportive Data

During laboratory verification studies, 745 fecal samples previously tested with the Meridian Premier Platinum HpSA Plus fecal antigen test were assayed with this test. The assay detected Helicobacter pylori DNA in 306/335 antigen positive fecal samples (91% sensitivity [87.5-93.9%, 95% CI]). The Helicobacter pylori with Clarithromycin Resistance Prediction (HPFRP) assay also detected H pylori DNA in 12/410 antigen negative fecal samples (97.1% specificity [94.9%-98.5%, 95% CI]). Positive and negative predictive values were 96.2% (93.5-98.0%, 95% CI) and 93.0% (90.1-95.2%, 95% CI), respectively. Simple Kappa Coefficient measurement of the performance of the assay against that of the antigen test was 0.89 (0.85-0.92, 95%CI), an almost perfect correlation.(Landis JR, Koch GG, Biometrics 1977;33:159-174)


Assessment of clarithromycin resistance prediction was made by performing bidirectional Sanger sequencing on all HPFRP positive samples. All 76 samples with predicted clarithromycin susceptible H pylori, demonstrated wild-type 23S ribosomal RNA gene sequence at positions 2142 and 2143. All 37 samples with predicted clarithromycin resistant, pylori demonstrated single nucleotide polymorphisms of A2143G, A2142G, or A2142C in the detected H pylori 23S ribosomal RNA gene.

Clinical Reference Recommendations for in-depth reading of a clinical nature

1. Malfertheiner P, Megraud F, O'Morain CA, et al: Management of Helicobacter pylori infection--the Maastricht IV/Florence Consensus Report. Gut. 2012 May;61(5):646-664 doi: 10.1136/gutjnl-2012-302084

2. Chen D, Cunningham SA, Cole N, et al: Phenotypic and molecular antimicrobial susceptibility of Helicobacter pylori. Antimicrob Agents Chemother. 2017 Mar 24;61(4):e02530-16

3. Beckman E, Saracino I, Fiorini G, et al: A novel stool PCR test for Helicobacter pylori may predict Clarithromycin resistance and eradication of infection at a high rate. J Clin Microbiol. 2017 Aug;55:2400-2405

4. Monteiero L, Gras N, Vidal R, et al: Detection of Helicobacter pylori DNA in human feces by PCR: DNA stability and removal of inhibitors. J Microbiol Methods. 2001 Jun;45(2):89-94

Special Instructions Library of PDFs including pertinent information and forms related to the test