Test Catalog

Test ID: HPCRP    
Helicobacter pylori with Clarithromycin Resistance Prediction, Molecular Detection, PCR, Varies

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

Assessing pure isolates of Helicobacter pylori to predict clarithromycin resistance or susceptibility

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.


When this test is ordered, the reflex test may be performed at an additional charge.

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 its 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 clinical 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; the presence or absence of the 3 most common 23S ribosomal RNA gene single nucleotide variations (A2143G, A2142G, and A2142C) is reported.


A not detected result indicates the absence of detectable H pylori DNA.

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

This assay is used for testing of isolates of Helicobacter pylori. Request HPFRP / Helicobacter pylori with Clarithromycin Resistance Prediction, Molecular Detection, PCR, Feces if testing directly from feces is desired.

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


This assay examines the 3 most common 23S ribosomal RNA point variants associated with clarithromycin resistance in H pylori. Other mechanisms of clarithromycin resistance are not assessed, nor are mechanisms of resistance to nonclarithromycin antimicrobial agents. The ZMMLS / Antimicrobial Susceptibility, Aerobic Bacteria, MIC, Varies assay is preferentially recommended for culture isolates to define a fuller spectrum of antimicrobial susceptibility (ie, to include antimicrobial agents beyond clarithromycin).

Supportive Data

During laboratory verification studies, 111 isolates of Helicobacter pylori (grown on Columbia agar with 5% sheep blood) with previous clarithromycin phenotypic susceptibility testing performed and which had undergone partial 23S ribosomal RNA gene sequencing were studied. This test matched phenotypic testing for 106/111 isolates (95.5% categorical agreement); a major error rate of 8.7% (2/23) and very major error rate of 3.4% (3/88) were observed. The assay results perfectly matched partial 23S ribosomal RNA gene sequencing data, including that performed on the 5 discordant isolates.


A subset of 45 of the isolates (including 1/5 isolates demonstrating a discordant result in the earlier study) were re-grown on tryptic soy agar with 5% sheep blood and re-assayed with this assay. The assay matched phenotypic testing in 44/45 isolates (97.8% categorical agreement); a major error rate of 0% and very major error rate of 3% (1/33) were observed. The PCR assay perfectly matched partial 23S ribosomal RNA gene sequencing data, including that performed on the single discordant isolates.

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