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
Highlights
This test detects the Helicobacter pylori 23S ribosomal RNA gene and the 3 most common 23S ribosomal RNA gene single nucleotide variations (A2143G, A2142G, and A2142C) that lead to resistance to clarithromycin.
Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.
For more information see Helicobacter pylori Diagnostic Algorithm.
Method Name
A short description of the method used to perform the test
Real-Time Polymerase Chain Reaction (PCR)
NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.
Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test
Aliases
Lists additional common names for a test, as an aid in searching
Clarithromycin
H pylori
H. pylori
Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.
For more information see Helicobacter pylori Diagnostic Algorithm.
Specimen Type
Describes the specimen type validated for testing
Fecal
Ordering Guidance
Confirmation of eradication testing should not be ordered until 4 or more weeks after cessation of treatment.
Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete testing
The high sensitivity of amplification by polymerase chain reaction requires the specimen to be processed in an environment in which contamination of the specimen by Helicobacter pylori DNA is unlikely.
Patient Preparation:
1. For 4 weeks prior to testing, patient should not take antibiotics.
2. For 2 weeks prior to testing, patient should not take proton pump inhibitors or bismuth compounds.
Supplies: Culture and Sensitivity Stool Transport Vial (T058)
Specimen Type: Preserved feces
Submission Container/Tube: Commercially available transport system specific for recovery of enteric pathogens from fecal specimens (15 mL of nonnutritive transport medium containing phenol red as a pH indicator, either Cary-Blair or Para-Pak C and S)
Specimen Volume: 5 mL
Collection Instructions:
1. Collect fresh fecal specimen and submit 1 gram or 5 mL in container with transport medium.
2. Place feces in preservative within 2 hours of collection.
3. Place vial in a sealed plastic bag and send ambient or refrigerated. Specimens sent frozen will be rejected.
Special Instructions
Library of PDFs including pertinent information and forms related to the test
Forms
If not ordering electronically, complete, print, and send one of the following with the specimen:
1. Microbiology Test Request (T244)
Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the testing laboratory. The minimum volume is sufficient for one attempt at testing.
1 mL
Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected
| Fecal swab ESwab transport medium Feces in gel transport medium ECOFIX preservative formalin PVA fixative Unpreserved stool | Reject |
Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included
| Specimen Type | Temperature | Time | Special Container |
|---|---|---|---|
| Fecal | Ambient (preferred) | 7 days | |
| Refrigerated | 7 days |
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.
For more information see Helicobacter pylori Diagnostic Algorithm.
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 noninvasive 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 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 detected
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
Proton pump inhibitors (PPI) and bismuth compounds should be avoided for 2 weeks prior to initial testing; antibiotics should be avoided for 4 weeks prior to initial testing. False-negative results may occur if testing occurs prior to these recommended timeframes. If testing is performed to determine response to therapy, testing should be performed at least 4 weeks after completion of antibiotic therapy and after PPI therapy has been withheld for 2 weeks. Histamine 2-receptor antagonists have been shown to slightly decrease the sensitivity of some Helicobacter pylori tests and, if possible, should be discontinued 2 weeks before testing. Antacids do not appear to impair test performance and may be taken until one day before testing.
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 H 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.(3)
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 wildtype 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;61(5):646-664. doi:10.1136/gutjnl-2012-302084
2. Chen D, Cunningham SA, Cole N, Kohner PC, Mandrekar JN, Patel R. Phenotypic and molecular antimicrobial susceptibility of Helicobacter pylori. Antimicrob Agents Chemother. 2017;61(4):e02530-16. doi:10.1128/AAC.02530-16
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;55(8):2400-2405
4. Marrero Rolon R, Cunningham SA, Mandrekar JN, Polo ET, Patel R. Clinical evaluation of a real-time PCR assay for simultaneous detection of helicobacter pylori and genotypic markers of clarithromycin resistance directly from stool. J Clin Microbiol. 2021;59(5):e03040-20. doi:10.1128/JCM.03040-20
5. Savarino V, Tracci D, Dulbecco P, et al. Negative effect of ranitidine on the results of urea breath test for the diagnosis of Helicobacter pylori. AM J Gastroenterol. 2001;96(2):348-52. doi:10.1111/j.1572-0241.2001.03517.x
6. Chey WD, Grigorios L, Howden CW, Moss SF. ACG Clinical Guideline: Treatment of Helicobacter pylori infection. Am J Gastroenterol. 2017;112(2):p 212-239. doi:10.1038/ajg.2016.563
7. Jones NL, Koletzko S, Goodman K, et al. Joint ESPGHAN/NASPGHAN Guidelines for the Management of Helicobacter pylori in Children and Adolescents. J Pediatr Gastroenterol Nutr. 2017:64(6):p 991-1003. doi:10.1097/MPG.0000000000001594
8. Malfertheiner P, Megraud F, O'Morain CA, et al. Management of Helicobacter pylori infection-the Maastricht V/Florence Consensus Report. Gut. 2017;66(1):6-30. doi:10.1136/gutjnl-2016-312288
Method Description
Describes how the test is performed and provides a method-specific reference
Fecal samples (approximately 50-100 mg) are placed into 50% STAR buffer and extracted on a Hamilton Microlab STAR device using a Mayo Microlab Maxwell HT Fecal DNA Purification Kit. The polymerase chain reaction (PCR) assay employs a target-specific detection system including primers as well TaqMan detection probes alongside a SimpleProbe for melt curve analysis-based genotyping targeting the 23S ribosomal RNA gene. The LightCycler 480 II instrument amplifies and monitors target nucleic acid sequences by fluorescence during PCR cycling. Detection of amplified product is based on the TaqMan probe principle. For PCR product detection, the TaqMan probe binds the complementary strand of amplified target. Specific PCR Taq polymerase with 5'-3' exonuclease activity degrades the probe, releasing the fluorophore and breaking the proximity to the quencher molecule, allowing fluorescence of the fluorophores. At the conclusion of PCR cycling, amplified product is thermally denatured and then cooled to allow for a fluorescein labeled SimpleProbe to anneal to an 18-base pair region of the amplified target that includes 2 positions mutations at which are known to confer clarithromycin resistance. The temperature is slowly raised while consistently monitoring fluorescence. The process is completed in a closed system to mitigate contamination. Further, contamination control is achieved through UNG enzymatic treatment and a master mix which includes dUTPs.(Chen D, Cunningham SA, Cole NC, Kohner PC, Mandrekar JN, Patel R. Phenotypic and molecular antimicrobial susceptibility of Helicobacter pylori. Antimicrob Agents Chemother. 2017;61(4):e02530-16. doi:10.1128/AAC.02530-16)
PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information
Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.
Monday, Wednesday, Friday
Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.
Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded
Performing Laboratory Location
Indicates the location of the laboratory that performs the test
Fees :
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.
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- Prospective clients should contact their account representative. For assistance, contact Customer Service.
Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.
This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. It has not been cleared or approved by the US Food and Drug Administration.
CPT Code Information
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.
CPT codes are provided by the performing laboratory.
CPT codes are provided by the performing laboratory.
87513
LOINC® Information
Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the order and results codes of this test. LOINC values are provided by the performing laboratory.
| Test Id | Test Order Name | Order LOINC Value |
|---|---|---|
| HPFRP | H pylori + Clarithro Resist, PCR, F | 88509-5 |
| Result Id | Test Result Name |
Result LOINC Value
Applies only to results expressed in units of measure originally reported by the performing laboratory. These values do not apply to results that are converted to other units of measure.
|
|---|---|---|
| 608002 | Helicobacter pylori Result | 91061-2 |
| 608003 | Clarithromycin Resistance Result | 88509-5 |
| HPSRC | Specimen Source | 31208-2 |