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
Highlights
This test detects the Helicobacter pylori 23S ribosomal RNA gene and the three most common 23S ribosomal RNA gene single nucleotide variations (A2143G, A2142G, and A2142C) leading to resistance to clarithromycin using viable or nonviable isolates to molecularly predict clarithromycin resistance or susceptibility.
Reflex Tests
Lists tests that may or may not be performed, at an additional charge, depending on the result and interpretation of the initial tests.
| Test Id | Reporting Name | Available Separately | Always Performed |
|---|---|---|---|
| PCRID | Identification by PCR | No, (Bill Only) | No |
Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.
When this test is ordered, the reflex test may be performed at an additional charge.
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.
When this test is ordered, the reflex test may be performed at an additional charge.
For more information see Helicobacter pylori Diagnostic Algorithm.
Specimen Type
Describes the specimen type validated for testing
Varies
Ordering Guidance
This test uses isolates of Helicobacter pylori for testing. If testing directly from feces is desired, order HPFRP / Helicobacter pylori with Clarithromycin Resistance Prediction, Molecular Detection, PCR, Varies.
Additional Testing Requirements
1. If identification testing is needed; also order IDENT / Organism Referred for Identification, Aerobic Bacteria.
2. If susceptibility testing is needed; also order ZMMLS / Antimicrobial Susceptibility, Aerobic Bacteria, MIC, Varies.
Shipping Instructions
1. For shipping information see Infectious Specimen Shipping Guidelines.
2. Place specimen in a large infectious container and label as an etiologic agent/infectious substance, if appropriate.
Necessary Information
Organism identification and specimen source are required.
ORDER QUESTIONS AND ANSWERS
| Question ID | Description | Answers |
|---|---|---|
| HPORG | Organism Identified by Client | |
| HPS2 | Specimen Source |
Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete testing
Supplies: Infectious Container, Large (T146)
Container/Tube: Agar slant or other appropriate media
Specimen Volume: Isolate
Collection Instructions:
1. Perform isolation of Helicobacter pylori in culture.
2. H pylori isolate must be submitted in pure culture. Do not submit mixed cultures.
Special Instructions
Library of PDFs including pertinent information and forms related to the test
Forms
If not ordering electronically, complete, print, and send Gastroenterology and Hepatology Test Request (T728)
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.
See Specimen Required
Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected
| Agar plate ESwab Port-a-Cult | 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 |
|---|---|---|---|
| Varies | Ambient (preferred) | ||
| Refrigerated | |||
| Frozen | |||
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.
When this test is ordered, the reflex test may be performed at an additional charge.
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 a risk factor for gastric cancer when left untreated. 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 clinical microbiology laboratories that perform H pylori susceptibility testing. In an internal study of local and referred isolates, 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 non-pylori 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 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 non-clarithromycin antimicrobial agents. The ZMMLS / Antimicrobial Susceptibility, Aerobic Bacteria, 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 polymerase chain reaction 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 NC, Kohner PC, Mandrekar JN, Patel R: 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(8):2400-2405
4. Monteiro L, Gras N, Vidal R, Megraud F: 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
Method Description
Describes how the test is performed and provides a method-specific reference
Viable and nonviable clinical isolates are processed by transferring up to a 1 mcL loop full of isolate into a swab neutralization buffer tube for thermal/physical lysis and then diluted 1:100 prior to testing. 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 its 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 the 2 position mutations associated 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 that includes deoxyuridine triphosphates.(Chen D, Cunningham SA, Cole NC, Kohner PC, Mandrekar JN, Patel R: Phenotypic and molecular antimicrobial susceptibility of Helicobacter pylori. Antimicrob Agents Chemother. 2017 Mar 24;61(4):e02530-16)
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 through 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.
- Authorized users can sign in to Test Prices for detailed fee information.
- Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
- 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 |
|---|---|---|
| HPCRP | H pylori + Clarithro Resist PCR | 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.
|
|---|---|---|
| HPS2 | Specimen Source | 31208-2 |
| 608005 | Helicobacter pylori Result | 49101-9 |
| 608006 | Clarithromycin Resistance Result | 88509-5 |
| HPORG | Organism Identified by Client | In Process |