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

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.

See Helicobacter pylori Diagnostic Algorithm in Special Instructions.

 

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

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

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.

Yes

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

H pylori + Clarithro Resist PCR

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.

See Helicobacter pylori Diagnostic Algorithm in Special Instructions.

 

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

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. See Infectious Specimen Shipping Guidelines in Special Instructions for shipping information.

2. Place specimen in a large infectious container (T146) and label as an etiologic agent/infectious substance, if appropriate.

Necessary Information

Organism identification and specimen source are required.

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 Client Test Request (T728) with the specimen

Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the Testing Laboratory

NA

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)
Frozen
Refrigerated

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

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 (NB) tube for thermal/physical lysis and then diluted 1:100 prior to testing. The 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 which includes dUTPs.(Chen D, Cunningham SA, Cole N, et al: Phenotypic and Molecular Antimicrobial Susceptibility of Helicobacter pylori in the United States. Antimicrob Agents Chemother 2016;61:e02530-16)

PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information

No

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.

3 to 4 days

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

30 days

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Rochester

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 Regional Manager. 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. This test 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.

87150

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 43409-2

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | Create a PDF

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports