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Test Code LAB3783 Helicobacter pylori with Clarithromycin Resistance Prediction, Molecular Detection, PCR, Feces

Important Note

Requires collection in 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) OR delivery to the lab within 2 hrs of collection.


Notify Lab Client Services with requests for collection kits (

Ordering Guidance

Confirmation of eradication testing should not be ordered until 4 or more weeks after cessation of treatment.

Specimen Required

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: Proton pump inhibitors and bismuth compounds should be avoided for 2 weeks prior to testing; antibiotics should be avoided for 4 weeks prior to testing.

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.

Useful For

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

Testing Algorithm

For more information see Helicobacter pylori Diagnostic Algorithm.

Method Name

Real-Time Polymerase Chain Reaction (PCR)

Reporting Name

H pylori + Clarithro Resist, PCR, F
Seattle Children's Hospital Note:

SCH Clinical System Name: Miscellaneous Lab Test

Specimen Type


Specimen Minimum Volume

1 mL

Specimen Stability Information

Specimen Type Temperature Time Special Container
Fecal Ambient (preferred) 7 days
  Refrigerated  7 days

Reject Due To

Fecal swab ESwab transport medium Feces in gel transport medium ECOFIX preservative formalin PVA fixative Unpreserved stool Reject

Reference Values

Not detected

Method Description

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 Mar 24;61(4):e02530-16. doi: 10.1128/AAC.02530-16)

Performing Laboratory

Mayo Clinic Laboratories in Rochester

Test Classification

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

87798 x 2

LOINC Code Information

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
HPSRC Specimen Source 31208-2
608002 Helicobacter pylori Result 91061-2
608003 Clarithromycin Resistance Result 88509-5

Day(s) Performed

Monday through Friday

Report Available

4 to 6 days


If not ordering electronically, complete, print, and send one of the following with the specimen:

1. Microbiology Test Request (T244)

2. Gastroenterology and Hepatology Client Test Request (T728)