Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 Sep-Oct;30(5):e70075.
doi: 10.1111/hel.70075.

Droplet Digital PCR-Based Detection of Clarithromycin Resistance on Rapid Urease Test Samples Predicts Helicobacter pylori Eradication Success: A New Zealand Cohort Study

Stephen James Inns  1   2 , Samantha Sowerbutts  1 , Bibek Yumnam  3 , Kate Payne  3 , Georgina Wheller  3 , Mali Camberis  3 , Thomas Mules  1   2   3
Affiliations

Droplet Digital PCR-Based Detection of Clarithromycin Resistance on Rapid Urease Test Samples Predicts Helicobacter pylori Eradication Success: A New Zealand Cohort Study

Stephen James Inns et al. Helicobacter. 2025 Sep-Oct.

Abstract

Background: Helicobacter pylori (H. pylori) infection is a major cause of peptic ulcer disease and gastric cancer. Rising clarithromycin resistance has significantly reduced the efficacy of standard triple therapy. In Aotearoa New Zealand, the prevalence and impact of antibiotic resistance remain incompletely defined, limiting the development of effective treatment strategies.

Methods and aims: This study evaluated the feasibility and clinical utility of detecting clarithromycin resistance genes using droplet digital polymerase chain reaction (ddPCR) on stored Rapid Urease Test (RUT) samples-a relatively novel application of molecular diagnostics. We also assessed the association between resistance status and treatment outcomes following empiric first-line triple therapy. Patients with positive RUT tests during gastroscopy were treated with omeprazole-based triple therapy and followed up with H. pylori stool antigen testing to confirm eradication.

Results: Among 84 patients, clarithromycin resistance genes were detected in 13 (15.5%). Overall eradication was achieved in 74 (88.1%) patients. However, eradication success was significantly lower in those with resistance (38.5%) compared to those without (97.2%, p < 0.001). Infection burden, treatment regimen, and duration were not associated with eradication rates, supporting resistance status as the primary determinant of treatment outcome. Resistance rates were similar between Māori and Pacific patients (18.2%) and other ethnic groups (14.8%), although sample sizes limited definitive conclusions.

Conclusions: ddPCR testing on stored RUT samples is a feasible and effective method for detecting clarithromycin resistance. This study demonstrates that clarithromycin resistance, rather than infection burden, treatment regimen, or duration, drives eradication failure in New Zealand. Tailored therapy based on molecular resistance testing may enhance treatment success and support antibiotic stewardship. These findings justify the development of PCR-guided treatment pathways and provide a strong rationale for extending this approach to non-invasive stool-based testing suitable for use in primary care and screening programs.

Keywords: Helicobacter pylori; clarithromycin resistance; tailored therapy.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflicts of interest.

Figures

FIGURE 1
FIGURE 1
Number of patients receiving different therapies and durations. OAC, omeprazole, amoxicillin, clarithromycin. OMC, omeprazole, metronidazole, clarithromycin.
FIGURE 2
FIGURE 2
Eradication rates of H. pylori by clarithromycin resistance gene status, with 95% confidence intervals.
FIGURE 3
FIGURE 3
Comparison of the concentration (copies/ng) of the mutant 23S rRNA allele between patients who failed eradication and those who achieved successful eradication. When two mutant genes were present, the concentrations of the two genes were added together. Median with IQR. Data were analyzed with the Mann–Whitney U test.
See this image and copyright information in PMC

References

    1. Correa P., “Human Gastric Carcinogenesis: A Multistep and Multifactorial Process—First American Cancer Society Award Lecture on Cancer Epidemiology and Prevention1,” Cancer Research 52, no. 24 (1992): 6735–6740. - PubMed
    1. International Agency for Research on Cancer , “Schistosomes, Liver Flukes and <styled-content style="fixed-case"> Helicobacter Pylori </styled-content> ,” in IARC Monographs on the Evaluation of Carcinogenic Risks to Humans (World Health Organisation, 1994). - PMC - PubMed
    1. Hooi J. K. Y., Lai W. Y., Ng W. K., et al., “Global Prevalence of <styled-content style="fixed-case"> Helicobacter pylori </styled-content> Infection: Systematic Review and Meta‐Analysis,” Gastroenterology 153, no. 2 (2017): 420–429, 10.1053/j.gastro.2017.04.022. - DOI - PubMed
    1. Malfertheiner P., Megraud F., Rokkas T., et al., “Management of Helicobacter pylori Infection: The Maastricht VI/Florence Consensus Report,” Gut (2022): 2022‐327745, 10.1136/gutjnl-2022-327745. - DOI - PubMed
    1. Hsiang J., Selvaratnam S., Taylor S., et al., “Increasing Primary Antibiotic Resistance and Ethnic Differences in Eradication Rates of <styled-content style="fixed-case"> Helicobacter pylori </styled-content> Infection in New Zealand—A New Look at an Old Enemy,” New Zealand Medical Journal 126, no. 1384 (2013): 64–76. - PubMed

MeSH terms