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Updated: Dec 30, 2025
Gastric Mucosa Quantitative Polymerase Chain Reaction Analysis for Detecting Helicobacter pylori and Antibiotic Resistance
Published on: March 7, 2025
Treatment of Helicobacter pylori infection and its long-term impacts on gut microbiota
Jyh-Ming Liou1,2,3, Yi-Chia Lee1,2, Ming-Shiang Wu1,2
1Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
Abstract:
The rising prevalence of antibiotic resistance and the long-term safety following eradication therapy are important issues in the management of Helicobacter pylori infection. The prevalence of clarithromycin, levofloxacin, and metronidazole resistance of H. pylori has increased to 21%, 27%, and 45%, respectively, in the Asia-Pacific region. Personalized treatment guided by susceptibility testing may provide a reliably excellent eradication rate in the first-line treatment but is costly and not widely available. Population-specific empirical therapy according to the local prevalence of antibiotic resistance may be an alternative strategy. Levofloxacin-based therapy and bismuth quadruple therapy are the recommended second-line rescue therapy. Susceptibility testing or genotypic resistance-guided therapy is the preferred treatment for refractory H. pylori infection, but empirical therapy may be an acceptable alternative. Eradication of H. pylori leads to short-term perturbation of gut microbiota. The diversity of gut microbiota can be restored months after eradication therapy, but the speed of recovery varies with regimens. The short-term increases of antibiotic resistance of Escherichia coli and Klebsiella pneumoniae may be restored to basal states months after H. pylori eradication. Future studies that apply in-depth sequencing, such as shotgun metagenomics sequencing, are needed to clarify whether the compositions of gut microbiota at the species level are fully restored.
Insights
Antibiotic resistance in Helicobacter pylori is rising, especially in the Asia-Pacific. Personalized or population-specific therapies are key for effective eradication and managing gut microbiota changes post-treatment.
Area of Science:
- Microbiology
- Gastroenterology
- Pharmacology
Background:
- Rising antibiotic resistance of Helicobacter pylori (H. pylori) is a significant clinical challenge.
- Prevalence of resistance to clarithromycin (21%), levofloxacin (27%), and metronidazole (45%) is high in the Asia-Pacific.
- Long-term safety and gut microbiota impact of H. pylori eradication therapies require careful consideration.
Purpose of the Study:
- To review current strategies for H. pylori eradication in the context of increasing antibiotic resistance.
- To evaluate the effects of H. pylori eradication on gut microbiota composition and antibiotic resistance.
- To discuss future research directions for optimizing H. pylori treatment and understanding its ecological impact.
Main Methods:
- Literature review of studies on H. pylori resistance patterns and eradication therapies.
- Analysis of data on the impact of eradication regimens on gut microbiota diversity and antibiotic resistance.
- Synthesis of evidence regarding susceptibility testing, empirical therapy, and rescue treatments.
Main Results:
- Antibiotic resistance, particularly to levofloxacin and metronidazole, is a growing concern in H. pylori management.
- Personalized susceptibility testing offers high eradication rates but faces accessibility and cost barriers.
- H. pylori eradication causes transient gut microbiota disruption, with variable recovery depending on the regimen.
- Short-term increases in antibiotic resistance of other gut bacteria may resolve post-eradication.
Conclusions:
- Population-specific empirical therapy is a viable alternative to susceptibility testing for H. pylori eradication.
- Levofloxacin-based and bismuth quadruple therapies are recommended for second-line treatment.
- Further research using advanced sequencing techniques is needed to confirm full gut microbiota restoration post-eradication.
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