Treatment For H. Pylori Didn't Work. Now What?

In our latest question and answer, the pharmacist discusses what to do if your initial treatment for an H. Pylori infection doesn't work.

3 min read Updated Jun 2026 Read by 6,383 people
Treatment For H. Pylori Didn't Work. Now What?
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Emilio asked

My doctor has me on treatment with Prilosec, clarithromycin, and amoxicillin for acid reflux. I have finished the treatment and pills last Wednesday. The issue is that I have some effects still and still feel some acid reflux, but not as much now. Should I ask for a refill or am I missing something?

Dec 06, 2022
The quick answer
  • If your H. pylori treatment didn't work, talk to your doctor right away because about 20% of people fail initial treatment and there are several alternative medication regimens available. Your doctor can test you to confirm whether the infection is still present using a urea breath test, fecal antigen test, or upper endoscopy. Treatment failure can happen for reasons like not taking all your medication, antibiotic resistance, or not enough acid suppression, and your doctor may adjust your dose or try a different combination of antibiotics.
A quick summary of Dr. Brian Staiger, PharmD's full answer below, condensed by AI from that answer only (not from any outside source). The pharmacist's answer is the source of record.

Answer

Thanks so much for reaching out! Based on the medications you stated you are taking in your question (amoxicillin, clarithromycin, and Prilosec [omeprazole]), I'm assuming you are being treated for more than acid reflux.

That combination of medications (two antibiotics and a proton pump inhibitor) is a common treatment regimen for an H. Pylori infection. It is known as 'triple therapy' and is generally given for 14 days.

I don't know if you have been tested for H. Pylori, which was confirmed positive, or if your doctor has simply given you empiric treatment (assumed diagnosis, but not confirmed with testing).

Nevertheless, since you state you are continuing to have symptoms, it is important to discuss this with your doctor.

Assuming you are being treated for an active H. Pylori infection, studies suggest that nearly 20% of individuals fail initial treatment, so you aren't alone. 

In the next section, I discuss some options for the treatment of H. Pylori if you failed the initial treatment, which it seems like you may have.

H. Pylori Treatment Failure - Next Steps

As mentioned, failing initial treatment for H. Pylori isn't uncommon, and there are plenty of reasons why it could occur, including:

  • Poor medication adherence

  • Microbial resistance to antibiotics (common with clarithromycin)

  • Inadequate suppression of stomach acid

The therapy you were started on (amoxicillin, clarithromycin, and Prilosec) is the most common initial therapy. If that fails, which could be for any of the reasons I mentioned above, there are alternative treatments available. These treatments include:

  • Bismuth quadruple therapy: Bismuth subsalicylate, metronidazole, tetracycline, and a proton pump inhibitor (like Prilosec) given for 14 days

  • Concomitant therapy: Clarithromycin, amoxicillin, metronidazole, and a proton pump inhibitor for 10-14 days

  • Hybrid therapy: Amoxicillin and a PPI for seven days followed by amoxicillin, clarithromycin, a nitroimidazole, and a proton pump inhibitor for 7 days

  • Levofloxacin triple therapy: Levofloxacin, amoxicillin, and a proton pump inhibitor for 10 to 14 days

  • Levofloxacin quadruple therapy: Levofloxacin, omeprazole, metronidazole, and doxycycline for 10-14 days

  • Levofloxacin sequential therapy: Amoxicillin and a proton pump inhibitor for five to seven days followed by levofloxacin, amoxicillin, metronidazole, and a proton pump inhibitor for 5-7 days.

  • Rifabutin triple therapy: Rifabutin, amoxicillin, and a proton pump inhibitor twice daily for 14 days.

As you can see, there are plenty of alternative regimens you could try since your first treatment didn't work. I urge you to connect with your doctor about how you are feeling and to be re-evaluated.

Your doctor can perform tests to confirm your infection has been adequately treated. Tests include:

It is important to point out here too that generally a proton pump inhibitor, when used as part of a treatment plan to treat H. Pylori, should be given twice daily, especially if your first treatment ended in failure.

Final Words

I hope you found this answer helpful. I am making an educated guess about what you are treating based on the drugs you gave me, so please, if you have any further questions or clarifications to send my way, please do so.

References & sources
  1. Clinical practice. Helicobacter pylori infection. — PubMed
  2. American College of Gastroenterology guideline on the management of Helicobacter pylori infection. — PubMed
  3. Bismuth-based quadruple therapy using a single capsule of bismuth biskalcitrate, metronidazole, and tetracycline given with omeprazole versus omeprazole, amoxicillin, and clarithromycin for eradication of Helicobacter pylori in duodenal ulcer patients: a prospective, randomized, multicenter, North American trial — PubMed
  4. ACG Clinical Guideline: Treatment of Helicobacter pylori Infection — PubMed
  5. Update on non-bismuth quadruple (concomitant) therapy for eradication of Helicobacter pylori — PubMed
  6. Review: efficacy and safety of hybrid therapy for Helicobacter pylori infection: a systematic review and meta-analysis — PubMed
  7. A randomized study comparing levofloxacin, omeprazole, nitazoxanide, and doxycycline versus triple therapy for the eradication of Helicobacter pylori — PubMed
  8. The relationship among previous antimicrobial use, antimicrobial resistance, and treatment outcomes for Helicobacter pylori infections — PubMed
  9. Review article: rifabutin in the treatment of refractory Helicobacter pylori infection — PubMed
Glossary — Terms in This Answer
Proton pump inhibitor
A medication that reduces stomach acid production by blocking acid-secreting cells in the stomach lining.
Triple therapy
A treatment regimen using three medications together, in this case two antibiotics and an acid-reducing drug.
H. Pylori
A bacterium that infects the stomach and can cause ulcers and digestive problems.
Empiric treatment
Medical treatment started based on a suspected diagnosis without confirming tests.
Microbial resistance
When bacteria develop the ability to survive and multiply despite antibiotic treatment.
Bismuth quadruple therapy
A four-drug treatment regimen using bismuth subsalicylate, metronidazole, tetracycline, and a proton pump inhibitor.
Urea breath test
A diagnostic test that detects H. Pylori infection by measuring carbon dioxide in a patient's breath after drinking labeled urea.
Upper endoscopy
A procedure where a thin viewing tube is inserted down the throat to visually examine the stomach and intestines.
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Dr. Brian Staiger, PharmD
About the pharmacist

Dr. Brian Staiger, PharmD

Clinical Pharmacy

Doctor of Pharmacy, board certified clinical pharmacist (BCPS), American Herbalist Guild, Medication Therapy Management certified

Brian Staiger, PharmD, BCPS, is a licensed pharmacist with more than 13 years of experience across retail pharmacy, clinical pharmacy, medication safety, pharmacy program development, and healthcare administration. He is the founder of HelloPharmacist.com, where he helps patients...

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