Can I continue taking omeprazole (proton pump inhibitor) during antibiotic treatment for small intestine bacterial overgrowth (SIBO) with metronidazole and rifaximin, given my history of norovirus infection, gastropathy, and irritated stomach lining, and then taper off the omeprazole after completing the antibiotics?

PPI Use During SIBO Antibiotic Treatment

You should discontinue omeprazole immediately and not restart it after completing your SIBO antibiotics, as proton pump inhibitors are a well-established risk factor for SIBO development and recurrence. 1

Why PPIs Likely Caused Your SIBO Recurrence

• Gastric acid suppression is one of the key mechanisms that normally prevents bacterial overgrowth in the small intestine. 1
• One month of omeprazole therapy is sufficient to reduce gastric acid enough to allow bacterial proliferation in the small intestine. 1
• Your symptom pattern strongly suggests PPI-induced SIBO: symptoms resolved after the norovirus cleared (when motility normalized within 2-4 weeks), then recurred after starting omeprazole. 1
• Gut motility typically normalizes within 2-4 weeks after acute viral gastroenteritis, making it highly unlikely that norovirus from 3 months ago is still causing dysmotility. 1

The Critical Problem with Continuing PPI During Treatment

• Continuing omeprazole during SIBO treatment directly contradicts the goal of eradicating bacterial overgrowth—you would be simultaneously treating SIBO while maintaining the primary factor causing it. 1
• The American Gastroenterological Association specifically recommends considering SIBO risk when prescribing proton pump inhibitors. 1
• Discontinuing omeprazole immediately removes the SIBO predisposing factor and is essential for successful treatment. 1

Your Antibiotic Regimen

• Rifaximin 550 mg twice daily for 14 days is the most effective first-line treatment for SIBO, achieving 60-80% eradication rates. 1, 2, 3
• Metronidazole has lower documented efficacy for SIBO treatment and should not be first choice. 1, 2
• Your plan to run metronidazole for 10 days and rifaximin for 14 days with staggered end dates is acceptable, though rifaximin alone would be more effective. 1, 2
• Doxycycline, ciprofloxacin, or amoxicillin-clavulanic acid are equally effective alternatives to rifaximin if needed. 1, 2

Managing Your Gastropathy Without PPIs

• Do not restart omeprazole after SIBO treatment unless absolutely necessary. 1
• Consider H2-blockers (like famotidine) as alternatives if acid suppression is required—these have lower SIBO risk than PPIs. 1
• For your irritated stomach lining, dietary modifications and time off the PPI may allow healing without perpetuating the SIBO cycle. 1

Common Pitfalls to Avoid

• Do not assume persistent motility dysfunction from a 3-month-old viral illness when acid suppression is the more likely culprit for your recurrent symptoms. 1
• If symptoms persist after completing antibiotics, consider repeat breath testing 2-4 weeks after treatment completion to confirm SIBO eradication. 2
• Be aware that failure to respond to antibiotics may indicate resistant organisms, absence of actual SIBO, or coexisting disorders like bile acid diarrhea or pancreatic insufficiency. 1, 2

What to Expect

• Rifaximin is not absorbed from the gastrointestinal tract, which minimizes systemic antibiotic resistance risk and side effects. 1, 2, 3
• No adverse events are typically reported with rifaximin, making it safer than systemic antibiotics like metronidazole. 4, 5
• If SIBO recurs after successful treatment while off PPIs, then consider structured antibiotic cycling with repeated courses every 2-6 weeks, rotating different antibiotics with 1-2 week antibiotic-free periods between courses. 2, 3