Impact of co-amoxiclav versus amoxicillin on the gastrointestinal microbiota in sub-Saharan children hospitalized with pneumonia

Journal article

Community-acquired pneumonia (CAP) causes high pediatric mortality especially in sub-Saharan Africa. In a secondary analysis of samples from the PediCAP trial (ISRCTN63115131), we tracked gastrointestinal resistome and microbiota dynamics of 149 children (<6 years) from South Africa, Zambia, Zimbabwe and Uganda presenting with severe CAP. Patients received initial WHO-standard IV therapy before being randomized to continue IV therapy or step-down to oral amoxicillin or co amoxiclav for different total treatment durations. Samples were obtained after starting IV antibiotics, at discharge, and at four weeks follow-up. Microbiota dynamics were strongly associated with age and country of origin with specific bacterial genera unique to each country. Oral step-down to either antibiotic regimen or duration did not show any differential effects on the gastrointestinal microbiota and resistome dynamics compared to continuous IV therapy. The data of this secondary analysis complement the primary PediCAP trial analysis, supporting earlier hospital discharge for paediatric CAP patients.

Authors: Rodriguez-Ruiz, JP; Hiel, S; Musiime, V; Mulenga, V; Mujuru, HA

• Publication status: Accepted
• Peer review status: Peer reviewed
• Publisher: Springer Nature
• Journal: npj Antimicrobials and Resistance
• Acceptance date: 2026-05-08
• EISSN: 2731-8745
• Language: English
• Keywords: community-acquired pneumonia; microbiome; gastrointestinal; shotgun metagenomics; antimicrobial resistance