A randomized phase 1 study investigating gut microbiome changes with moxifloxacin vs. oral vancomycin: Implications for Clostridioides difficile risk.

Authors

Hossaena Ayele, Jinhee Jo, Khurshida Begum, Chenlin Hu, Thanh M Le, M Jahangir Alam, Taryn A Eubank, Sigmund J Haidacher, Thomas Horvath, Blake M Hanson, Kevin W Garey

Published in

The Journal of infectious diseases. Oct 13, 2025. Epub Oct 13, 2025.

Abstract

The epidemic, hypervirulent Clostridioides difficile ribotype (RT) 027 strain is associated with bacterial virulence traits, including faster germination time and resistance to moxifloxacin, a second-generation fluoroquinolone. Although linked to the RT 027 epidemic, studies to understand moxifloxacin as a high-risk antibiotic for C. difficile infection (CDI) are limited. This study assessed the microbial taxonomic profile and metabolomic changes in healthy volunteers given moxifloxacin or oral vancomycin, an antibiotic known to increase CDI risk via gut perturbation.
This was a phase 1, nonblinded, randomized clinical trial of healthy volunteers aged 18-40 who received moxifloxacin or vancomycin for 10 days (clinicaltrials.gov NCT06030219). Stool samples were collected at baseline and 12 follow-up visits. Metataxonomics was completed by 16S V1-V3 rRNA sequencing and bile acid metabolites by LC-MS/MS.
Moxifloxacin therapy caused minimal microbial disruption, although changes in bacterial species from the Clostridiales order during-therapy were observed. Secondary bile acid concentrations decreased from Day 0 to Day 7 with moxifloxacin therapy. Vancomycin caused more significant changes in the microbiome, including increased Proteobacteria, decreased Clostridiales abundance, and a longer duration of decreased secondary bile acids.
Moxifloxacin use was associated with specific microbiome and metabolomic changes increasing CDI risk albeit for a shorter period than vancomycin. This window of vulnerability may help to explain the risk of fluoroquinolones with the faster germination time for RT 027 strains.

PMID:
41081530
Bibliographic data and abstract were imported from PubMed on 13 Oct 2025.

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