Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota

Recent treatment guidelines for uncomplicated urinary tract infections (UTIs) discourage fluoroquinolone prescription because of collateral damage to commensal microbiota, but the ecologic impact of alternative agents has not been evaluated by culture-free techniques. We prospectively collected faec...

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Bibliographic Details
Published in:Clinical microbiology and infection 2015-04, Vol.21 (4), p.344.e1-344.e11
Main Authors: Stewardson, A.J., Gaïa, N., François, P., Malhotra-Kumar, S., Delémont, C., Martinez de Tejada, B., Schrenzel, J., Harbarth, S., Lazarevic, V.
Format: Article
Language:English
Subjects:
Adult
Anti-Bacterial Agents - therapeutic use
Antibiotics
Bacteria - classification
Bacteria - drug effects
Bacteria - genetics
Bacteria - isolation & purification
Ciprofloxacin - therapeutic use
DNA, Bacterial - chemistry
DNA, Bacterial - genetics
DNA, Ribosomal - chemistry
DNA, Ribosomal - genetics
ecologic damage
Feces - microbiology
Female
Gastrointestinal Microbiome - drug effects
Humans
Male
microbiomics
microbiota
Middle Aged
Nitrofurantoin - therapeutic use
Outpatients
Prospective Studies
RNA, Ribosomal, 16S - genetics
Sequence Analysis, DNA
urinary tract infection
Urinary Tract Infections - drug therapy
Young Adult
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Summary:Recent treatment guidelines for uncomplicated urinary tract infections (UTIs) discourage fluoroquinolone prescription because of collateral damage to commensal microbiota, but the ecologic impact of alternative agents has not been evaluated by culture-free techniques. We prospectively collected faecal samples at three time points from ambulatory patients with UTIs treated with ciprofloxacin or nitrofurantoin, patients not requiring antibiotics and household contacts of ciprofloxacin-treated patients. We described changes in gut microbiota using a culture-independent approach based on pyrosequencing of the V3–V4 region of the bacterial 16S rRNA gene. All groups were similar at baseline. Ciprofloxacin had a significant global impact on the gut microbiota whereas nitrofurantoin did not. The end of ciprofloxacin treatment correlated with a reduced proportion of Bifidobacterium (Actinobacteria), Alistipes (Bacteroidetes) and four genera from the phylum Firmicutes (Faecalibacterium, Oscillospira, Ruminococcus and Dialister) and an increased relative abundance of Bacteroides (Bacteroidetes) and the Firmicutes genera Blautia, Eubacterium and Roseburia. Substantial recovery had occurred 4 weeks later. Nitrofurantoin treatment correlated with a reduced relative proportion of the genus Clostridium and an increased proportion of the genus Faecalibacterium. This study supports use of nitrofurantoin over fluoroquinolones for treatment of uncomplicated UTIs to minimize perturbation of intestinal microbiota.
ISSN:1198-743X
1469-0691
DOI:10.1016/j.cmi.2014.11.016