title: Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota.
abstract: 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.
authors: Infection Control Program, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland; Department of Medicine (Austin Health), University of Melbourne, Heidelberg, Australia. Electronic address: andrew.stew@rdson.net.
authors: A J
authors: AJ
authors: Stewardson
authors: Service of Infectious Diseases, Genomic Research Laboratory, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland.
authors: N
authors: N
authors: Gaïa
authors: Service of Infectious Diseases, Genomic Research Laboratory, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland.
authors: P
authors: P
authors: François
authors: Department of Medical Microbiology, Universiteit Antwerpen, Antwerp, Belgium; Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium.
authors: S
authors: S
authors: Malhotra-Kumar
authors: Department of Primary Care, Community and Emergency Medicine, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland.
authors: C
authors: C
authors: Delémont
authors: Department of Obstetrics and Gynaecology, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland.
authors: B
authors: B
authors: Martinez de Tejada
authors: Service of Infectious Diseases, Genomic Research Laboratory, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland.
authors: J
authors: J
authors: Schrenzel
authors: Infection Control Program, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland.
authors: S
authors: S
authors: Harbarth
authors: Service of Infectious Diseases, Genomic Research Laboratory, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland.
authors: V
authors: V
authors: Lazarevic
mesh_terms: D000328:Adult; D000900:Anti-Bacterial Agents / Q000627:therapeutic use*; D001419:Bacteria / Q000145:classification* / Q000187:drug effects* / Q000235:genetics / Q000302:isolation & purification; D002939:Ciprofloxacin / Q000627:therapeutic use*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005243:Feces / Q000382:microbiology; D005260:Female; D000069196:Gastrointestinal Microbiome / Q000187:drug effects*; D006801:Humans; D008297:Male; D008875:Middle Aged; D009582:Nitrofurantoin / Q000627:therapeutic use*; D010045:Outpatients; D011446:Prospective Studies; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D014552:Urinary Tract Infections / Q000188:drug therapy*; D055815:Young Adult
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D002939:Ciprofloxacin; D009582:Nitrofurantoin
keywords: Antibiotics; ecologic damage; microbiomics; microbiota; urinary tract infection