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.

Influence of dairy by-product waste milk on the microbiomes of different gastrointestinal tract components in pre-weaned dairy calves

“…Certain members of the genus Anaerovibrio are able to utilise glycerol24 and have been associated with propionate and butyrate production in the rumen2425. Previous studies revealed that squid ink polysaccharide and ciprofloxacin treatment were correlated with a reduced proportion of the genus Oscillospira in the gut2627. Hence, rumen concentrations of propionate and butyrate may be increased by feeding dairy calves UWM.…”

Ecophysiological consequences of alcoholism on human gut microbiota: implications for ethanol-related pathogenesis of colon cancer

“…In this context, a culture-based analysis revealed that oral administration of ciprofloxacin decreases the rate of ethanol elimination in humans16, probably because this drug reduces the proportions of aerobes and facultative anaerobes in the human intestine16. However, in recent culture-free GM analysis, ciprofloxacin administration to human subjects (outpatients with urinary tract infections) decreased the relative abundances of various obligate anaerobes, including Bifidobacterium and Ruminococcus 45. Thus, ciprofloxacin adversely affects not only aerobes and facultative anaerobes, but also obligate anaerobes.…”

Effects of Antibiotics on Gut Microbiota

“…Dysbiosis is commonly characterized by a reduced diversity of the phyla Firmicutes and Bacteroidetes, and often accompanied by an overgrowth of the family Enterobacteriaceae [12,13,22,23,24,25]. This may become critical, as the healthy microbiota conveys colonization resistance towards invading pathogenic bacteria [26], and dysbiosis increases vulnerability for post-antibiotic expansion of enteropathogenic strains like Clostridium difficile [27] and antibiotic-resistant pathogens such as vancomycin-resistant Enterococcus [28].…”