Metagenomic analysis of the impact of nitrofurantoin treatment on the human faecal microbiota

Objectives: The objective was to study changes in the faecal microbiota of patients with uncomplicated urinary tract infections (UTIs) treated with nitrofurantoin and of non-treated healthy controls using 16S rRNA analysis. Methods: Serial stool samples were collected from patients receiving nitrofurantoin treatment at different timepoints [before treatment (day 1; T1), within 48 h of end of treatment (days 5-15; T2) and 28 days after treatment (days 31-43; T3)], as well as from healthy controls. Direct DNA extraction (PowerSoil DNA Isolation Kit, MoBio Laboratories, Carlsbad, CA, USA) from stool samples was followed by pyrosequencing (454 GS FLX Titanium) of the V3-V5 region of the bacterial 16S rRNA gene. Results: Among UTI patients, mean proportions of the Actinobacteria phylum increased by 19.6% in the first follow-up sample (T2) in comparison with the pretreatment baseline stool sample (T1) (P = 0.026). However, proportions of Actinobacteria reversed to 'normal' pre-antibiotic levels, with a mean difference of 1.0% compared with baseline proportions, in the second follow-up sample (T3). The increase in Actinobacteria was specifically due to an increase in the Bifidobacteriaceae family (Bifidobacterium genus), which constituted 81.0% (95% CI +/- 7.4%) of this phylum. Conclusions: No significant impact was observed other than a temporary increase in the beneficial Bifidobacterium genus following nitrofurantoin treatment, which supports its reintroduction into clinical use.