title: Metagenomic analysis of the impact of nitrofurantoin treatment on the human faecal microbiota.
abstract: OBJECTIVE
  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.
authors.affiliation: Department of Medical Microbiology, Universiteit Antwerpen, Antwerp, Belgium Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium.
authors.forename: Jascha
authors.initials: J
authors.lastname: Vervoort
authors.affiliation: Department of Medical Microbiology, Universiteit Antwerpen, Antwerp, Belgium Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium.
authors.forename: Basil Britto
authors.initials: BB
authors.lastname: Xavier
authors.affiliation: Infection Control Program, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia.
authors.forename: Andrew
authors.initials: A
authors.lastname: Stewardson
authors.affiliation: Department of Medical Microbiology, Universiteit Antwerpen, Antwerp, Belgium Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium.
authors.forename: Samuel
authors.initials: S
authors.lastname: Coenen
authors.affiliation: Centre for Family and Community Medicine, Medical University of Lodz, Lodz, Poland.
authors.forename: Maciek
authors.initials: M
authors.lastname: Godycki-Cwirko
authors.affiliation: Department of Medical Microbiology, Universiteit Antwerpen, Antwerp, Belgium Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium.
authors.forename: Niels
authors.initials: N
authors.lastname: Adriaenssens
authors.affiliation: Centre for Family and Community Medicine, Medical University of Lodz, Lodz, Poland.
authors.forename: Anna
authors.initials: A
authors.lastname: Kowalczyk
authors.affiliation: Department of Medical Microbiology, Universiteit Antwerpen, Antwerp, Belgium Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium.
authors.forename: Christine
authors.initials: C
authors.lastname: Lammens
authors.affiliation: Infection Control Program, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland.
authors.forename: Stephan
authors.initials: S
authors.lastname: Harbarth
authors.affiliation: Department of Medical Microbiology, Universiteit Antwerpen, Antwerp, Belgium Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium.
authors.forename: Herman
authors.initials: H
authors.lastname: Goossens
authors.affiliation: Department of Medical Microbiology, Universiteit Antwerpen, Antwerp, Belgium Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium surbhi.malhotra@uantwerpen.be.
authors.forename: Surbhi
authors.initials: S
authors.lastname: Malhotra-Kumar
mesh_terms: D000890:Anti-Infective Agents / Q000008:administration & dosage / Q000494:pharmacology*; D001419:Bacteria / Q000145:classification* / Q000302:isolation & purification; D016000:Cluster Analysis; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005243:Feces / Q000382:microbiology*; D000069196:Gastrointestinal Microbiome / Q000187:drug effects*; D006801:Humans; D008137:Longitudinal Studies; D056186:Metagenomics; D064307:Microbiota / Q000187:drug effects*; D008969:Molecular Sequence Data; D009582:Nitrofurantoin / Q000008:administration & dosage / Q000494:pharmacology*; D010802:Phylogeny; D011446:Prospective Studies; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D014552:Urinary Tract Infections / Q000188:drug therapy
chemical_list: D000890:Anti-Infective Agents; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D009582:Nitrofurantoin
keywords: 16S rDNA; 16S rRNA; antibiotic resistance; compositional changes; culture independent; faecal flora; gastrointestinal flora; stool; urinary tract infections