title: Methodology for a vaginal and urinary microbiome study in women with mixed urinary incontinence.
abstract: OBJECTIVE
  We describe the rationale and methods of a study designed to compare vaginal and urinary microbiomes in women with mixed urinary incontinence (MUI) and similarly aged, asymptomatic controls.
  
  
  METHODS
  This paper delineates the methodology of a supplementary microbiome study nested in an ongoing randomized controlled trial comparing a standardized perioperative behavioral/pelvic floor exercise intervention plus midurethral sling versus midurethral sling alone for MUI. Women in the parent study had at least "moderate bother" from urgency and stress urinary incontinence symptoms (SUI) on validated questionnaire and confirmed MUI on bladder diary. Controls had no incontinence symptoms. All participants underwent vaginal and urine collection for DNA analysis and conventional urine culture. Standardized protocols were designed, and a central lab received samples for subsequent polymerase chain reaction (PCR) amplification and sequencing of the bacterial16S ribosomal RNA (rRNA) gene. The composition of bacterial communities will be determined by dual amplicon sequencing of variable regions 1-3 and 4-6 from vaginal and urine specimens to compare the microbiome of patients with controls. Sample-size estimates determined that 126 MUI and 84 control participants were sufficient to detect a 20 % difference in predominant urinary genera, with 80 % power and 0.05 significance level.
  
  
  RESULTS
  Specimen collection commenced January 2015 and finished April 2016. DNA was extracted and stored for subsequent evaluation.
  
  
  CONCLUSIONS
  Methods papers sharing information regarding development of genitourinary microbiome studies, particularly with control populations, are few. We describe the rigorous methodology developed for a novel urogenital microbiome study in women with MUI.
authors.affiliation: Division of Female Pelvic Medicine and Reconstructive Surgery, Department of Obstetrics and Gynecology MSC10-5580, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131-0001, USA. ykomesu@salud.unm.edu.
authors.forename: Yuko M
authors.initials: YM
authors.lastname: Komesu
authors.affiliation: Division of Urogynecology and Pelvic Reconstructive Surgery, Department of Obstetrics and Gynecology, University of Alabama at Birmingham, Birmingham, AL, USA.
authors.forename: Holly E
authors.initials: HE
authors.lastname: Richter
authors.affiliation: Clinical Translational Sciences Center and Department of Pediatrics, University of New Mexico of New Mexico Health Sciences Center, Albuquerque, NM, USA.
authors.forename: Darrell L
authors.initials: DL
authors.lastname: Dinwiddie
authors.affiliation: Division of Urogynecology and Reconstructive Pelvic Surgery, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA.
authors.forename: Nazema Y
authors.initials: NY
authors.lastname: Siddiqui
authors.affiliation: Division of Urogynecology and Reconstructive Pelvic Surgery, Department of Obstetrics and Gynecology, Alpert Medical School of Brown University, Providence, RI, USA.
authors.forename: Vivian W
authors.initials: VW
authors.lastname: Sung
authors.affiliation: Division of Female Pelvic Medicine and Reconstructive Surgery, Department of Reproductive Medicine, UC San Diego Health System, San Diego, CA, USA.
authors.forename: Emily S
authors.initials: ES
authors.lastname: Lukacz
authors.affiliation: Center for Urogynecology and Reconstructive Pelvic Surgery, Obstetrics and Gynecology and Women's Health Institute, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: Beri
authors.initials: B
authors.lastname: Ridgeway
authors.affiliation: Division of Urogynecology and Reconstructive Pelvic Surgery, Hospital of University of Pennsylvania, Philadelphia, PA, USA.
authors.forename: Lily A
authors.initials: LA
authors.lastname: Arya
authors.affiliation: Division of Urogynecology and Reconstructive Pelvic Surgery, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
authors.forename: Halina M
authors.initials: HM
authors.lastname: Zyczynski
authors.affiliation: Division of Female Pelvic Medicine and Reconstructive Surgery, Department of Obstetrics and Gynecology MSC10-5580, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131-0001, USA.
authors.forename: Rebecca G
authors.initials: RG
authors.lastname: Rogers
authors.affiliation: Social, Statistical and Environmental Sciences, RTI International, Research Triangle Park, Durham, NC, USA.
authors.forename: Marie
authors.initials: M
authors.lastname: Gantz
mesh_terms: D005260:Female; D006801:Humans; D064307:Microbiota / Q000235:genetics; D008875:Middle Aged; D016133:Polymerase Chain Reaction; D012107:Research Design; D017422:Sequence Analysis, DNA; D011795:Surveys and Questionnaires; D014550:Urinary Incontinence, Stress / Q000382:microbiology*; D053202:Urinary Incontinence, Urge / Q000382:microbiology*; D014621:Vagina / Q000382:microbiology
keywords: Female urinary microbiome; Mixed urinary incontinence; Next-generation sequencing; Urinary taxa; Vaginal microbiome