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Urinary microbiota of women with recurrent urinary tract infection: collection and culture methods


Introduction and hypothesis

Many clinicians utilize standard culture of voided urine to guide treatment for women with recurrent urinary tract infections (RUTI). However, despite antibiotic treatment, symptoms may persist and events frequently recur. The cyclic nature and ineffective treatment of RUTI suggest that underlying uropathogens pass undetected because of the preferential growth of Escherichia coli. Expanded quantitative urine culture (EQUC) detects more clinically relevant microbes. The objective of this study was to assess how urine collection and culture methods influence microbial detection in RUTI patients.


This cross-sectional study enrolled symptomatic adult women with an established RUTI diagnosis. Participants contributed both midstream voided and catheterized urine specimens for culture via both standard urine culture (SUC) and EQUC. Presence and abundance of microbiota were compared between culture and collection methods.


Forty-three symptomatic women participants (mean age 67 years) contributed specimens. Compared to SUC, EQUC detected more unique bacterial species and consistently detected more uropathogens from catheterized and voided urine specimens. For both collection methods, the most commonly detected uropathogens by EQUC were E. coli (catheterized: n = 8, voided: n = 12) and E. faecalis (catheterized: n = 7, voided: n = 17). Compared to catheterized urine samples assessed by EQUC, SUC often missed uropathogens, and culture of voided urines by either method yielded high false-positive rates.


In women with symptomatic RUTI, SUC and assessment of voided urines have clinically relevant limitations in uropathogen detection. These results suggest that, in this population, catheterized specimens analyzed via EQUC provide clinically relevant information for appropriate diagnosis.

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The authors gratefully acknowledge funding by NIH/NICHD R01 DK104718 (Drs. Wolfe and Brubaker) for support for the conduct of this research. For this study, no funding, supplies, or services were received from any commercial organization.

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Authors and Affiliations



BR Hochstedler and L Burnett: Data collection, Data management, Data analysis, Manuscript writing/editing, and Overall study supervision.

TK Price and C Jung: Protocol/project development, Data collection, Manuscript editing.

AJ Wolfe and L Brubaker: Protocol/project development, Data analysis, Overall study supervision, and Manuscript editing.

Corresponding author

Correspondence to Alan J. Wolfe.

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Conflicts of interest

Dr. Wolfe discloses research support from the NIH, the DOD and Kimberly Clark Corporation. He also discloses membership on the Scientific Advisory Boards of Pathnostics and Urobiome Therapeutics. Dr. Brubaker discloses research funding from NIH and editorial stipends from Female Pelvic Medicine & Reconstructive Surgery, UpToDate, and JAMA. The remaining authors report no disclosures.

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Hochstedler, B.R., Burnett, L., Price, T.K. et al. Urinary microbiota of women with recurrent urinary tract infection: collection and culture methods. Int Urogynecol J 33, 563–570 (2022).

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  • Enhanced urine culture
  • Recurrent urinary tract infection
  • Urine collection
  • Urinary microbiome
  • Urinary pathogen detection