Molecular Diagnosis of Vaginitis: Comparing Quantitative PCR and Microbiome Profiling Approaches to Current Microscopy Scoring

J Clin Microbiol. 2019 Aug 26;57(9):e00300-19. doi: 10.1128/JCM.00300-19. Print 2019 Sep.


Vaginitis is often diagnosed by microscopy and limited to testing for bacterial vaginosis (BV), vulvovaginal candidiasis, and trichomoniasis. Approximately 10% of vaginal swabs are negative but designated "altered flora" by BV Nugent score, leaving clinicians unsure how to treat patients. Accurate and comprehensive vaginitis diagnostics are needed to direct treatment and reduce risks of recurrent or more severe infections. Vaginal swabs were collected from 93 women (mean age, 23.53 years; range, 18 to 42 years) in a cross-sectional study. Microscopy results for BV and Candida were compared to those from two molecular approaches: (i) a comprehensive quantitative PCR (qPCR) assay, including testing for aerobic vaginitis (AV), Candida, sexually transmitted infections (STI), and BV (Applied Biosystems) with an accompanying BV interpretive algorithm (Coriell Life Sciences), and (ii) microbiome profiling of the 16S rRNA gene (Illumina). Microscopy plus BV Nugent score had 76% overall agreement with the qPCR plus BV interpretive algorithm method (24 positive, 47 negative). OF the nine samples designated altered flora by Nugent, five were categorized BV positive and four were BV negative by the qPCR method. Although BV negative, 3/4 of the latter samples had positive AV targets with one also was STI positive. Microscopic identification of Candida versus that by qPCR had 94% agreement (9 positive, 78 negative). The comprehensive qPCR assay revealed alternative etiologies summarized as 38% BV, 10% AV, 5% Candida, 2% STI, 10% mixed infection (positive targets in multiple panels), and 35% negative for all targets. 16S microbiome analysis confirmed the bacterial qPCR results and identified differentiating patterns between AV, BV, and Lactobacillus-dominated vaginal microbiomes.

Keywords: 16s rRNA gene; Nugent score; aerobic vaginitis; bacterial vaginosis; dysbiosis; microbiome; microscopy; molecular diagnostics; qPCR.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Candidiasis, Vulvovaginal / diagnosis*
  • Cross-Sectional Studies
  • Diagnostic Tests, Routine / methods*
  • Female
  • Humans
  • Microscopy / methods*
  • Real-Time Polymerase Chain Reaction / methods*
  • Vagina / microbiology
  • Vaginosis, Bacterial / diagnosis*
  • Young Adult