Ann Lab Med 2016; 36(5): 441-449  https://doi.org/10.3343/alm.2016.36.5.441
Analysis of the Vaginal Microbiome by Next-Generation Sequencing and Evaluation of its Performance as a Clinical Diagnostic Tool in Vaginitis
Ki Ho Hong, M.D.1,2, Sung Kuk Hong, M.D.2,3, Sung Im Cho, M.T.4, Eunkyung Ra, M.T.4, Kyung Hee Han, M.D.5,
Soon Beom Kang, M.D.6, Eui-Chong Kim, M.D.3,4, Sung Sup Park, M.D.3,4, and Moon-Woo Seong, M.D.3,4
Department of Laboratory Medicine1, Seoul Medical Center, Seoul, Korea; Department of Laboratory Medicine2, College of Medicine, Seoul National University, Seoul, Korea; Department of Laboratory Medicine3, Sheikh Khalifa Specialty Hospital, Ras Al Khaimah, United Arab Emirates; Department of Laboratory Medicine4, Seoul National University Hospital, Seoul, Korea; Department of Obstetrics & Gynecology5, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, Korea; Department of Obstetrics & Gynecology6, Konkuk University Medical Center, Seoul, Korea
Received: November 30, 2015; Revised: April 3, 2016; Accepted: May 30, 2016
© Korean Society for Laboratory Medicine. All rights reserved.

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Abstract
Background: Next-generation sequencing (NGS) can detect many more microorganisms of a microbiome than traditional methods. This study aimed to analyze the vaginal microbiomes of Korean women by using NGS that included bacteria and other microorganisms. The NGS results were compared with the results of other assays, and NGS was evaluated for its feasibility for predicting vaginitis.
Methods: In total, 89 vaginal swab specimens were collected. Microscopic examinations of Gram staining and microbiological cultures were conducted on 67 specimens. NGS was performed with GS junior system on all of the vaginal specimens for the 16S rRNA, internal transcribed spacer (ITS), and Tvk genes to detect bacteria, fungi, and Trichomonas vaginalis. In addition, DNA probe assays of the Candida spp., Gardnerella vaginalis, and Trichomonas vaginalis were performed. Various predictors of diversity that were obtained from the NGS data were analyzed to predict vaginitis.
Results: ITS sequences were obtained in most of the specimens (56.2%). The compositions of the intermediate and vaginitis Nugent score groups were similar to each other but differed from the composition of the normal score group. The fraction of the Lactobacillus spp. showed the highest area under the curve value (0.8559) in ROC curve analysis. The NGS and DNA probe assay results showed good agreement (range, 86.2-89.7%).
Conclusions: Fungi as well as bacteria should be considered for the investigation of vaginal microbiome. The intermediate and vaginitis Nugent score groups were indistinguishable in NGS. NGS is a promising diagnostic tool of the vaginal microbiome and vaginitis, although some problems need to be resolved.
Keywords: Vaginal microbiome, NGS, Vaginitis

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