Analysis of the Vaginal Microbiome by Next-Generation Sequencing and Evaluation of its Performance as a Clinical Diagnostic Tool in Vaginitis.
10.3343/alm.2016.36.5.441
- Author:
Ki Ho HONG
1
;
Sung Kuk HONG
;
Sung Im CHO
;
Eunkyung RA
;
Kyung Hee HAN
;
Soon Beom KANG
;
Eui Chong KIM
;
Sung Sup PARK
;
Moon Woo SEONG
Author Information
1. Department of Laboratory Medicine, Seoul Medical Center, Seoul, Korea.
- Publication Type:Evaluation Studies ; Original Article
- Keywords:
Vaginal microbiome;
NGS;
Vaginitis
- MeSH:
Area Under Curve;
Bacteria/*genetics/isolation & purification;
Bacterial Proteins/genetics;
Candida/*genetics/isolation & purification;
Female;
Fungal Proteins/genetics;
Gardnerella vaginalis/genetics/isolation & purification;
High-Throughput Nucleotide Sequencing;
Humans;
*Microbiota;
RNA, Ribosomal, 16S/chemistry/genetics/metabolism;
ROC Curve;
Sequence Analysis, DNA;
Trichomonas vaginalis/genetics/isolation & purification;
Vagina/*microbiology;
Vaginitis/*diagnosis/microbiology
- From:Annals of Laboratory Medicine
2016;36(5):441-449
- CountryRepublic of Korea
- Language:English
-
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.
