title: Comparison of detection methods for vaginal lactobacilli.
abstract: Vaginal lactobacilli offer protection against microbiota imbalance and genitourinary tract infections. We compared vaginal lactobacilli in 50 Estonian women of child-bearing age applying culture-based methods, quantitative PCR and next-generation sequencing (NGS). The culture-based methods found three different lactobacilli: Lactobacillus crispatus, Lactobacillus jensenii and Lactobacillus gasseri. Using NGS revealed the presence of L. crispatus in 76%, Lactobacillus iners in 52%, L. jensenii in 47% and L. gasseri in 33% of the samples. According to qPCR, L. iners was present in 67% and L. crispatus in 64% of the samples. The proportions of L. crispatus revealed by qPCR and NGS were in good correlation (R=0.79, P<0.001), while that of L. iners correlated poorly (R=0.13, P>0.05). Good concordance for L. crispatus was also found between the results of the culture-based method and qPCR. Finally, good overlap between the results of the culture-based method and NGS was revealed: in case of a positive NGS result for L. crispatus, the same species was isolated in 95% of samples. The corresponding percentages were 82% for L. jensenii and 86% for L. gasseri. Our data indicate fairly general concordance of the three methods for detecting vaginal lactobacilli, except for L. iners. This points out the importance of standardisation of techniques, and the respective studies should involve cultures applying a medium suitable for the fastidious L. iners.
authors: 1 Department of Microbiology, Faculty of Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia.|2 Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia.
authors: I
authors: I
authors: Smidt
authors: 2 Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia.|3 Faculty of Science and Technology, University of Tartu, Ravila 19, Tartu 50411, Estonia.
authors: R
authors: R
authors: Kiiker
authors: 1 Department of Microbiology, Faculty of Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia.
authors: H
authors: H
authors: Oopkaup
authors: 1 Department of Microbiology, Faculty of Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia.|2 Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia.
authors: E
authors: E
authors: Lapp
authors: 1 Department of Microbiology, Faculty of Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia.|2 Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia.
authors: T
authors: T
authors: Rööp
authors: 1 Department of Microbiology, Faculty of Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia.
authors: K
authors: K
authors: Truusalu
authors: 1 Department of Microbiology, Faculty of Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia.|2 Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia.
authors: J
authors: J
authors: Štšepetova
authors: 2 Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia.|3 Faculty of Science and Technology, University of Tartu, Ravila 19, Tartu 50411, Estonia.
authors: J
authors: J
authors: Truu
authors: 1 Department of Microbiology, Faculty of Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia.|2 Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia.
authors: R
authors: R
authors: Mändar
mesh_terms: D001431:Bacteriological Techniques / Q000379:methods*; D004957:Estonia; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007778:Lactobacillus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification* / Q000502:physiology; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D014621:Vagina / Q000382:microbiology*
keywords: Lactobacillus iners; next generation sequencing; qPCR; vaginal lactobacilli