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Comparison of self-collected and physician-collected vaginal swabs for microbiome analysis.

ABSTRACT: To our knowledge, no data are available on whether the microbial species composition and abundance sampled with self-collected vaginal swabs are comparable to those of swabs collected by clinicians. Twenty healthy women were recruited to the study during a routine gynecological visit. Eligible women were between 18 and 40 years old with regular menstrual cycles. Participants self-collected a vaginal swab using a standardized protocol and then were examined by a physician, who collected an additional five swabs from the lateral wall of the mid-vagina. In this study, the self-collected and three physician-obtained swabs were analyzed and compared using terminal restriction fragment length polymorphism and sequence analyses of the 16S rRNA genes. Vaginal microbial community comparative statistical analyses of both T-RFLP and 16S rRNA gene sequence datasets revealed that self-collected vaginal swabs sampled the same microbial diversity as physician collected swabs of the mid-vagina. These findings enable large-scale, field-based studies of the vaginal microbiome.

SUBMITTER: Forney LJ

PROVIDER: S-EPMC2863907 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature

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Comparison of self-collected and physician-collected vaginal swabs for microbiome analysis.

Forney Larry J LJ Gajer Pawel P Williams Christopher J CJ Schneider G Maria GM Koenig Sara S K SS McCulle Stacey L SL Karlebach Shara S Brotman Rebecca M RM Davis Catherine C CC Ault Kevin K Ravel Jacques J

Journal of clinical microbiology 20100303 5

To our knowledge, no data are available on whether the microbial species composition and abundance sampled with self-collected vaginal swabs are comparable to those of swabs collected by clinicians. Twenty healthy women were recruited to the study during a routine gynecological visit. Eligible women were between 18 and 40 years old with regular menstrual cycles. Participants self-collected a vaginal swab using a standardized protocol and then were examined by a physician, who collected an additi ...[more]

PMID: 20200290

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Project description:BackgroundPolymerase chain reaction-based Xpert human papillomavirus (HPV) assay is a rapid test that detects high-risk HPV (hrHPV) infection. This point-of-care test is usually performed by collecting a cervical specimen in a vial of PreservCyt® transport medium. We compared HPV test positivity and accuracy between self-collected sample with a dry swab (s-DRY) versus physician-collected cervical sampling using a broom like brush and immediate immersion in PreservCyt (dr-WET).MethodsIn this cross-sectional study, we recruited 150 women ? 18 years old attending the colposcopy clinic in the University Hospital of Geneva. Each participant first self-collected a vaginal sample using a dry swab and then the physician collected a cervical specimen in PreservCyt. HPV analysis was performed with Xpert. Part of the PreservCyt-collected sample was used for hrHPV detection with the cobas® HPV test. HPV test positivity and performance of the two collection methods was compared.ResultsHPV positivity was 49.1% for s-DRY, 41.8% for dr-WET and 46.2% for cobas. Good agreement was found between s-DRY and dr-WET samples (kappa±Standard error (SE) = 0.64±0.09,), particularly for low-grade squamous intraepithelial lesions (LSIL+) (kappa±SE = 0.80±0.17). Excellent agreement was found between the two samples for HPV16 detection in general (kappa±SE = 0.91±0.09) and among LSIL+ lesions (kappa±SE = 1.00±0.17). Sensitivities and specificities were, respectively, 84.2% and 47.1%(s-DRY), 73.1% and 58.7%. (dr-WET) and 77.8% and 45.7% (cobas) for CIN2+ detection. The median delay between sampling and HPV analysis was 7 days for the Xpert HPV assay and 19 days for cobas. There were 36 (24.0%) invalid results among s-DRY samples and 4 (2.7%) among dr-WET (p = 0.001). Invalid results happened due to the long interval between collection and analysis.ConclusionSelf-collected vaginal dry swabs are a valid alternative to collecting cervical samples in PreservCyt solution for HPV testing with the Xpert HPV assay.ImpactHPV self-collection with dry cotton swabs might assist in the implementation of an effective screening strategy in developing countries.Trial registrationInternational Standard Randomized Controlled Trial Number Registry ISRCTN83050913.

Project description:ObjectivesSelf-collected vaginal swabs can facilitate diagnosis of vaginal discharge (VD) in resource-limited settings, provided reliability of the method is established. The aim of this study was to evaluate the concordance between self-collected and physician-collected vaginal swabs for aetiological diagnosis of VD and to determine the prevalence of bacterial vaginosis (BV), vulvovaginal candidiasis (VVC) and trichomonas vaginitis (TV).MethodsA total of 550 females (median age: 32 years; range: 18-45 years) attending two sexually transmitted infection/reproductive tract infection (STI/RTI) clinics with VD from January 2015 to May 2016 were included in the study after obtaining written informed consent. Swabs were self-collected by patients after instructions and subsequently by a physician under speculum examination. Samples were processed for standard bedside tests, Gram staining, wet mount and culture (gold standard) according to the national guidelines. Concordance between the two methods was determined by the Cohen's kappa value.ResultsBV, VVC and TV were diagnosed in 79 (14.4%), 144 (26.2%) and 3 (0.5%) patients, respectively. VVC coexisted with BV in 58 (10.5%) patients. There was no coinfection of TV with BV or VVC. Candida albicans was isolated in 84 (58.3%) VVC cases. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of self-collected swabs for diagnosing BV was 91.1%, 100%, 100% and 98.5%, respectively, while for the C. albicans VVC and TV, sensitivity, specificity, PPV and NPV all were 100% as compared with physician-collected swabs. Highly concordant results were obtained between two methods by the Kappa values of 0.95 (BV), 0.99 (VVC) and 1.0 (TV).ConclusionThe comparative performance of self-collected and physician-collected vaginal swabs establishes self-collection of samples for BV, VVC and TV as a viable alternative tool in the management of STIs/RTIs, especially in peripheral and resource-constrained settings. This would be effective in implementing the diagnostic approaches for STIs/RTIs in community-based surveillance studies at national or regional level and therefore strengthening the National STI/RTI Control Programme.

Project description:Background: The composition of the microbiome in human body sites plays an important role in health. The vaginal environment is colonized by several species of bacteria that have a major influence on reproductive health. The advancement of sequencing technologies has made the assessment of the composition of the microbiota possible through microbial DNA extraction and sequencing. Therefore, it is of a paramount importance to select a sensitive and reproducible DNA extraction method, that facilitates isolation of microbial DNA with a sufficient quantity and purity, from microbial species living in the vaginal environment. Here, we have evaluated four different DNA extraction protocols from self-collected vaginal swabs. Methods: Five healthy female volunteers were enrolled in the study. Each donor was asked to self-collect 4 samples using Copan ESwab. DNA was extracted using Qiagen DNeasy kit and three modified protocols of the MoBio PowerSoil kit ("DNeasy PowerSoil" after acquisition from Qiagen). DNA quantity and integrity was checked through Nanodrop and LabChip GX. DNA was further tested through quantitative real-time PCR (qPCR) and 16S sequencing. Vaginal microbiota diversities were determined using MiSeq-Illumina high-throughput sequencing of bacterial 16S rDNA V1-V3 fingerprint. Sequencing data were analyzed using QIIME pipeline. Results: Qiagen DNeasy protocol resulted in the highest DNA yield as compared to the modified protocols of MoBio Powersoil kit. The size of the DNA extracted using each protocol was ~40 kb. Qiagen DNeasy protocol gave the highest Genomic Quality Score (average ± standard deviation: 4.24 ± 0.36), followed by the different MoBio Powersoil protocols. A substantial variability in microbial DNA abundance was found across the protocols. The vaginal microbiota of the healthy volunteers was dominated by Lactobacillus species. MoBio Powersoil kit provided a significantly higher alpha diversity as compared to the Qiagen DNeasy kit, while beta diversity measures did not reveal any significant cluster changes, except when the Bray-Curtis method was applied. Conclusion: We were able to isolate microbial DNA from the vaginal swabs. Qiagen DNeasy method gave the highest DNA yield and quality but was not optimal in detecting microbial diversity. The modified MoBio PowerSoil protocols showed higher microbial diversities as compared to the standard protocol.

Dataset Information

Comparison of self-collected and physician-collected vaginal swabs for microbiome analysis.

Publications

Comparison of self-collected and physician-collected vaginal swabs for microbiome analysis.

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