Dataset Information

A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis.

ABSTRACT: The composition of the vaginal microbiome, including both the presence of pathogens involved in sexually transmitted infections (STI) as well as commensal microbiota, has been shown to have important associations for a woman's reproductive and general health. Currently, healthcare providers cannot offer comprehensive vaginal microbiome screening, but are limited to the detection of individual pathogens, such as high-risk human papillomavirus (hrHPV), the predominant cause of cervical cancer. There is no single test on the market that combines HPV, STI, and microbiome screening. Here, we describe a novel inclusive vaginal health assay that combines self-sampling with sequencing-based HPV detection and genotyping, vaginal microbiome analysis, and STI-associated pathogen detection. The assay includes genotyping and detection of 14 hrHPV types, 5 low-risk HPV types (lrHPV), as well as the relative abundance of 31 bacterial taxa of clinical importance, including Lactobacillus, Sneathia, Gardnerella, and 3 pathogens involved in STI, with high sensitivity, specificity, and reproducibility. For each of these taxa, reference ranges were determined in a group of 50 self-reported healthy women. The HPV sequencing portion of the test was evaluated against the digene High-Risk HPV HC2 DNA test. For hrHPV genotyping, agreement was 95.3% with a kappa of 0.804 (601 samples); after removal of samples in which the digene hrHPV probe showed cross-reactivity with lrHPV types, the sensitivity and specificity of the hrHPV genotyping assay were 94.5% and 96.6%, respectively, with a kappa of 0.841. For lrHPV genotyping, agreement was 93.9% with a kappa of 0.788 (148 samples), while sensitivity and specificity were 100% and 92.9%, respectively. This novel assay could be used to complement conventional cervical cancer screening, because its self-sampling format can expand access among women who would otherwise not participate, and because of its additional information about the composition of the vaginal microbiome and the presence of pathogens.

SUBMITTER: Bik EM

PROVIDER: S-EPMC6493738 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis.

Bik Elisabeth M EM Bird Sara W SW Bustamante Juan P JP Leon Luis E LE Nieto Pamela A PA Addae Kwasi K Alegría-Mera Víctor V Bravo Cristian C Bravo Denisse D Cardenas Juan P JP Carson Glenn A GA Caughey Adam A Covarrubias Paulo C PC Pérez-Donoso José J Gass Graham G Gupta Sarah L SL Harman Kira K Hongo Donna Marie B DMB Jiménez Juan C JC Kraal Laurens L Melis-Arcos Felipe F Morales Eduardo H EH Morton Amanda A Navas Camila F CF Nuñez Harold H Olivares Eduardo E Órdenes-Aenishanslins Nicolás N Ossandon Francisco J FJ Phan Richard R Pino Raul R Soto-Liebe Katia K Varas Ignacio I Vera-Wolf Patricia P Walton Nathaniel A NA Almonacid Daniel E DE Goddard Audrey D AD Ugalde Juan A JA Zneimer Susan S Richman Jessica J Apte Zachary S ZS

PloS one 20190501 5

The composition of the vaginal microbiome, including both the presence of pathogens involved in sexually transmitted infections (STI) as well as commensal microbiota, has been shown to have important associations for a woman's reproductive and general health. Currently, healthcare providers cannot offer comprehensive vaginal microbiome screening, but are limited to the detection of individual pathogens, such as high-risk human papillomavirus (hrHPV), the predominant cause of cervical cancer. The ...[more]

PMID: 31042762

Similar Datasets

Project description:High-risk human papillomavirus (hr-HPV) infection of the cervicovaginal tract is known to be the major cause of cervical cancer. Similar to various other countries, Germany introduced an organized combined screening including cytology and HPV testing in 2020. The participation rate was around 70% in the past. Self-testing for hr-HPV infections could be an option to increase the participation rate. Two dry vaginal self-sampling devices and a device for the self-collection of first-void urine were evaluated in combination with a PCR-based hr-HPV test regarding their clinical performance (sensitivity for high-grade cervical intraepithelial neoplasia, CIN 2+). A cervical smear taken by a clinician during colposcopy was used as reference. This open prospective multicenter trial recruited patients referred to the two participating colposcopy clinics (Hannover Medical School and IZD Hannover, Germany) with abnormal results from cervical cancer screening from 05/2020 to 11/2020. All patients received three CE-certified self-sampling devices (FLOQSwabs, COPAN, Italy; Evalyn Brush, Rovers Medical Devices, the Netherlands; Colli-Pee FV-5000, Novosanis, Wijnegem, Belgium) with instructions to read and apply at home in a pre-specified alternating order without medical assistance. HPV testing was performed after adequate preservation and DNA extraction. Histological results from colposcopy or cervical excisional surgery after self-sampling were used as the gold-standard. The data of 65 patients were analyzed. All invasive cancer cases and over 90% of the CIN 3 lesions were found to be hr-HPV positive with all three self-collection devices. All devices were considered easy to use without any difficulties following the written instructions. Hr-HPV testing of self-collected first-void urine and dry vaginal self-samples showed a high sensitivity for CIN 3+ comparable to that of a clinician-taken smear. Self-sampling was well accepted as it is convenient and easy to use.

Project description:BackgroundAccording to international guidelines, Human Papillomavirus (HPV) DNA tests represent a valid alternative to Pap Test for primary cervical cancer screening, provided that they guarantee balanced clinical sensitivity and specificity for cervical intraepithelial neoplasia grade 2 or more (CIN2+) lesions. The study aimed to assess whether HPV Selfy (Ulisse BioMed - Trieste, Italy), a full-genotyping HPV DNA test that detects and differentiates 14 high-risk HPV (HR-HPV) types, meets the criteria for primary cervical cancer screening described in the international guidelines, on clinician-collected as well as on self-collected samples.MethodsFor each participant woman, consecutively referring to Azienda Sanitaria Universitaria Giuliano Isontina (Trieste, Italy) and CRO-National Cancer Institute (Aviano, Italy) for the cervical cancer screening program, the following samples were tested: (a) a clinician-collected cervical specimen, analyzed with the reference test (Hybrid Capture®2 test, HC2) and HPV Selfy; and (b) a self-collected vaginal sample, analyzed with HPV Selfy. Enrolled women were also asked to fulfill a questionnaire about self-sampling acceptability. As required by guidelines, a non-inferiority test was conducted to compare the clinical performance of the test under evaluation with its reference test.ResultsHPV Selfy clinical sensitivity and specificity resulted non-inferior to those of HC2. By analysis of a total of 889 cervical liquid-based cytology samples from a screening population, of which 98 were from women with CIN2+, HPV Selfy showed relative sensitivity and specificity for CIN2+ of 0.98 and 1.00 respectively (non-inferiority score test: P = 0.01747 and P = 0.00414, respectively); the test reached adequate intra- and inter-laboratory reproducibility. Moreover, we demonstrated that the performance of HPV Selfy on self-collected vaginal samples was non-inferior to the performance obtained on clinician-collected cervical specimen (0.92 relative sensitivity and 0.97 relative specificity). Finally, through HPV Selfy genotyping, we were able to describe HPV types prevalence in the study population.ConclusionsHPV Selfy fulfills all the requirements of the international Meijer's guidelines and has been clinically validated for primary cervical cancer screening purposes. Moreover, HPV Selfy has also been validated for self-sampling according to VALHUDES guidelines. Therefore, at date, HPV Selfy is the only full-genotyping test validated both for screening purposes and for self-sampling. Trial registration ASUGI Trieste n. 16008/2018; CRO Aviano n.17149/2018.

Dataset Information

A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis.

Publications

A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets