A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis
| العنوان: | A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis |
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| المؤلفون: | Harold Nuñez, Amanda Morton, Nathaniel A. Walton, Kira Harman, Juan Cristobal Jimenez, Elisabeth M. Bik, Victor Alegria-Mera, Donna Marie B. Hongo, Laurens Kraal, Felipe Melis-Arcos, Raul Pino, Susan Zneimer, Ignacio Varas, Pamela A. Nieto, Richard Phan, Jessica Richman, Audrey D. Goddard, Luis E. Leon, Eduardo H. Morales, Glenn A. Carson, Patricia Vera-Wolf, Sarah Gupta, Zachary Apte, Sara W. Bird, Camila F. Navas, Cristian Bravo, Graham Gass, José M. Pérez-Donoso, Nicolás Órdenes-Aenishanslins, Juan Pablo Cárdenas, Daniel Almonacid, Denisse Bravo, Kwasi Addae, Eduardo Olivares, Francisco J. Ossandon, Katia Soto-Liebe, Paulo C. Covarrubias, Juan Pablo Bustamante, Juan A. Ugalde, Adam Caughey |
| المصدر: | PLoS ONE, Vol 14, Iss 5, p e0215945 (2019) PLoS ONE CONICET Digital (CONICET) Consejo Nacional de Investigaciones Científicas y Técnicas instacron:CONICET |
| بيانات النشر: | Public Library of Science (PLoS), 2019. |
| سنة النشر: | 2019 |
| مصطلحات موضوعية: | 0301 basic medicine, Gardnerella, Viral Diseases, Ciencias de la Salud, Artificial Gene Amplification and Extension, Pathology and Laboratory Medicine, Cervical Cancer, Polymerase Chain Reaction, law.invention, Limit of Detection, law, RNA, Ribosomal, 16S, Genotype, Medicine and Health Sciences, Medicine, Papillomaviridae, DNA extraction, Polymerase chain reaction, Cervical cancer, Multidisciplinary, Microbiota, Gene Pool, Genomics, Middle Aged, Otras Ciencias de la Salud, Infectious Diseases, Oncology, Medical Microbiology, Viral Pathogens, Vagina, Viruses, purl.org/becyt/ford/3 [https], Female, Pathogens, Research Article, Adult, Human Papillomavirus Infection, Genotyping, CIENCIAS MÉDICAS Y DE LA SALUD, Adolescent, Papillomaviruses, Urology, Science, 030106 microbiology, Sexually Transmitted Diseases, VAGINAL MICROBIOME ANALYSIS, Microbial Genomics, Hpv detection, Sensitivity and Specificity, Microbiology, purl.org/becyt/ford/3.3 [https], Young Adult, 03 medical and health sciences, Extraction techniques, Genetics, Humans, Microbiome, Molecular Biology Techniques, Microbial Pathogens, Molecular Biology, Evolutionary Biology, Biology and life sciences, Population Biology, Genitourinary Infections, business.industry, Papillomavirus Infections, Organisms, Reproducibility of Results, Human Papillomavirus, Cancers and Neoplasms, Oncogene Proteins, Viral, medicine.disease, Virology, Research and analysis methods, Lactobacillus, MICROBIOME, 030104 developmental biology, HPV DETECTION, DNA, Viral, Capsid Proteins, DNA viruses, business, Gynecological Tumors, Population Genetics, Kappa, VAGINAL HEALTH ASSAY |
| الوصف: | 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. Fil: Bik, Elisabeth M.. Ubiome; Fil: Bird, Sara W.. Ubiome; Fil: Bustamante, Juan Pablo. Universidad Nacional de Entre Ríos. Instituto de Investigación y Desarrollo en Bioingeniería y Bioinformática - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación y Desarrollo en Bioingeniería y Bioinformática; Argentina Fil: Leon, Luis E.. Ubiome |
| وصف الملف: | application/pdf |
| تدمد: | 1932-6203 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::77ef7d3814522f61adbcbab0a3bbc67fTest https://doi.org/10.1371/journal.pone.0215945Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....77ef7d3814522f61adbcbab0a3bbc67f |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 19326203 |
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