A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis
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 can...
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| Published in | PloS one Vol. 14; no. 5; p. e0215945 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Public Library of Science
01.05.2019
Public Library of Science (PLoS) |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1932-6203 1932-6203 |
| DOI | 10.1371/journal.pone.0215945 |
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| 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. |
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| AbstractList | 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. 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.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. 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. |
| Audience | Academic |
| Author | Nuñez, Harold Ossandon, Francisco J. Bravo, Denisse Pérez-Donoso, José Kraal, Laurens Goddard, Audrey D. Nieto, Pamela A. Gupta, Sarah L. Leon, Luis E. Alegría-Mera, Víctor Gass, Graham Harman, Kira Olivares, Eduardo Hongo, Donna Marie B. Soto-Liebe, Katia Morton, Amanda Addae, Kwasi Bravo, Cristian Jiménez, Juan C. Bustamante, Juan P. Melis-Arcos, Felipe Navas, Camila F. Varas, Ignacio Bird, Sara W. Órdenes-Aenishanslins, Nicolás Ugalde, Juan A. Zneimer, Susan Cardenas, Juan P. Apte, Zachary S. Covarrubias, Paulo C. Carson, Glenn A. Pino, Raul Morales, Eduardo H. Vera-Wolf, Patricia Richman, Jessica Walton, Nathaniel A. Almonacid, Daniel E. Phan, Richard Caughey, Adam Bik, Elisabeth M. |
| AuthorAffiliation | Istituto Nazionale Tumori IRCCS Fondazione Pascale, ITALY 2 Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, United States of America 1 uBiome, San Francisco, CA, United States of America |
| AuthorAffiliation_xml | – name: 1 uBiome, San Francisco, CA, United States of America – name: Istituto Nazionale Tumori IRCCS Fondazione Pascale, ITALY – name: 2 Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, United States of America |
| Author_xml | – sequence: 1 givenname: Elisabeth M. orcidid: 0000-0001-5477-0324 surname: Bik fullname: Bik, Elisabeth M. – sequence: 2 givenname: Sara W. surname: Bird fullname: Bird, Sara W. – sequence: 3 givenname: Juan P. surname: Bustamante fullname: Bustamante, Juan P. – sequence: 4 givenname: Luis E. surname: Leon fullname: Leon, Luis E. – sequence: 5 givenname: Pamela A. surname: Nieto fullname: Nieto, Pamela A. – sequence: 6 givenname: Kwasi surname: Addae fullname: Addae, Kwasi – sequence: 7 givenname: Víctor surname: Alegría-Mera fullname: Alegría-Mera, Víctor – sequence: 8 givenname: Cristian surname: Bravo fullname: Bravo, Cristian – sequence: 9 givenname: Denisse surname: Bravo fullname: Bravo, Denisse – sequence: 10 givenname: Juan P. surname: Cardenas fullname: Cardenas, Juan P. – sequence: 11 givenname: Glenn A. surname: Carson fullname: Carson, Glenn A. – sequence: 12 givenname: Adam surname: Caughey fullname: Caughey, Adam – sequence: 13 givenname: Paulo C. surname: Covarrubias fullname: Covarrubias, Paulo C. – sequence: 14 givenname: José surname: Pérez-Donoso fullname: Pérez-Donoso, José – sequence: 15 givenname: Graham surname: Gass fullname: Gass, Graham – sequence: 16 givenname: Sarah L. surname: Gupta fullname: Gupta, Sarah L. – sequence: 17 givenname: Kira surname: Harman fullname: Harman, Kira – sequence: 18 givenname: Donna Marie B. surname: Hongo fullname: Hongo, Donna Marie B. – sequence: 19 givenname: Juan C. surname: Jiménez fullname: Jiménez, Juan C. – sequence: 20 givenname: Laurens surname: Kraal fullname: Kraal, Laurens – sequence: 21 givenname: Felipe surname: Melis-Arcos fullname: Melis-Arcos, Felipe – sequence: 22 givenname: Eduardo H. surname: Morales fullname: Morales, Eduardo H. – sequence: 23 givenname: Amanda surname: Morton fullname: Morton, Amanda – sequence: 24 givenname: Camila F. surname: Navas fullname: Navas, Camila F. – sequence: 25 givenname: Harold surname: Nuñez fullname: Nuñez, Harold – sequence: 26 givenname: Eduardo surname: Olivares fullname: Olivares, Eduardo – sequence: 27 givenname: Nicolás surname: Órdenes-Aenishanslins fullname: Órdenes-Aenishanslins, Nicolás – sequence: 28 givenname: Francisco J. surname: Ossandon fullname: Ossandon, Francisco J. – sequence: 29 givenname: Richard surname: Phan fullname: Phan, Richard – sequence: 30 givenname: Raul surname: Pino fullname: Pino, Raul – sequence: 31 givenname: Katia surname: Soto-Liebe fullname: Soto-Liebe, Katia – sequence: 32 givenname: Ignacio surname: Varas fullname: Varas, Ignacio – sequence: 33 givenname: Patricia surname: Vera-Wolf fullname: Vera-Wolf, Patricia – sequence: 34 givenname: Nathaniel A. surname: Walton fullname: Walton, Nathaniel A. – sequence: 35 givenname: Daniel E. surname: Almonacid fullname: Almonacid, Daniel E. – sequence: 36 givenname: Audrey D. surname: Goddard fullname: Goddard, Audrey D. – sequence: 37 givenname: Juan A. surname: Ugalde fullname: Ugalde, Juan A. – sequence: 38 givenname: Susan surname: Zneimer fullname: Zneimer, Susan – sequence: 39 givenname: Jessica surname: Richman fullname: Richman, Jessica – sequence: 40 givenname: Zachary S. surname: Apte fullname: Apte, Zachary S. |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/31042762$$D View this record in MEDLINE/PubMed |
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| ContentType | Journal Article |
| Copyright | COPYRIGHT 2019 Public Library of Science 2019 Bik et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2019 Bik et al 2019 Bik et al |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Competing Interests: All of the authors of the paper are current or past employees of uBiome, Inc. and have received stock options as well as other compensation. Some authors have patents pending in relation to this work: US Application No 15/198,818, Method and system for diagnostic testing, Application No 16/084,945, Method and system for microbiome-derived diagnostics and therapeutics for bacterial vaginosis, and Application No 16/115,542, Method and system for characterization for female reproductive system-related conditions associated with microorganisms. The data in this article were used in the development of a commercially available test product developed and marketed by uBiome. This does not alter our adherence to PLOS ONE policies on sharing data and materials. These authors are co-first authors on this work. |
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| SubjectTerms | Abundance Adolescent Adult Assaying Bioassay Biology and life sciences Cancer Cancer screening Capsid Proteins - genetics Cellular biology Cervical cancer Cervix Composition Criminal investigation Cross-reactivity Deoxyribonucleic acid Diagnosis DNA DNA sequencing DNA, Viral - genetics DNA, Viral - isolation & purification Female Gardnerella - genetics Gardnerella - isolation & purification Genotype Genotyping Health care Health care industry Health risks Human papillomavirus Humans Lactobacillus - genetics Lactobacillus - isolation & purification Limit of Detection Medical screening Medicine and Health Sciences Microbiomes Microbiota Microbiota (Symbiotic organisms) Middle Aged Novels Oncogene Proteins, Viral - genetics Papillomaviridae - genetics Papillomaviridae - isolation & purification Papillomavirus Papillomavirus infections Papillomavirus Infections - diagnosis Papillomavirus Infections - virology Pathogenic microorganisms Pathogens Relative abundance Reproducibility Reproducibility of Results Research and analysis methods Risk RNA, Ribosomal, 16S - genetics RNA, Ribosomal, 16S - metabolism Sampling Sensitivity Sensitivity and Specificity Sexually transmitted diseases Sexually Transmitted Diseases - diagnosis Sexually Transmitted Diseases - virology STD Vagina Vagina - microbiology Vagina - virology Women's health Womens health Young Adult |
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| Title | A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis |
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