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...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2019-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0215945 |
| _version_ | 1819108582251036672 |
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| author | Elisabeth M Bik Sara W Bird Juan P Bustamante Luis E Leon Pamela A Nieto Kwasi Addae Víctor Alegría-Mera Cristian Bravo Denisse Bravo Juan P Cardenas Glenn A Carson Adam Caughey Paulo C Covarrubias José Pérez-Donoso Graham Gass Sarah L Gupta Kira Harman Donna Marie B Hongo Juan C Jiménez Laurens Kraal Felipe Melis-Arcos Eduardo H Morales Amanda Morton Camila F Navas Harold Nuñez Eduardo Olivares Nicolás Órdenes-Aenishanslins Francisco J Ossandon Richard Phan Raul Pino Katia Soto-Liebe Ignacio Varas Patricia Vera-Wolf Nathaniel A Walton Daniel E Almonacid Audrey D Goddard Juan A Ugalde Susan Zneimer Jessica Richman Zachary S Apte |
| author_facet | Elisabeth M Bik Sara W Bird Juan P Bustamante Luis E Leon Pamela A Nieto Kwasi Addae Víctor Alegría-Mera Cristian Bravo Denisse Bravo Juan P Cardenas Glenn A Carson Adam Caughey Paulo C Covarrubias José Pérez-Donoso Graham Gass Sarah L Gupta Kira Harman Donna Marie B Hongo Juan C Jiménez Laurens Kraal Felipe Melis-Arcos Eduardo H Morales Amanda Morton Camila F Navas Harold Nuñez Eduardo Olivares Nicolás Órdenes-Aenishanslins Francisco J Ossandon Richard Phan Raul Pino Katia Soto-Liebe Ignacio Varas Patricia Vera-Wolf Nathaniel A Walton Daniel E Almonacid Audrey D Goddard Juan A Ugalde Susan Zneimer Jessica Richman Zachary S Apte |
| author_sort | Elisabeth M Bik |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-22T03:12:13Z |
| format | Article |
| id | doaj.art-5898905ae8a940088488e6ace215245f |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-22T03:12:13Z |
| publishDate | 2019-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-5898905ae8a940088488e6ace215245f2022-12-21T18:40:54ZengPublic Library of Science (PLoS)PLoS ONE1932-62032019-01-01145e021594510.1371/journal.pone.0215945A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis.Elisabeth M BikSara W BirdJuan P BustamanteLuis E LeonPamela A NietoKwasi AddaeVíctor Alegría-MeraCristian BravoDenisse BravoJuan P CardenasGlenn A CarsonAdam CaugheyPaulo C CovarrubiasJosé Pérez-DonosoGraham GassSarah L GuptaKira HarmanDonna Marie B HongoJuan C JiménezLaurens KraalFelipe Melis-ArcosEduardo H MoralesAmanda MortonCamila F NavasHarold NuñezEduardo OlivaresNicolás Órdenes-AenishanslinsFrancisco J OssandonRichard PhanRaul PinoKatia Soto-LiebeIgnacio VarasPatricia Vera-WolfNathaniel A WaltonDaniel E AlmonacidAudrey D GoddardJuan A UgaldeSusan ZneimerJessica RichmanZachary S ApteThe 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.https://doi.org/10.1371/journal.pone.0215945 |
| spellingShingle | Elisabeth M Bik Sara W Bird Juan P Bustamante Luis E Leon Pamela A Nieto Kwasi Addae Víctor Alegría-Mera Cristian Bravo Denisse Bravo Juan P Cardenas Glenn A Carson Adam Caughey Paulo C Covarrubias José Pérez-Donoso Graham Gass Sarah L Gupta Kira Harman Donna Marie B Hongo Juan C Jiménez Laurens Kraal Felipe Melis-Arcos Eduardo H Morales Amanda Morton Camila F Navas Harold Nuñez Eduardo Olivares Nicolás Órdenes-Aenishanslins Francisco J Ossandon Richard Phan Raul Pino Katia Soto-Liebe Ignacio Varas Patricia Vera-Wolf Nathaniel A Walton Daniel E Almonacid Audrey D Goddard Juan A Ugalde Susan Zneimer Jessica Richman Zachary S Apte A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis. PLoS ONE |
| title | A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis. |
| title_full | A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis. |
| title_fullStr | A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis. |
| title_full_unstemmed | A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis. |
| title_short | A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis. |
| title_sort | novel sequencing based vaginal health assay combining self sampling hpv detection and genotyping sti detection and vaginal microbiome analysis |
| url | https://doi.org/10.1371/journal.pone.0215945 |
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