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

Date Published: May 1, 2019

Publisher: Public Library of Science

Author(s): 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, Maria Lina Tornesello.


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.

Partial Text

A woman’s vaginal health is critical for her general well-being and reproductive success, and is in part determined by the vaginal microbiome composition, the presence of pathogens associated with sexually transmitted infections (STI), and the presence of human papillomavirus (HPV) types that can cause genital warts or cervical cancer. Current clinical vaginal health assays focus on the detection of STI or that of HPV, but there is no single test that combines these targets with vaginal microbiome analysis or with self-sampling.

Here, we describe a novel vaginal health assay combining vaginal microbiome analysis, STI-associated pathogen detection, and HPV detection and identification in a self-sampling format. Although each of these components have been described before, to our knowledge, this assay is the first to combine all of these parts, thus offering women a unique opportunity to gain a broad perspective into their vaginal and reproductive health.




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