A new sequencing-based women's health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis. A new women’s health assay

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 women’s 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 32 bacterial taxa of clinical importance, including Lactobacillus, Sneathia, Gardnerella, and 4 pathogens involved in STI, with high sensitivity, specificity, and reproducibility. For each of these taxa, healthy 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. 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

阴道微生物组的组成，包括性传播感染（sexually transmitted infections, STI）相关病原体与共生菌群，已被证实与女性生殖健康及全身健康存在重要关联。当前医疗从业者无法提供全面的阴道微生物组筛查服务，仅能开展单一病原体检测，例如引发宫颈癌的主要致病原——高危型人乳头瘤病毒（high-risk human papillomavirus, hrHPV）。目前市场上尚无同时整合HPV检测、性传播感染筛查与微生物组分析的综合检测项目。
本文介绍一种新型女性健康综合检测方案，该方案将自我采样技术与基于测序的HPV检测分型、阴道微生物组分析以及性传播感染相关病原体检测相结合。该检测可完成14种高危型HPV、5种低危型HPV（low-risk HPV, lrHPV）的分型与检测，同时定量分析32种具有临床重要性的细菌类群的相对丰度，涵盖乳杆菌属（Lactobacillus）、斯涅瑟菌属（Sneathia）、加德纳菌属（Gardnerella），以及4种性传播感染相关病原体，且具备高灵敏度、特异性与可重复性。
研究团队从50名自我报告健康的女性队列中，确定了上述各类细菌类群的健康参考范围。该检测的HPV测序模块以Digene高危型HPV HC2 DNA检测作为金标准进行性能验证。针对高危型HPV分型检测，601份样本的检测一致性达95.3%，Kappa值为0.804；剔除Digene高危型探针与低危型HPV存在交叉反应的样本后，高危型HPV分型检测的灵敏度与特异性分别为94.5%与96.6%。对于低危型HPV分型检测，148份样本的一致性为93.9%，Kappa值为0.788，其灵敏度与特异性分别达100%与92.9%。
这种新型检测方案可作为传统宫颈癌筛查的有效补充：其一，其自我采样模式能够覆盖原本无法参与筛查的女性群体；其二，该方案可提供阴道微生物组组成及病原体存在情况的额外临床信息。