Prospective study of cervicovaginal microbiome and incident Chlamydia trachomatis

Chlamydia trachomatis (CT) is the most common bacterial sexually transmitted infection that continues to rise in incidence and disproportionately affects Black and Hispanic adolescent and young adult (AYA) populations. We utilized a cohort of sexually active AYA women in NYC to prospectively study risk factors for development of CT. We matched AYA women with incident-CT to controls who were CT-negative for molecular assessment of their cervicovaginal microbiomes (CVMs) approximately 6 months prior to infection (t-1), at infection (t0) and approximately 6 months following treatment (t+1). We demonstrate that CT risk increases when molecular bacterial vaginosis (molBV) is detected prior to infection at t-1. We further show that the closer the time molBV-BV is detected the higher the risk for incident CT and this risk is strongly dependent on a subtype of BV dominated by Candidatus Lachnocurva vaginae (formerly BVAB1). Subsequent treatment partially recovers an optimal CVM state. This report is the first to consider CVM prior, during and after an incident CT infection and presents evidence for a significant relationship between the CVM and the risk of acquisition of CT with implications for public health management via screening and tailored intervention. Note that this upload breaks the nested case control design (i.e. there are no duplicate samples) due to Qiita upload rules. While this data will be sufficient for reproducing the core study results (only about 7% of samples are duplicated), please contact the corresponding author of the CT study for the structured matched nested-case control analysis map to match exact numbers in published paper. Additionally the original sequencing contains sample replicated (~10%), positive controls (ZYMO standards) and negatives. At time of upload (October 2024), there was a 1,500 sample upload limit to a study prep, so these control samples were not included as part of submission. If you are interested in using these secondary samples for QC work, please contact the CT study corresponding authors.

沙眼衣原体（Chlamydia trachomatis, CT）是最常见的细菌性性传播感染病原体，其发病率持续攀升，且对黑人与西班牙裔青少年及年轻成人（Adolescent and Young Adult, AYA）群体的影响尤为显著不均。本研究依托纽约市性活跃的AYA女性队列，前瞻性探究CT感染的危险因素。研究将新发CT感染的AYA女性与对照人群进行匹配，对照人群分别在感染前约6个月（t-1）、感染时（t0）及治疗后约6个月（t+1）的宫颈阴道微生物组（Cervicovaginal Microbiome, CVM）分子检测结果均为CT阴性。本研究证实，若在感染前的t-1时间点检测到分子细菌性阴道病（molecular bacterial vaginosis, molBV），则CT感染风险会显著升高。进一步分析显示，molBV检测时间与CT感染时间越接近，新发CT感染的风险越高，且该风险高度依赖于以Candidatus Lachnocurva vaginae（原BVAB1）为优势菌的BV亚型。后续抗感染治疗可部分恢复最优宫颈阴道微生物组状态。本报告首次针对新发CT感染的感染前、感染中及感染后三个阶段的宫颈阴道微生物组进行系统分析，证实宫颈阴道微生物组与CT感染风险间存在显著关联，该发现可为通过筛查与个性化干预开展公共卫生管理提供理论依据。请注意，受Qiita上传规则限制，本次上传打破了嵌套病例对照研究设计（即无重复样本）。尽管本次数据仅存在约7%的重复样本，已足够复现核心研究结果，但如需获取与已发表论文中精确匹配数值对应的结构化匹配嵌套病例对照分析映射表，请联系本CT研究的通讯作者。此外，原始测序数据包含约10%的重复样本、阳性对照（Zymo标准品）及阴性对照。本次上传时间为2024年10月，受单研究项目1500样本的上传限额限制，本次提交未纳入上述对照样本。若您希望使用这些二级样本开展质控相关工作，请联系CT研究的通讯作者。