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.