Microbiome and metabolomic changes associated with HPV clearance in women undergoing local excisional treatment for cervical intraepithelial neoplasia.

Cervical intraepithelial neoplasia (CIN) is a common gynecological condition often associated with persistent human papillomavirus (HPV) infections. Although the loop electrosurgical excision procedure (LEEP) is effective in removing lesions, some patients remain HPV positive post-treatment. In this prospective study, we enrolled reproductive-age women diagnosed with HPV-related CIN and employed a multi-omics analysis of cervicovaginal secretion and cervical tissue microbiomes, alongside non-targeted and targeted metabolomic assessments. We aim to explore the role of the cervicovaginal and intratissue microbiota and associated metabolites on HPV clearance following LEEP. We observed significant shifts in bacterial diversity and composition in both cervicovaginal secretion and cervical tissue samples. Notably, distinct bacterial species, such as IMPORTANCE: The clearance of human papillomavirus (HPV) after local excisional treatment for cervical intraepithelial neoplasia is crucial for patient health. This study reveals significant alterations in the cervicovaginal secretion and cervical tissue microbiomes, alongside metabolomic changes, which are associated with HPV clearance. Through a comprehensive multi-omics approach, we identified specific bacterial species and metabolic changes that correlate with successful HPV clearance post-loop electrosurgical excision procedure. Notably, the presence of beneficial