The vaginal microbiome is increasingly studied using sequencing approaches; however, the exact bacterial community structure in vaginal diseases, e.g. bacterial vaginosis (BV), remains unclear. Vaginal Pap smears routinely obtained in preventive screening programs can also be evaluated with high accuracy regarding microbial colonization by means of microscopy.

This longitudinal retrospective case control study aims to investigate the relationship between microscopic vaginal flora observed in Pap-smears and Human Papilloma Virus (HPV) clearance, persistence or progression using HPV-PCR tests and the results of the Pap-smears. Two cohorts of high-risk HPV positive patients were formed. Cohort A (n = 136) was observed over a two-year time period 2020–2022, while cohort B (n = 160) was observed over a one-year period from 2021 to 2022. Each case group consisted of BV-positive patients that were compared to BV negative patients as controls.

It was found that the case groups in both cohorts had a higher HPV persistence rate and a higher rate of progression at follow-up. Lactobacillus flora was consistently associated with favorable outcomes, particularly higher HPV clearance rates across both cohorts and the entire observation period. In contrast patients with bacterial vaginosis (BV) were associated with significantly increased risk of HPV progression, especially in Cohort B, supporting its role as risk factor in the development of precancerous cervical lesions.

The integration of microscopic flora assessment into screening programs for cervical cancer may help to improve risk stratification in HPV positive women. Our findings suggest that, BV-positive patients may benefit from a closer follow-up period and earlier therapeutic intervention.

Not applicable.