Introduction/Background Increasing evidence suggests vaginal dysbiosis is associated with persistence of human papillomavirus (HPV) infection and cervical intraepithelial neoplasia (CIN1–3) development. In this pilot study we aimed to investigate the potential of vaginal microbiome biomarkers to predict CIN3 development in high risk HPV positive (hr-HPV+) women.

Methodology 59 women with normal cytology at initial screening and follow-up over six years were enrolled from ARTISTIC trial. The cohort included 14 hr-HPV negative (hr-HPV-) and 15 hr-HPV+ women through whole follow-up. Additionally, 30 hr-HPV+ women, who developed CIN3 at the first follow-up, then were surgically treated for the disease and testing hr-HPV- after, were also included. Exfoliated cervical specimens were used for whole genomic and bacterial DNA extraction. Vaginal microbiota composition was determined by 16S rRNA gene fragments sequencing. The S5 methylation classifier assays were performed as previously described (Brentnall et al, 2015).

Results We identified unique microbial biomarkers associated with CIN3 development and recovery after surgical treatment. Hr-HPV+ women with CIN3 showed a significant overrepresentation of following microbial species: Sneathia amnii, Megasphaera genomosp., Peptosterptoccocus anaerobius and Achromobacter spanius. Sneathia amnii was the only bacteria consistently associated with CIN3 in all group comparisons performed (p<0.01). Conversely, after successful treatment women were hr-HPV- and exhibited an increased representation of Lactobacillus species, especially Lactobacillus gasseri (p<0.01). Higher proportions of Lactobacillus helveticus, Lactobacillus suntoryeus and Lactobacillus vaginalis showed a potential protective role against CIN3 development in women with persistent hr-HPV infection. We confirmed S5 scores are increasing with cervical disease severity. Increasing Sneathia amnii abundance was directly proportional to S5 score increase during cervical disease development.

Conclusion Our results might indicate Sneathia amnii possible role in modifying the epigenetic landscape of the cervicovaginal space. Further investigations are required to establish a link between the identified potential vaginal microbiome biomarkers and their influence on epigenetic mechanisms.