Frontiers in Endocrinology · Oct 30, 2026
Vaginal microbiome alterations associated with HPV infection and cervical dysplasia in apparently healthy Togolese women
By EYA KAMASSA, Gnatoulma KATAWA, Righteous Kwaku Agoha et al.
Background: Persistent high-risk human papillomavirus (HR-HPV) infection is the main cause of cervical cancer; however, the role of vaginal microbiome dysbiosis in HPV positivity and cervical dysplasia remains poorly characterized in sub-Saharan Africa. This study examined cervicovaginal microbiome profiles associated with HR-HPV infection and cervical dysplasia among apparently healthy women in Togo. Methods: A cross-sectional, community-based cervical cancer screening study was conducted in Lomé, Togo. Vaginal dysbiosis was assessed using Nugent scoring, cervical cytology using the Bethesda 2014 system, and HR-HPV genotyping using the Anyplex II HPV HR Detection Kit. Vaginal microbiome profiling was performed by Illumina MiSeq sequencing of the V3-V4 region of the 16S rRNA gene. Bioinformatics included DADA2 for processing, phyloseq and vegan in R for diversity analyses, DESeq2 for differential abundance, and PICRUSt2 with MetaCyc for functional prediction. Results: Among 338 women, HR-HPV prevalence was 31.33% and cervical dysplasia 10.06%. HPV16 was the most frequent genotype, followed by HPV51 and HPV58. HR-HPV infection and dysplasia were associated with significantly higher Nugent scores (p = 0.001 and p = 0.008). Alpha and beta diversity analyses showed no significant global microbiome restructuring by HPV or dysplasia status. However, compositional shifts showed depletion of Lactobacillus and enrichment of anaerobic and opportunistic taxa, including Atopobium vaginae, Sneathia sanguinegens, Prevotella spp., Peptostreptococcus anaerobius, and Peptoniphilus faecalis. Community state type analysis revealed a shift from Lactobacillus-dominated CSTs to dysbiotic CST IV. Functional prediction showed enrichment of sucrose degradation II, chorismate biosynthesis II, and anaerobic pathways in affected groups. No correlation was observed between HPV viral load and dysbiosis score. Conclusion: HR-HPV infection and cervical dysplasia in Togolese women are linked to vaginal microbiome dysbiosis characterized by Lactobacillus depletion and enrichment of anaerobic, potentially pro-inflammatory taxa. These findings suggest a microbiome contribution to HPV positivity and cervical lesions and support its integration into prevention strategies in sub-Saharan Africa. This is the first West African community-based study combining blinded cervical screening, Nugent scoring, and sequencing-based microbiome profiling.