Metagenomic profiling in hr-HPV positive women

Increasing evidence in the latest years has highlighted the role of the vaginal microbiome (VM) in the severity of HPV infection and its potential link to cervical intraepithelial neoplasia, however there is still a lot that remains unclear regarding the precise role of certain bacteria in the context of HPV positivity and persistence of infection. Here, we applied an NGS methodology to comprehensively profile the VM in a series of 877 women who tested positive for at least one high risk HPV (hrHPV) type with the COBAS® 4800 assay, after self-collection of a vaginal smear sample. Starting from gDNA, we PCR amplified the V3-V4 region of the bacterial 16S rRNA gene and applied a paired-end NGS protocol (Illumina). Our results show significant differences in the abundance of certain bacteria compared to negative controls, and among different HPV-subtypes, more particularly in the abundance of species assigned to Lacticaseibacillus Megasphaera and Sneathia genera). Especially for Lacticaseibacillus, we observed significant depletion in the case of HPV16, HPV18 vs. HPVother. Overall, our results suggest that the presence or absence of specific microbial genera may be linked to the observed severity in hrHPV infection, particularly in the case of HPV16, 18 subtypes.