Vaginal microbiome and metabolome profiling identifies candidate signatures associated with persistent high-risk HPV infection

Abstract The role of vaginal microbiota dysbiosis in the progression of human papillomavirus (HPV) infection is increasingly recognized. Yet, the factors determining why only a minority of infections persist and evolve into clinically significant disease remain poorly defined. From a large screening cohort of 4572 women, we rigorously selected 640 participants, categorizing them into HPV-negative, high-risk HPV, and low-risk HPV groups, with 70 high-risk individuals monitored over one year. Integrated metagenomic, genome-resolved, and metabolomic analyses identified distinct taxonomic and predicted functional profiles across HPV infection statuses. Lactobacillus iners emerged as a prominent hr-HPV-associated taxon and was linked to selected predicted functions involving redox processes, stress responses, and bacterial mobile genetic elements. Genome-resolved analyses further identified group-associated differences in taxonomic composition and predicted contributions to biofilm- and short-chain-fatty-acid-related pathways. Although overall microbial diversity and community state type distributions and transitions did not distinguish persistent infection from transient clearance, the two outcomes were associated with specific taxonomic and baseline metabolic features. These included an exploratory baseline signal for Streptococcus agalactiae in transient clearance, increased Bifidobacterium breve and B. bifidum during clearance, and increased Ewingella americana and Pseudomonas fluorescens during persistence, together with differences in energy, nicotinate/nicotinamide, glycerophospholipid, and redox-related metabolism. An exploratory integrated microbial–metabolic classifier yielded internal AUC estimates of 0.820–0.970. Targeted next-generation sequencing complemented metagenomic sequencing and conventional PCR for reproductive tract pathogen detection and HPV genotyping. Our findings demonstrate that shifts in vaginal microbial and metabolic profiles are linked to HPV infection clinical outcomes, which paves the way for novel microbiome-targeted diagnostics and therapies.