Longitudinal Dynamics of Vaginal Microbiome Reconstitution After Antibiotic Therapy and Its Influence on STI Susceptibility in Reproductive-Age Women in Oyo State

Antibiotic-induced perturbation of the vaginal microbiome disrupts the Lactobacillus-dominant community state that protects against sexually transmitted infections, but the temporal dynamics of microbiome reconstitution and its implications for STI susceptibility windows in Nigerian women remain uncharacterized. This longitudinal cohort study recruited 120 reproductive-age women in Ibadan, Oyo State, in the South West geopolitical zone of Nigeria, who received systemic antibiotic therapy (amoxicillin-clavulanate, metronidazole, or doxycycline) for non-gynecological indications. Vaginal swabs were collected at baseline, 48 hours, one week, two weeks, and four weeks post-therapy. 16S rRNA V3-V4 amplicon sequencing was performed at each time point. STI incidence including Trichomonas vaginalis, Chlamydia trachomatis, and Neisseria gonorrhoeae was assessed by NAAT at baseline and four weeks. Community state type transitions were modeled using Markov chain analysis. Forty-three percent of women experienced community state type transitions from Lactobacillus-dominant to diverse anaerobe-enriched states within 48 hours post-therapy. Full Lactobacillus reconstitution occurred in only 61 percent of women by four weeks. Women with non-restored Lactobacillus dominance at two weeks had a 3.8-fold higher STI incidence at four weeks. Metronidazole produced the most sustained disruption. These findings demonstrate time-dependent post-antibiotic STI vulnerability windows and advocate for targeted probiotic interventions, partner STI management, and microbiome-aware prescribing during antibiotic therapy in reproductive-age women. Keywords: vaginal microbiome, antibiotic perturbation, STI susceptibility, Lactobacillus reconstitution, Oyo State.