Incident sexually transmitted infections associated with vaginal microbiome and sexual behaviors in a prospective cohort of adolescent girls and young women

Background Adolescent girls and young women (AGYW) disproportionately bear the burden of sexually transmitted infections (STI). We assessed risk factors for incident STIs among AGYW in western Kenya. Methods We enrolled girls from six secondary schools beginning in May 2018 and followed them prospectively for five years. Demographic and sexual behaviors were collected via self-administered survey. From self-collected vaginal swabs, STIs were assessed annually and microbiome every six months. Vaginal microbiome (16s rRNA sequencing) was analyzed according to community state type (CST). Multivariable interval-censored Cox regression models assessed risk factors for each incident outcome separately: Chlamydia trachomatis (CT), Trichomonas vaginalis (TV), and composite STI (CT, TV, and/or Neisseria gonorrhoeae ). Results Among 436 AGYW (median age at enrollment:16.9 years) cumulative incidence of composite STI was 43.1%. The rate of first incident CT, TV, and composite STI was 7.7, 3.1, and 10.6 per 100 person years, respectively. In multivariable modelling, participants with CST-IV (non-optimal) and CST-III ( Lactobacillus iners dominant) versus CST -I, -II, or -V (optimal) had a 4-fold higher risk of incident CT and nearly 3-fold higher risk of composite STI. CST-IV was associated with 2-fold increased risk of incident TV. Exposures associated with sexual activity were also associated with STI incidence: having a boyfriend/partner, sexual activity, hormonal contraceptive use, younger age at sexual debut, and pregnancy. Conclusions Incident STIs were common in a population-based cohort of AGYW in western Kenya and associated with non-optimal vaginal microbial composition and sexual practices. Interventions targeting non-optimal vaginal microbiome and factors underlying sexual risk behaviors could mitigate STI incidence and adverse reproductive consequences.