Introduction Hormonal contraception (HC) has been associated with a reduced risk of bacterial vaginosis (BV). We conducted a prospective study to evaluate the relationship between vaginal microbiota and several HC methods.

Methods During 2-years of follow-up, 108 women provided 2,662 mid-vaginal samples. Participants reported three HC methods [oral contraceptive pill (OCP), vaginal ring, implanon]. Controls not taking HC were also followed. Visits were scheduled at baseline, 2 weeks, 4 weeks, 3 months, 6 months, 12 months, 18 months, and 24 months. Additionally, participants self-collected mid-vaginal swabs twice-weekly in the two weeks before each visit. Vaginal microbiota composition was characterised on all samples by 16S rRNA gene analysis of the V3-V4 hypervariable regions. We identified four community state types (CSTs) which were dominated by Lactobacillus species. CST-IV-B was characterised by a low relative abundance of Lactobacillus spp. and higher proportions of BV-associated bacteria (Gardnerella and Atopobium). A multinomial model for dependence of proportions was used to evaluate the association between CST and HC. Jensen-Shannon distances between all pairs of samples were analysed to assess stability of the microbiota longitudinally.

Results Women on OCPs had more stable bacterial communities than controls during the 2-year follow-up (p = 0.04). HC (overall) also tended toward greater stability (p = 0.10). The low-Lactobacillus CST-IV-B had an 83% lower probability among OCP users and a 55% lower probability among implanon users. CST-II (L. gasseri-dominated) was significantly higher in all HC types compared to controls. Additionally, OCP users were more likely to be CST-III-A (L. iners-dominated) and CST-V (L. jensenni-dominated), while CST-III-A was also high among ring users. CST-I (L. crispatus-dominated) was associated with implanon. All reported findings were statistically significant (p < 0.03).

Conclusion Women on HC experienced greater stability of the vaginal microbiota over time compared to controls. OCPs and the vaginal ring were protective against transition to a Lactobacillus-depleted state.

Disclosure of interest statement The study was funded by the US National Institute of Allergy and Infectious Diseases (NIAID) R01-AI089878. No pharmaceutical grants were received in the development of this study.