Background Although Sub-Saharan Africa is one of the most important areas in the world to study the complex relationships between the vaginal microbiome and reproductive health outcomes, data are limited.

Methods Endocervical samples of 174 female sex workers in Kigali, Rwanda, were analysed cross-sectionally using a phylogenetic microarray specifically designed for the cervicovaginal microbiome. Women with sexually transmitted infections (STI) were purposefully oversampled. Two hundred fifty one probes were used for co-regularised spectral clustering analysis and 123 probes (specific at species or genus level) to describe the vaginal microbiome clusters. Demographic, behavioural, and clinical correlates of the clusters were also determined.

Results The prevalence of HIV (36%) and other STIs (bacterial STI 46%, HPV 48%, and HSV-2 78%) in the analysis sample were high by design. Six distinct vaginal microbiome clusters were identified. Two clusters were dominated by Lactobacillus crispatus and L. iners, respectively, and were associated with a Nugent score of 0–3. Three clusters were dominated by Gardnerella vaginalis, Atopobium spp. and Prevotella spp in different compositions, and were associated with a Nugent score of 7–10. The sixth cluster, also dominated by anaerobic bacteria, was not associated with a particular Nugent score category. Women belonging to the L. crispatus cluster were significantly less likely to have bacterial (0% compared to 32–67%) and viral STIs (36% compared to 89–100%) than women in the other 5 clusters.

Conclusion In this sample of African sex workers with a high prevalence of HIV and STIs, six vaginal microbiome clusters were identified. Sex workers with a vaginal microbiome dominated by L. crispatus (but not L. iners) did not have bacterial STIs and were less likely to have viral STIs than women with other microbiome compositions. Longitudinal studies are needed to determine the temporal relationships between the vaginal microbiome and various STIs.