Background Studies characterising the normal and disturbed vaginal microbiome in African women are scarce.

Methods Women were recruited in three African countries and followed up over seven visits. Vaginal specimens were examined using Nugent score defined by 0–3 (normal), a score 4–6 (intermediate) and a score of 7–10 (bacterial vaginosis (BV)) and analysed by quantitative PCR to detect and quantify lactobacilli, Gardnerella vaginalis (GV) and Atopobium vaginae (AV). The preliminary baseline data are presented.

Results Out of 376 women, 55.3% had a normal Nugent score, 7.7% an intermediate and 34.6% a BV score. A significant difference in prevalence of all species was seen between the three Nugent score groups (p = < 0.001 except L. gasseri p = 0.044). Almost all (99.5%) women with normal Nugent score harboured lactobacilli: L. iners and L. vaginalis were frequently detected; L. crispatus, L. jensenii, L. gasseri were less prevalent. The percentage of women harbouring lactobacilli was lower in the intermediate group and near absent in the BV group, except for L. iners. GV and AV were detected in a high proportion of the BV group, in more than half of the women in the intermediate group and were less prevalent, but still present in the normal group.

Conclusion This is the first study to our knowledge showing a higher presence of L. vaginalis compared to L. crispatus mostly so in the women with normal Nugent scores. L. iners remains highly present independent of the Nugent score compared to the other lactobacilli.