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High rates of bacterial vaginosis and Chlamydia in a low-income, high-population-density community in Cape Town. Young South African women, from resource-poor communities, face several sexual and reproductive health challenges. Here we describe the vaginal microbiota and sexually transmitted infection (STI) prevalence of 102; 16-22-year-old, HIV-negative South African women from a low-income, high-population-density community in Cape Town (CPT). Vaginal microbiota were profiled using 16S rRNA amplicon sequencing; bacterial vaginosis (BV) status was established using Nugent scoring; and STIs were determined by multiplex polymerase chain reaction. STIs were common, with 55% of women having at least one STI; 41% were infected with high-risk human papilloma virus (HPV) and a further 28% with low-risk HPV; 44% were infected with Chlamydia, 16% of whom had at least one additional STI. Similarly, BV rates were very high, with 55% of women classified as BV-positive (Nugent score -7); 7% as BV-intermediate (Nugent score 3-6) and 38% as BV-negative (Nugent 0-2). Group B Streptococcus (Streptococcus agalactiae), the leading cause of neonatal sepsis, was present in 25% of BV-positive women and 28% of BV-negative women, and was significantly more abundant among BV-negative women. Both Chlamydia infection and BV may adversely affect reproductive health and place these women at additional risk for HIV acquisition. The high abundance of Prevotella amnii, in particular, may increase HIV risk, given its inflammatory capacity. Laboratory-based testing for STIs (Chlamydia and Gonorrhoeae in particular) appears to be warranted in this community, together with further monitoring and/or treatment of BV. [ABSTRACT FROM AUTHOR]