Prevalence of Chlamydia trachomatis and Neisseria gonorrhoeae infections and associated risk factors among pregnant women and key populations in Kenya: A multi-centre cross-sectional study

Sexually-transmitted pathogens Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) cause curable but often asymptomatic bacterial infections. Missed diagnoses and treatment, leading to chronic infections, can cause clinical complications and increase transmission. Accurate prevalence estimates are essential for the effective public health control of these sexually transmitted infections, especially in Africa, where data are scarce. This cross-sectional study was undertaken across five sites in Nairobi, Mombasa, and Homabay in Kenya. Between February and July 2022, vaginal, urethral, or rectal swab samples were collected in pregnant women and populations at higher risk of sexually transmitted infections (key populations) aged ≥15 years and analysed using an NG/CT nucleic acid amplification test. The primary objective was to determine the prevalence of NG and CT in pregnant women and key populations in Kenya to provide input in developing national prevalence estimates. Multivariate regression analysis examined infection status based on participants characteristics. NG prevalence was significantly lower among pregnant women [1.0% (95%CI: 0.5-1.9)] compared to key populations [9.4% (95%CI: 6.9-12.5)], while CT prevalence was similar between the two populations: 9.6% (95%CI: 7.8-11.7) in pregnant women and 11.2% (95%CI: 8.4-14.5) in key populations. NG and CT prevalence were highest among younger individuals, reaching 5.7% and 15.1% in pregnant women <20 years and 25.0% and 50.0% in key populations <20 years, respectively. Prevalence of both pathogens decreased with increasing age. These findings support the development of national prevalence estimates, which will support better management of NG and CT infections in Kenya by directing preventive and control measures.