Prevalence of Chlamydia trachomatis and Neisseria gonorrhoeae among Ugandan Adolescents and Adults Vulnerable to HIV

Background: Chlamydia and gonorrhea are common sexually transmitted infections (STIs) in populations with behavioral vulnerability to HIV. In Uganda, routine syndromic STI management underdiagnoses infections. Methods: Between October 2022 and September 2024, we enrolled participants in Kampala, Uganda, aged 14-55 years, without HIV, who reported a recent documented STI, injection drug use, transactional sex, condomless sex, or anal sex with males. Urine and anorectal/oropharyngeal swabs were tested for Chlamydia trachomatis and Neisseria gonorrhoeae (Xpert CT/NG, Cepheid). Multivariable robust Poisson regression with purposeful variable selection estimated adjusted prevalence ratios (aPRs) and 95% confidence intervals (CIs) for factors potentially associated with each STI. Results: Among 420 participants with a median age of 21 years (interquartile range 19-24), 241 (57.4%) were female, and 136 (32.4%) were males who have sex with men (MSM). Chlamydia was more prevalent than gonorrhea (21.9% vs. 13.1%, p <0.001). The anorectum was the most common site of infection with 75 chlamydia cases (17.9% [95%CI: 14.5%-21.8%]) and 51 gonorrhea cases (12.1% [9.4%-15.6%]), followed by the urogenital site with 45 chlamydia cases (10.7% [8.1%-14.0%]) and 23 gonorrhea cases (5.5% [3.7%-8.1%]). Urogenital-only screening would have missed 51.1% and 58.2% of chlamydia and gonorrhea cases, respectively, while urogenital+anorectal screening would have missed 1.1% and 0%. Male sex was independently associated with increased prevalence of chlamydia (aPR 2.06 [1.37-3.11], p =0.001) and gonorrhea (PR 2.81 [1.56-5.06], p =0.001). Chlamydia was also more common among participants aged 15-24 years compared to 25-40 (aPR 2.11 [1.02-4.35], p =0.043). Conclusions: Ugandan healthcare policies should consider anorectal chlamydia and gonorrhea testing, particularly among youth and MSM, to improve STI detection and reduce transmission.