Introduction Multiple studies identify a high prevalence of STIs among men who have sex with men (MSM) in sub-Saharan Africa, though few have measured incidence and associated factors. We measured the incidence and associated factors of urethral and rectal N. gonorrhoeae (NG) and C. trachomatis (CT) among a Kenyan cohort of MSM.

Methods Enrolled MSM underwent audio computer assisted self-interview for behaviour and socio-demographics, with medical examination every 6 months. Antibody testing detected HIV. NG and CT were diagnosed by polymerase chain reaction assay in urine and rectal swabs. We identified factors associated with incident urogenital infection using multivariable Cox regression and report adjusted hazard ratios (aHR) and 95% confidence intervals (CI).

Results By September 2016, 713 participants were enrolled, with 20% completing 12 month follow-up at time of analysis: median age 23% and 11% with HIV. At baseline, 15.2% (107/702) of men were infected with CT and/or NG, 8.4% (33/392) at 6 months, and 15.6% (10/64) at 12 months. The incidence of anorectal and/or urogenital infection was 6.0 per 100 person-years (P-Y), and 4.6 per 100 P-Ys for urogenital infection alone. Increased risk of urogenital infection was associated drug use in the past year (aHR=2.44; 95% CI: 1.17–5.08), versatile (compared to insertive) usual sexual positioning (aHR=2.40; 95% CI: 1.01–5.71) or water-based lubricant use compared to no lubricant use (aHR=5.72; 95% CI: 1.28–25.5). Protective factors (p<0.10 each) included increasing age (aHR=0.94), condom use at last sex (aHR=0.53), and increasing social support (aHR=0.73 per quartile increase). Child abuse scores, depressive symptom measures, HIV status, and alcohol use were not associated with incidence.

Conclusions NG and/or CT and incidence was high despite baseline testing and treatment, quarterly visits, and peer counselling and support for reducing HIV risk. Partner treatment and program exposure measures will be analysed as data accrual completes with follow-up continuing to September 2017.