Introduction Men who have sex with men (MSM) are considered an important key population in South Africa. Insight in the dynamics of sexually transmitted infections (STI) is of paramount importance to address the burden of infection. We aim to characterise incident STI among South African MSM.

Methods This prospective cohort study was conducted at two primary healthcare clinics that specifically target MSM in Johannesburg City Centre and Soweto, South Africa. We recruited MSM presenting with urethral discharge and provided standard syndromic management. Participants were requested to return for follow-up testing after six weeks, or earlier in case of symptoms. A urine specimen and rectal swab were collected for molecular microbiological investigations at both visits.

Results We recruited 78 MSM of whom 69% identified as gay; 43% was HIV-infected. Neisseria gonorrhoeae was the main cause of discharge in 46 men (59%), followed by Chlamydia trachomatis in 9 (12%), Mycoplasma genitalium in 1 (1.3%) and Trichomonas vaginalis in 3 (3.8%). Rectal swabs were positive for N. gonorrhoeae (28%), C. trachomatis (13%) and T. vaginalis (3.8%). Sixty-one (78%) men came for follow-up visit. Twenty-three men (38%) had a total of 34 STI diagnosed at follow-up, including 20 urethral and 14 rectal infections. The majority of these infections (68%) were considered newly acquired STI based on microorganism detected and anatomic site involved. This includes all infections with C. trachomatis (n=5), M. genitalium (n=3) and T. vaginalis (n=9). Seventeen MSM tested positive for N. gonorrhoeae at follow-up; six of which were new infections.

Conclusion We demonstrate a high rate of repeat STI in this unique cohort of South African MSM and show that most of these infections are newly acquired. This supports the effectiveness of syndromic management for most STI, but also highlights that strengthening of prevention efforts is highly warranted. The observation of repeat N. gonorrhoeae infections is concerning and molecular typing for further analysis of these strains is underway.