Sexually transmitted infection prevalence and Neisseria gonorrhoeae antimicrobial resistance patterns in men who have sex with men with or without urethral discharge syndrome in Johannesburg, South Africa, 2024.

We conducted a cross-sectional study to estimate the prevalence of urogenital and extragenital sexually transmitted infections (STIs) among men who have sex with men (MSM) with and without urethral discharge syndrome, to assess infections missed by syndromic management, and to describe phenotypic antimicrobial susceptibility patterns of Neisseria gonorrhoeae. The study included 189 MSM attending the Engage Men's Health Clinic in Johannesburg, South Africa, in 2024. Urethral, rectal and oropharyngeal swabs were tested by multiplex PCR for Neisseria gonorrhoeae (NG), Chlamydia trachomatis (CT), Mycoplasma genitalium (MG) and Trichomonas vaginalis (TV). Genital ulcer swabs were tested for HSV-1/2, lymphogranuloma venereum (LGV), Haemophilus ducreyi (HD) and Treponema pallidum (TP). Serological diagnostic testing for HIV, hepatitis B virus (HBV) and syphilis was performed. NG isolates underwent culture and antimicrobial susceptibility testing. Among MSM with urethritis, NG was most prevalent (urethra: 80.3%, rectum: 41.7%), followed by CT (urethra: 14.8%, rectum: 11.7%). Pharyngeal NG was more common among MSM with urethritis than those without (18.0% vs 3.1%, p = 0.001). Among MSM without urethritis, rectal NG and CT prevalence were 13.5% and 9.5%; rectal LGV was detected in three cases. Among 22 participants with genital ulcers, an aetiology was identified in eight: HSV-2 (n = 3), TP (n = 4) and LGV (n = 1). All NG isolates were susceptible to ceftriaxone, cefixime, and azithromycin, and had low MICs of gentamicin. HIV, HBsAg and treponemal antibody seroprevalence were 31.4%, 3.2% and 50.8%. Active syphilis (RPR titres ≥1:32) was more frequent among MSM without urethral symptoms. Among MSM with urethritis, CT infection was less likely in those reporting recent insertive oro-anal sex and HIV pre-exposure prophylaxis (PrEP) use. Among MSM without urethritis, any discharge STI was associated with homosexual orientation, HIV positivity and lack of circumcision, NG with HIV positivity and being uncircumcised and CT with HIV positivity. Extragenital and asymptomatic STIs remain common among MSM in Johannesburg, stressing the need for routine multi-site molecular screening and inclusion of rapid serological syphilis testing in national STI guidelines for key populations.