Chlamydia trachomatis and Neisseria gonorrhoeae are the two most common curable bacterial sexually transmitted infections worldwide, yet most Nigerian health facilities still practice syndromic management because nucleic acid testing is rarely available outside research settings. Facility-based estimates using molecular diagnostics are correspondingly scarce, and the proportion of infection that would be missed by syndromic management are not well described in this population.

Methods. We conducted a cross-sectional study at a tertiary hospital in southern Nigeria between April 2020 and April 2022. consenting adults who had not taken antibiotics recently were enrolled; women who were menstruating were excluded. Participants completed an interviewer-administered questionnaire covering demographic characteristics, sexual behavior and genitourinary symptoms. Genital specimens were tested with the Xpert CT/NG assay. Prevalence was estimated with Jeffreys 95% confidence intervals, and correlates of infection were examined using Pearson chi-square tests followed by multivariable logistic regression.

Results. Of 472 participants (243 women, 229 men; mean age 29.8 years, SD 8.2), 212 had C. trachomatis, N. gonorrhoeae or both (44.9%, 95% CI 40.5–49.4). N. gonorrhoeae was detected in 211 participants (44.7%, 95% CI 40.3–49.2) and C. trachomatis in 165 (35.0%, 95% CI 30.8–39.3); 164 participants (34.7%) carried both organisms, and all but one chlamydial infection occurred as a co-infection. Prevalence did not differ by sex (47.2% in men, 42.8% in women; p = 0.39). Ninety-two of the 212 infections (43.4%) occurred in participants who reported no genitourinary symptoms. In the adjusted model, infection was associated with self-reported HIV-positive status (aOR 7.05, 95% CI 4.02–12.37), sexual debut between 15 and 20 years (aOR 3.78, 95% CI 1.73–8.25) and before 15 years (aOR 3.10, 95% CI 1.38–6.99), non-use of a condom at the most recent sexual encounter (aOR 2.98, 95% CI 1.49–5.97) and symptomatic presentation (aOR 2.03, 95% CI 1.25–3.30). Sex, age group, marital status, education and employment were not independently associated with infection.

Conclusions. Nearly half of the adults tested carried at least one of the two organisms, and more than two in five infections would have been invisible to syndromic management. The concentration of chlamydial infection within co-infected participants and the strong association with early sexual debut argue for molecular screening of attendees who report HIV-positive status, early debut or condomless sex, rather than testing on the basis of symptoms alone.

Keywords: Chlamydia trachomatis; Neisseria gonorrhoeae; Xpert CT/NG; asymptomatic infection; syndromic management; Nigeria.