Introduction Non-urethral N. gonorrhoeae infections have been associated with antimicrobial resistance as well as increased HIV transmission and acquisition, however, incidence data from low and middle-income countries are lacking.

Methods We collected anal and pharyngeal specimens from MSM and transgender women seeking sexually transmitted disease clinical services quarterly for 2 years. Incident infection was defined as having a positive nucleic acid test among those with no prior infection or prior treatment. We used generalised estimating equations to calculate adjusted incident rate ratios (aIRR). We grouped infections by anatomic site. All models included any condomless sex and number of male sex partners in prior 3 months.

Results Of 401 participants, 22% identified as transgender and 31% had HIV infection at baseline. Incidence of anal infection was 30 and 40 cases per 100 person-years with N. gonorrhoeae and C. trachomatis, respectively, while incidence of pharyngeal infection was 22 and 12 cases per 100 person-years with N. gonorrhoeae and C. trachomatis, respectively. In the pharyngeal infection model with either organism, transgender identification was positively associated (aIRR=2.1; 95% CI 1.4–3.0) compared with MSM, whereas each decade increase in age was negatively associated (aIRR=0.7; 95% CI 0.6–0.9). In the anal infection model with either organism, HIV infection was positively associated (aIRR=1.6; 95% CI 1.2–2.1), whereas each decade increase in age was negatively associated (aIRR=0.7; 95% CI 0.6–0.9). Anal infection incidence was increased in those reporting receptive (aIRR=2.7; 95% CI 1.5–4.9) and both receptive/insertive (aIRR=2.6; 95% CI 1.5–4.6) sex versus reporting exclusively insertive sex.

Conclusion Incident non-urethral N. gonorrhoeae and C. trachomatis infections were common among MSM and transgender women in Lima, Peru, adding to the paucity of data from Latin America, especially among transgender women. Our findings support World Health Organisation recommendations for anal screening and argue for the addition of pharyngeal screening.