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Female anorectal Chlamydia trachomatis (chlamydia) infections are common irrespective of recent anal sex. We explored the role of anorectal infections in chlamydia transmission and estimated the impact of interventions aimed at improved detection and treatment of anorectal infections.We developed a pair compartmental model of heterosexuals aged 15–29 years attending STI clinics, in which women can be susceptible to or infected with chlamydia urogenitally and/or anorectally and men urogenitally. Transmission probabilities per vaginal and anal sex act, together with an autoinoculation probability, were estimated by fitting to anatomic site-specific prevalence data (14% urogenital; 11% anorectal prevalence). We investigated the 10-year reduction in female chlamydia prevalence of interventions (universal anorectal testing of female STI clinic attendees or doxycycline use for urogenital chlamydia) relative to continued current care (anorectal testing on indication and doxycycline for anorectal and azithromycin for urogenital chlamydia).The transmission probability per anal sex act was 5.8% (IQR 3.0–8.3%), per vaginal sex act 2.0% (IQR 1.7–2.2%) and the daily autoinoculation probability was 0.7% (IQR 0.5–1.0%). More anorectal chlamydia infections were caused by autoinoculation than by recent anal sex. Universal anorectal testing reduced population prevalence modestly with 8.7% (IQR 7.6–9.7%), yet the reduction was double that of doxycycline use for urogenital infections (4.3% (IQR 3.5–5.3%)) relative to continued current care.Autoinoculation between anatomic sites in women might play a role in sustaining high chlamydia prevalence. A shift to more anorectal testing of female STI clinic attendees may be considered for its (albeit modest) impact on reducing prevalence.