Background Little is known on the natural history of extragenital Chlamydia trachomatis (Ct) and Neisseria gonorrhoeae (Ng). More insight in the natural history of extragenital Ct and Ng could influence standard operating procedures in screening facilities such as STD clinics. We evaluated proportions of natural clearance of Ct and Ng in genital and extragenital samples.

Methods We included self collected Ct and/or Ng positive genital (urine and cervicovaginal) and extragenital (anorectal and oropharyngeal) samples from STD clinic attendees [April 2011-December 2012]. Data on demographics and sexual behaviour were collected in an electronic patient file at initial testing. At follow-up for treatment, subjects were retested prior to treatment at the same anatomic site(s) as initial testing and provided an additional questionnaire on sexual behaviour since initial testing. Natural clearance rates of Ct and Ng were compared between anatomic sites. Data on the first 238 individuals (299 samples) are presented, enrollment is ongoing.

Results In total, 38% of the participants were male and the median age was 27 years. The median interval between initial and follow-up sample was 11 days. Natural clearance of Ct was 10.5% (22/210) for genital samples (36% urine, 64% vaginal) and 25.9% (7/27) for extragenital samples (57% anorectal, 43% oropharyngeal) (P = 0.49). For Ng this was 22.2% (2/9) for genital samples (0% urine, 100% vaginal) and 18.8% (3/16) for extragenital samples (33% anorectal, 67% oropharyngeal) (P = 0.84). Overall, natural clearance of Ct was 12.2% (29/237) and Ng was 20.0% (5/25) (P = 0.14). Age < 25 years (P < 0.01) and female sex (P = 0.03) were associated with overall Ct clearance. Median interval was not associated with Ct/Ng clearance (P = 0.13 and P = 0.11 respectively).

Discussion Natural clearance of Ct and Ng was substantial in both genital and extragenital samples. Further analysis on associated determinants as well as bacterial load determinations will provide more insight into these results.