Background Pharyngeal Chlamydia trachomatis (PCt) must persist to contribute to ongoing transmission. We examined the prevalence, persistence and determinants of PCt among STI clinic clients.

Methods All men having sex with men (MSM) and women with a high risk profile were screened for anogenital and pharyngeal Ct with the APTIMA Combo 2 assay. After one week, clients with PCt were recalled for treatment, a follow-up pharyngeal swab and a questionnaire. Clients who used antibiotics since first visit were excluded from the analysis.

Results Between January 2011 and July 2012, we detected 148 PCt in MSM (13,111 visits; prevalence 1.1%) and 160 PCt in women (6,915 visits; 2.3%). In both groups, PCt was associated with being notified for STI, concurrent urogenital Ct and > 10 partners, but not with pharyngeal symptoms. Women reporting sex work had a lower risk, while women with pharyngeal gonorrhoea and MSM with anorectal Ct had a higher risk for PCt. 53% of MSM and 32% of women with PCt had no concurrent anogenitial Ct.

Of 43 (29%) MSM and 55 (34%) women, follow-up swabs and questionnaire data were available. The median time between both visits was 10 days. PCt persisted in 27 (63%) MSM and in 35 (64%) women. In both groups 50% had unprotected active oral sex between first and second visit, but this did not affect persistence.

Among MSM no determinants for persistence were detected; among women being notified for STI, younger age and urogenital Ct were significantly associated with persistence in univariate analysis.

Among clients (n = 16) whose second visit was more than 3 weeks after the first visit, 11 (69%) had PCt at second visit.

Discussion The prevalence of PCt is low among STI clinic clients, but persistence is common. Therefore, the pharynx is a potential reservoir for ongoing Ct transmission.