Introduction Pharyngeal Chlamydia trachomatis (PCt) must persist to contribute to ongoing transmission. In a retrospective study, we examined MLST-types of PCt in patients who had a positive pharyngeal swab on two visits, and had not been treated for this infection at first visit.

Methods From 1/1/2008 to 14/7/2010, pharyngeal swabs from patients at risk for pharyngeal gonorrhoea were tested with the AC2 (Hologic-GenProbe) test. Since at that time PCt detection was not considered to represent an infection, PCt results were not reported and patients were not treated, unless they had a chlamydial infection at another anatomic site. We looked for patients who had a positive PCt test on two different occasions with an interval of at least 3 weeks. For inclusion in the study, patients were required to have no Chlamydia infections at other anatomic locations at first visit and therefore received no treatment. PCt typing was done by MLST on stored specimens.

Results Sixteen patients could be included and paired pharyngeal samples from four of those patients contained enough DNA for MLST analysis. The intervals between the two visits were 112, 168, 207 and 268 days, respectively. In all four patients MLST types of both pharyngeal samples were completely identical. Patients were two women and two men who had sex with men (MSM). At second visit one woman and one MSM reported commercial sex work and had 30 and 150 sexual partners in the last 6 months, respectively. The second woman reported sex with two known persons and the second MSM reported sex with 15 known persons. None reported sex with a steady partner.

Conclusion Our findings of identical MLST types are consistent with persistent PCt infection for a period of 3–9 months, although repetitive exposure to untreated partners with identical C. trachomatis strains can not be excluded.