Background Since June 2009 we have routinely tested MSM in the drop-in clinic for Mycoplasma genitalium (MG), Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infections using nucleid acid amplification tests (NAAT) in both first void urine (FVU) and an anal swab from the same patient. In addition, a throat sample was tested for NG. The prevalence and sites of infection of these pathogens was determined in a retrospective study.

Methods We included 2408 MSM who have been registered for 4314 new visits from June 2009 to December 2012, of whom 188 (7.8%) patients representing 589 visits were HIV-positive. Two third were asymptomatic and asked for a self-taken anal swab, in addition to a throat sample taken by a nurse. One third was examined by a physician, who performed the sampling. A FVU was collected.

Results 372/4265 (8.7%) were positive for N. gonorrhoeae using a targeted NAAT (porA gene), 428/4314 (9.9%) were positive for C. trachomatis using COBAS^® TaqMan^® CT Test, v2.0 (Roche), and 223/4222 (5.3%) were positive for M. genitalium using an in-house real-time PCR.

The prevalence of any positive test in HIV-negative and HIV-positive patients was 19% and 34%, respectively.

Out of all positive samples in HIV-positive, FVU identified only 16% (13/82) CT, 19% (13/67) MG and 19% (13/67) NG. In HIV-negative, FVU identified 36% (122/335) CT, 34% (52/153 MG and 32% (94/293) NG.

Conclusion Our results supports that the MSM population carry a high burden of extra-genital STIs and that testing the ano-rectum and oro-pharynx, especially in HIV-positive, will identify a significantly higher percentage of infected patients than testing FVU alone. In addition to N. gonorrhoeae and C. trachomatis, anal M. genitalium may be a risk factor for HIV transmission.