Background Syndromic diagnosis of sexually transmitted infections (STIs) has shown its limits among MSM using PrEP due to the many asymptomatic infections. However, testing three biological sites (urethra, pharynx and anorectum) is expensive. Our objective was to implement and to evaluate a pooling method using the locally available GeneXpert instrument to test for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG ) in the framework of the West-African CohMSM-PrEP study (Togo and Burkina Faso).

Methods Duplicate pharyngeal (P) and anorectal (A) e-swabs and first-void urine (U) samples were taken from every participant (n=192 in total). A specimen pool per participant (400 µL of each sample) was made and tested using the Xpert CT/NG kit. If positive, the individual samples were tested to confirm the site of infection. Duplicate individual samples were also tested for evaluation purposes using the Abbott CT/NG molecular technique and in-house qPCR.

Results A total of 32 CT infections (10U-20A-2P) and 34 NG infections (5U-19A-10P) were found. Twelve results obtained by testing of the pools were discordant from the individual testing using Abbott CT/NG. When unpooling the samples, one discordant result was solved. Three CT infections (1 in each samplingsite) and four NG infections (2A and 2P) were missed; one CT (P) and three NG (A) infection were found to be false positive (one in each sampling site). This converts into a respective sensitivity and specificity of 91.2% (95%CI: 76.3–98.1%) and 99.8% (95%CI: 99.0–100.0%) for CT and 88.6% (95%CI: 73.3–96.8%) and 99.4% (95%: 98.3–99.9%) for NG of the pooling strategy. Cohen’s Kappa agreement was 0.94 for CT and 0.89 for NG which is an almost perfect agreement.

Conclusion We showed that this pooling strategy performs well using the FDA approved point-of-care assay GeneXpert. This may be a very cost-effective strategy and also feasible, as the assay is widespread throughout the African continent for tuberculosis testing.

Disclosure No significant relationships.