To pool or not to pool samples for Sexually Transmitted Infections detection in Men who have Sex with Men? An evaluation of a new pooling method using the GeneXpert instrument in West-Africa

Background Men who have sex with Men (MSM) using Pre-exposure prophylaxis (PrEP) are at risk for Sexually Transmitted Infections (STIs). Therefore, PrEP services should include regular screening for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) at urethra, anorectum and pharynx. However, financial and logistic challenges arise in low resource settings. We assessed a new STI sample pooling method using the GeneXpert instrument among MSM initiating PrEP in West-Africa. Methods Urine, anorectal and pharyngeal samples were pooled per individual for analysis. Unpooled samples were analyzed in case of an invalid or positive result of the pool, to identify the infection’s biological location. The results of two different pooling strategies were compared against a gold standard. Results We found a prevalence of 14.5% for chlamydia and 11.5% for gonorrhea, with a predominance of infections being extra-genital (77.6%). The majority of infections were asymptomatic (88.2%). The pooling strategy with unpooling of invalid results only, had a sensitivity, specificity and agreement for CT of 95.4%, 98.7% and 0.93, respectively; and 92.3%, 99.2% and 0.93 with additional unpooling of positive results. For NG, these figures were 88.9%, 97.7% and 0.85 for testing of invalid results, and 88.9%, 96.7% and 0.81 with unpooling of positive results. Conclusion West-African MSM have a high prevalence of extra-genital and asymptomatic STIs. The GeneXpert method provides an opportunity to move from syndromic towards etiological STI diagnosis in low income countries, as the platform is available in all African countries for tuberculosis testing. Pooling will reduce costs of triple site testing.