Unravelling the Dynamics of Chlamydia trachomatis and Neisseria gonorrhoeae Co-infections in Men who have Sex with Men: Insights from the Swiss PrEPared Program

Introduction: Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) are more commonly found in men who have sex with men (MSM) than in heterosexual men and women. Epidemiological data in recent years show that CT/NG co-infections occur more frequently than would be expected by chance, suggesting potential interaction between these pathogens that increases susceptibility, transmission, or both. Our study sought to better understand anorectal bacterial burdens and bacterial viability in single and CT/NG co-infections in MSM. Methods: MSM on HIV pre-exposure prophylaxis (PrEP) from the Swiss PrEPared program who were diagnosed with either NG or CT using a pooled swab (rectal, pharyngeal, and urethral samples in one tube) provided us with anorectal swab samples. We performed quantitative polymerase chain reaction (qPCR) for estimating the bacterial burden of both CT and NG, selective agar plate culture for NG, pathogen cell culture isolation combined with viability PCR (V-PCR) for CT, CT ompA genotyping, NG typing via MALDI-TOF analysis, and full-length 16S metabarcoding for microbiome taxonomical characterization. Results: At the time of submission, from 236 swabs 69 (29.2%) had rectal NG and 79 (33.5%) had rectal CT, with 16 (6.8%) having both pathogens. 46.8% of the CT-positive samples were isolated in cell culture, results that correlated with the CT V-PCR analysis (73.2% of PCR-viable samples were culture positive). Of NG-positive, 94.2% samples were isolated in plate culture, but only 62% were MALDI-TOF confirmed. We compared qPCR bacterial loads of single vs coinfection (NG Log10 loads mean = 4.58 vs CT/NG mean = 4.33; CT Log10 loads mean = 3.73, vs. CT/NG mean = 3.57). Discussion: In contrast to previous literature, our results suggest no statistically significant change in the bacterial burden as defined by qPCR copies/uL between CT/NG co-infections and single infections (p-values of 0.39 for NG load and 0.55 for CT loads). Strain diversity of CT based on ompA genotyping fell into the expected genital distribution, with genotypes G and J being the most abundant (23.5% each) followed by serovars E (17.2%), D/Da (14.1%) and others (>10% each). Conclusion: These cutting-edge techniques enable us to elucidate not only the prevalence and abundance of these pathogens but also the genetic diversity and pathogen viability in co-infections. Our goal is to provide the most complete and clinically relevant image possible of MSM risk for STI to ultimately contribute to development of targeted prevention strategies. While both sampling and analysis are ongoing at the time of writing, we decided to include non-PrEP user for further sampling, to rule out the influence of PrEP-use on the results. This study represents a crucial step toward enhancing our ability to address and manage STIs in high-risk populations, ultimately contributing to the advancement of global infectious disease control efforts.