Abbai, Nathlee Samantha.Ojo, Abidemi.Mofolorunsho, Kehinde Charles.2026-04-232026-04-2320242024https://hdl.handle.net/10413/24361Doctoral Degree. University of KwaZulu-Natal, Durban.Introduction: Gonorrhoea and chlamydia are amongst the most common sexually transmitted infections (STIs) worldwide, constituting a major public health problem. The incidence and prevalence of these infections are widespread, particularly in resource-poor countries due to the lack of access to health care facilities and ineffective diagnostic methods. In the African region, gonorrhoea and chlamydia have been reported to account for 11.4 and 12 million new cases per year, respectively. Gonorrhoea which is caused by the bacterium, Neisseria gonorrhoeae, and chlamydia, caused by the bacterium Chlamydia trachomatis have been found to be associated with serious health complications including infertility, pelvic inflammatory disease (PID), and epididymitis. Infections caused by these pathogens significantly increases the risk of Human Immunodeficiency Virus (HIV) transmission, particularly in men who have sex with men (MSM). Most MSM are asymptomatic, engaging in highrisk sexual behaviours, and have become an understudied group at greater risk for STI infections globally. C. trachomatis serovars have been linked to specific diseases, with serovars D-K detected in urogenital infections. In MSM, serovars reported were predominantly G, D and J. Microbiome variation has been found to be substantially affected by sexual practice. The bacterial composition of the male urinary microbiome is reported to influence the risk for the development of sexually transmitted infections. However, little is known about the urinary microbiome of MSM. The aim of this study was to determine the prevalence and risk factors associated with N. gonorrhoeae and C. trachomatis infections; characterize the distribution of C. trachomatis genotypes, and assess the bacterial composition of the urinary microbiome in a population of South African MSM. Methods: This study which was in two parts, was conducted over a 3-year period. The first part involved a systematic review and meta-analysis on the prevalence of N. gonorrhoeae and C. trachomatis among MSM in sub-Saharan Africa while the second part involved a cross-sectional laboratory based study. This cross-sectional laboratory based study included sexually active MSM, 18 years and older, willing to provide written informed consent and a urine sample to test for N. gonorrhoeae and C. trachomatis infections. A total of 200 MSM from the King Edward VIII hospital and the Aurum Institute both in Durban, South Africa were enrolled into the study. Urine samples were provided by each participant, and 10ml of each urine sample was centrifuged and the recovered pellets subjected to further molecular analyses. With a commercially available kit, deoxyribonucleic acid (DNA) was extracted from the sample pellets following the manufacturer’s protocol for the isolation of genomic DNA. N. gonorrhoeae and C. trachomatis were detected using the Applied Biosystems™ TaqMan® Assays. Amplification was performed on the QuantStudio 5 Real-time polymerase chain reaction (PCR) detection system. In addition, molecular genotyping of C. trachomatis positive samples was performed by an omp1 gene semi-nested PCR followed by restriction fragment length polymorphism (RFLP) analysis. The amplified product was digested with AluI, DdeI and HinfI restriction enzymes. Banding patterns obtained after digestion were used to determine the genotypes. The urinary microbiomes of study participants were characterized using 16S rRNA (V3 and V4) gene sequencing on the Illumina MiSeq platform. Participants’ demographics, sexual history, associated risk factors for each of the STIs as well as the barriers and facilitators to care were documented. All analyses were conducted using STATA 17.1 as well as the RStudio version 3.6.3 software. Results: The overall result of the meta-analysis gave a pooled prevalence of 27% (95% CI, 19–39%), with an I2 of 98% which indicates high heterogeneity amongst the studies. Subgroup analysis by country indicated that South Africa (n = 6) has a prevalence of 38%. Findings from our study showed that the prevalence of N. gonorrhoeae and C. trachomatis were 3.0% and 6.0%, respectively. Younger age was significantly associated with testing positive for C. trachomatis (p=0.037). Other factors significantly associated with testing positive for C. trachomatis included, education level, partner having other partners, sex practices, condom use and circumcision status (p<0.05). Being between the ages of 30-39 years old reduced the risk of acquiring C. trachomatis infection (OR: 0.10, 95% CI: 0.0120-0.7564, p=0.026). In addition, being circumcised reduced the risk of contracting C. trachomatis (adjusted OR: 0.01, 95% CI: 0.0005-0.3516, p=0.01). However, having between 2-4 sex partners increased the risk of testing positive for C. trachomatis (adjusted OR: 107.45, 95% CI: 1.3467- 8573.3130, p=0.036). Cohabiting with one’s sex partner, engaging in group sex, and drug use were significantly associated (p<0.05) with testing positive for N. gonorrhoeae infection. Fear and stigma were the main barriers to accessing health care in the studied population. The genotyping assays showed that genotype E was the most prevalent genotype present in 60% of the men infected with C. trachomatis. Other genotypes detected were Genotype I (30%) and Genotype J (10%). According to the bacterial taxonomic analysis, Prevotella and Lactobacillus were detected in urine samples of MSM. Alpha diversity metrics showed a slight increase in microbial diversity in positive samples. This was however not significant (ANOVA, P > 0.05). Principal coordinates analysis (PCoA) showed that the microbiome of C. trachomatis infected MSM was not clearly separated from those uninfected. Using normalized unweighted UniFrac dissimilarities, distinct bacterial communities were not detected between positive and negative samples (PERMANOVA F1,22= 1.0284, R2=0.047%, P=0.385). Conclusion: This study showed that C. trachomatis was prevalent in the study population and this finding was confirmed by previous studies conducted among MSM in South Africa. A proportion of the population who tested positive for both STIs were asymptomatic. In addition, finding from our review suggests that the burden of N. gonorrhoeae and C. trachomatis among MSM in South Africa and the rest of sub-Saharan Africa is higher when compared with other regions. These highlights the need for routine screening of these infections among MSM in order to facilitate proper management since some MSM engage in risky sexual behaviour. Genotyping, using the PCR-RFLP technique revealed the presence of three genotypes circulating in the study population. An important finding was the detection of genotype I. Since this genotype is common among women and heterosexual men, further research is needed to provide clarity as to why this genotype was present among MSM. The microbial composition of urine samples from our study participants showed diverse bacterial communities including Gardnerella and Sneathia which are associated with bacterial vaginosis in women. Therefore, more studies on the role of the female urinary microbiota in relation to MSM urinary health, needs to be conducted. This study adds to the growing body of literature on genitourinaryinfections in South African MSM and provides data that serves as a baseline for future research.enUrinary microbiota.Genotypes.Thesis