Molecular characterisation and macrolide resistance-associated mutations in Chlamydia trachomatis among symptomatic adults in East London, South Africa

Background Chlamydia trachomatis is an important sexually transmitted infection worldwide. This study aimed to characterise C. trachomatis strain diversity using ompA genotyping and high-resolution multilocus sequence typing (hr-MLST) and to investigate macrolide resistance-associated mutations in East London, South Africa. Methods In this retrospective analysis, stored C. trachomatis-positive urine and vaginal swab samples (n=136) obtained from symptomatic men and women visiting five public clinics were analysed. Genotyping of the ompA gene was performed using Sanger sequencing and alignment against a curated reference database. The hr-MLST profiling was conducted across six loci (ompA, hctB, CT058, CT144, CT172 and CT682) with sequences assembled in the Staden Package, edited in BioEdit, aligned with ClustalW in MEGA and compared against the pubMLST database. Minimum spanning trees were constructed in PHYLOViZ to visualise sequence type (ST) relationships. PCR and bidirectional Sanger sequencing were used to identify 23S rRNA macrolide resistance-associated mutations (A2058C, C2452A and T2611C). Results The ompA genotyping was successful in 83 samples and identified six genovars, with D (26.5%), G (18%) and E (16.8%) predominating. Complete hr-MLST profiles were obtained for 60 samples, revealing 49 distinct STs, including 38 novel STs. Most STs occurred as singletons with few larger clusters. Macrolide resistance-associated mutations were detected in two samples (2/72; 2.7%) (A2058C and T2611C, E. coli numbering). One sample was assigned to genovar G, while the second yielded insufficient amplification for complete genotyping. Conclusions This study demonstrates substantial C. trachomatis genetic diversity in our setting, with different STs and uncommon presence of macrolide resistance-associated mutations across multiple genovars. These findings support the need for continued molecular surveillance to monitor strain diversity and emerging antimicrobial resistance, which is critical for early detection of antimicrobial-resistant strains, guiding treatment recommendations and informing targeted STI control strategies in high-burden settings.