Genomic characterization of mobile genetic elements associated with antimicrobial resistance in Streptococcus pneumoniae from Australia

Abstract

The emergence and spread of antimicrobial resistance (AMR) in Streptococcus pneumoniae threatens current antibiotic treatment strategies. While β-lactams remain the first-line therapy for pneumococcal infections in Australia, resistance to macrolides, tetracyclines and other antibiotics, driven by resistance genes carried on mobile genetic elements (MGEs), is increasingly reported. In this study, we conducted a comprehensive analysis of 573 S. pneumoniae genomes from South Australia, Queensland and Victoria to investigate the distribution of MGEs and their association with acquired AMR genes. Resistance genes and MGEs were identified using AMRFinderPlus and MobileElementFinder. Serotypes, sequence types and global pneumococcal sequence clusters (GPSCs) were assigned using SeroBA, MLST and the GPS pipeline. Out of the 573 genomes, 547 passed quality checks. Tn916-like (Tn916, Tn6002, Tn2010, Tn6003 and ICESpnTw19F14) and Tn5253-like (Tn5253, ICESpn529IQ) integrative conjugative elements carried various combinations of ermB, mefA, msrD, tetM, catA and catA16 genes, supporting horizontal gene transfer as a key mechanism of resistance spread. Macrolide and tetracycline resistance genes co-occurred in 192/239 (80.7%) MGE-positive genomes. The most common MGE-positive serotypes were 33F/ST717/GPSC3 (15.6%, n=30), serotype 4/ST2759/GPSC162 (15.1%, n=29), serotype 15A/ST63/GPSC9 (7.3%, n=14), serotype 23A/ST338/GPSC5 (5.7%, n=11), serotype 15A/ST8625/GPSC9 (3.6%, n=7) and serotype 19A/ST3111/GPSC932 (3.6%, n=7). Our results reflect global trends of MGE-associated resistance in expanding non-vaccine serotypes (such as 15A and 23A) and multidrug-resistant clones. These findings underscore the evolutionary role of MGEs associated with AMR in shaping the pneumococcal resistome and highlight the continuous need for genomic surveillance to inform antibiotic stewardship and vaccine strategies in Australia.