Methicillin-resistant <i>Staphylococcus aureus</i> in China: a multicenter longitudinal study and whole-genome sequencing

The aim of this study was to investigate the genomic epidemiology of MRSA in China to identify predominant linages and their associated genomic and phenotypic characteristic. In this study, we conducted whole-genome sequencing on 565 MRSA isolates from 7 provinces and municipalities of China between 2014 and 2020. MRSA isolates were subjected to MLST, <i>spa</i> typing, SCC<i>mec</i> typing, analysis of virulence determinants and antimicrobial susceptibility testing. Among 565 MRSA isolates tested, clonal complex (CC) 59 (31.2%), CC5 (23.4%) and CC8 (13.63%) were the major lineages, and the clonal structure was dominated by ST59-t437-IV (14.9%), ST239-t030-III (6.4%) and ST5-t2460-II (6.0%). Of note, CC8, the predominant lineage in 2014-2015, was replaced by CC59 after 2016. Interestingly, the extension and unstable structure of CC5 population was observed, with ST5-t311-II, ST764-t1084-II, ST5-t2460-II and ST764-t002-II existed complex competition. Further analysis revealed that virulence determinant profiles and antibiograms were closely associated with the clonal lineage. The CC59 MRSA were less resistant to most tested antimicrobials and carried fewer resistance determinants, while rifampicin resistance and mupirocin resistance was closely linked with CC8 and CC5, respectively. MRSA isolates conservatively carried multiple virulence genes involved in various functions. PVL encoding genes were markedly more common in ST338, CC30, CC398, ST8 and CC22, while <i>tsst</i>-1 was associated with ST5. In conclusion, the community-associated CC59-ST59-t437-IV lineage was found to be predominant in China, with diverse clonal isolates alternately circulating in various geographical locations. Our study highlights the need for MRSA surveillance in China in order to monitor changes in MRSA epidemiology.