Using Core-genome Multilocus Sequence Typing to Monitor the Changing Epidemiology of Methicillin-resistant Staphylococcus aureus in a Teaching Hospital.

Abstract

This study was performed to elucidate the changing epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in a Chinese teaching hospital. We performed whole-genome sequencing and phylogenetic analysis on MRSA isolates recovered at Sir Run Run Shaw Hospital (SRRSH) from 2013 to 2015. MRSA isolates underwent susceptibility testing, resistance determinant screening, virulence assays and clinical data analysis. A total of 292 MRSA infections were identified during the study period. Of these, most belonged to sequence type (ST) 5 (51.4%; 150 of 292) and ST59 (23.3%; 68 of 292). The proportion of ST5 MRSA decreased from 68.3% in 2013 to 32.1% in 2015, and the proportion of ST59 MRSA increased from 8.9% to 41.0%. Core-genome phylogenetic analysis revealed that ST59 MRSA isolates exhibited wider genotypic diversity than ST5 MRSA isolates in both healthcare-onset and community-onset groups. Minimum spanning trees showed that a cluster of ST5 MRSA was circulating at SRRSH, whereas the ST59 MRSA infections were mostly sporadic. ST59 MRSA caused 45.2% of the 93 skin and soft-tissue infection cases and displayed lower levofloxacin (11.8%) and ciprofloxacin (19.1%) resistance rates than the ST239 and ST5 MRSA isolates. ST59 healthcare-onset MRSA displayed enhanced virulence in the skin infection model and hemolysis assays. Notably, these isolates had virulence levels similar to those of classic community-associated MRSA strains. ST59 MRSA strains with high virulence potential have been replacing ST5 MRSA in predominance in SRRSH and causing nosocomial infections. Whole-genome sequencing is a powerful tool to monitor changes in the epidemiology of MRSA in hospitals.