Genomic Epidemiology of Methicillin-Resistant Staphylococcus aureus (MRSA) in Healthcare Facilities

Abstract

Persistent endemicity versus recent transmission is often difficult to distinguish using standard epidemiology, a challenge for antimicrobial-resistant bacteria (AMR), such as methicillin-resistant Staphylococcus aureus (MRSA), in healthcare settings. This study demonstrated the genomic diversity, antimicrobial resistance gene carriage and transmission patterns of MRSA in tertiary health care facilities. A 2-year, multicentre (5 hospitals) observational study using a genomic epidemiology approach was conducted. MRSA isolates were obtained from patients with infection or colonisation, health care workers, and environmental surfaces. Species identification and susceptibility testing were carried out in a conventional microbiological manner. Whole-genome sequencing was conducted using Illumina short-read platforms. FastQC and Trimmomatic were used for quality control; SPAdes for assembly; Prokka for annotation; multilocus sequence typing for typing; and ResFinder and CARD were used to analyse for resistance and virulence determinants, respectively. To perform maximum-likelihood phylogenetic inference and cluster reconstruction of transmission, core-genome single-nucleotide polymorphisms (SNPs) were used. Multivariable logistic regression was used to assess the epidemiology and cluster membership. Of the 312 MRSA isolates, 238 (76.3%) were from patient samples, 42 (13.5%) from healthcare worker samples, and 32 (10.3%) were from environmental samples. WGS identified eight sequence types, with ST22/CC22 (35.6%), ST5/CC5 (24.4%), ST8/CC8 (14.7%), and ST239/CC8 (10.3%) dominating. MecA was found in all isolates, 71.5% of which also possessed either ermC or ermA, while 46.8% of which also possessed aac(6’)-aph(2”). Forty-seven transmission clusters were identified with 169 isolates, of which 14 comprised several different types of source-to-isolate linkage ( пациент– окружающая среда и пациент– здоровье-серия работника). ICU admission, exposure in the ward in the preceding 14 days, use of medical or physical devices, prior anti-MRSA treatment, and MRSA recovery in the environment independently correlated with membership in a cluster. Integrated genomic and epidemiological surveillance of MRSA populations determined population structure, revealed cryptic transmission networks, and identified actionable reservoirs not captured by routinely collected infection control data. Continuous WGS-based surveillance programmes should be built into HAI prevention and management programmes and antimicrobial stewardship programmes.