Whole genome sequencing of clinical Staphylococcus aureus isolates
Genomic DNA was extracted from 30 S. aureus isolates using the ESTstandPure Mag DNA Kit (Accurate Biology, Changsha, China). Whole-genome sequencing was performed on the Illumina HiSeq X Ten platform with 2 x 150 bp paired-end reads. Raw reads were quality filtered and trimmed using fastp v0.23.2 [27]. De novo assembly was performed on two representative isolates using the Oxford Nanopore platform, and hybrid genome assemblies were generated by combining short Illumina and long Nanopore reads with Unicycler v0.5.0 [28]. Genomes were annotated using Prokka [30]. Antimicrobial resistance genes were identified through the Comprehensive Antibiotic Resistance Database (CARD) [31], while virulence-associated genes were screened against BacWGSTdb [32]. Mobile genetic elements (MGEs) were predicted using mobileOG-db (beatrix-1.6), and plasmid maps were visualized with Proksee (33, 34). Spa typing was determined using the Ridom Spa Server [25], and Agr typing was performed with AgrVATE v1.0.2 [35].