Supplementary data for: Genomic characterization of methicillin-resistant Staphylococcus aureus clones during a decade of declining prevalence at a Mexican tertiary hospital

Supplementary data files accompanying the manuscript "Genomic characterization of methicillin-resistant Staphylococcus aureus clones during a decade of declining prevalence at a Mexican tertiary hospital." This dataset contains whole-genome sequencing analysis results for 26 S. aureus clinical isolates (13 MRSA, 13 MSSA) collected at the Antiguo Hospital Civil de Guadalajara, Mexico (2024–2025). Files included: - Supplementary_Data_S1_virulence_matrix.tsv — Full per-gene virulence factor matrix (26 isolates × 94 genes). - Supplementary_Data_S2_snp_distance_matrix.tsv — Complete 26×26 pairwise core-genome SNP distance matrix. - Supplementary_Data_S3_core_genome_alignment.fasta — Core-genome alignment after recombination filtering with Gubbins. - Supplementary_Data_S4A_26taxon_phylogeny.nwk — Newick tree for the 26-taxon core-genome phylogeny (IQ-TREE, TVM+F+ASC+R3, 1000 UFBoot). - Supplementary_Data_S4B_40taxon_contextual_phylogeny.nwk — Newick tree for the 40-taxon contextual phylogeny including international reference strains. Reference genome: S. aureus USA300 FPR3757 (GCF_000013465.1). All patient data are anonymized (SA001–SA027).