Phylogenomic Analysis Reveals Lineage-Specific AMR–Virulence Trade-offs in Staphylococcus aureus

Dataset supporting "Phylogenomic Analysis Reveals Lineage-Specific AMR–Virulence Trade-offs in Staphylococcus aureus". Contains genomic data, phylogenetic trees, AMR/VF gene counts, and supplementary materials for 232 S. aureus genomes. The dataset includes:- master_amr_vf_table.csv: AMR and VF gene counts- saureus_232_final.nwk: Phylogenetic tree file- isolates_database.tsv: Complete isolate database (162,472 isolates)- colab_session/: Analysis files and intermediate data- supplementary/: All supplementary tables (S1-S6) and figures (S1) Key findings reveal a global negative trade-off between AMR and VF genes (slope = -0.038, p = 7.5e-5), with CC8 driving the trend (r = -0.507) while CC30 shows an opposite pattern (r = +0.622). All data and code are provided for full reproducibility.