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

Abstract

This deposit contains the data, results, and scripts supporting the revised manuscript entitled “Phylogenomic Analysis Reveals Lineage‑Specific Antimicrobial Resistance–Virulence Factor Trade‑offs in Staphylococcus aureus”. The analysis is based on 1,255 high‑quality S. aureus genomes (CheckM2 completeness >95%, contamination <5%). AMR genes were identified with ABRicate (ResFinder, 80% identity, 60% coverage) and VF genes with VFDB (60% identity, 60% coverage). A core‑genome SNP tree was constructed using Snippy and FastTree. Eight hierarchical clusters were defined as lineage proxies. Phylogenetic signal (Pagel’s λ, Blomberg’s K) and phylogenetic generalized least squares (PGLS) with Pagel’s λ correlation were used to test AMR–VF associations, including interactions with cluster and isolation source. The archive (S_aureus_AMR_VF_tradeoff_complete.tar.gz) contains the following folders and files: data/ high_quality_genomes.txt – list of 1,255 genome accessions quality_report.tsv – CheckM2 completeness/contamination report amr_matrix_1255.csv – presence/absence matrix for 78 AMR genes vf_matrix_1255.csv – presence/absence matrix for 100 VF genes amr_vf_burden_final.csv – AMR and VF burdens per genome isolation_sources_clean.csv – categorised isolation source (clinical/non‑clinical/other/unknown) hclust_clusters_8.csv – hierarchical cluster assignments (8 clusters) core.tree – core‑genome SNP tree (Newick format) core_snps_sub100.aln – subsampled core SNP alignment (13,033 sites) results/ pgls_output.txt – global PGLS and AMR×source interaction results pgls_cluster_int_output.txt – AMR×cluster interaction results cohen_f2_correct.txt – corrected Cohen’s f² values (global, clinical, non‑clinical) log_transform_sensitivity.txt – sensitivity analysis using log‑transformed VF burden Supplementary_Table_S1.csv – prevalence of all AMR/VF genes by isolation source Supplementary_Table_S2.csv – prevalence of all AMR/VF genes by cluster scripts/ README_commands.txt – summary of key commands used (CheckM2, ABRicate, Snippy, FastTree, hierarchical clustering, PGLS, log‑transformation) All figures and the full manuscript text are not included here; they are part of the published article. This deposit provides all raw data, derived tables, and command summaries necessary to reproduce the analyses. Version note: This is the revised version of the dataset corresponding to the updated manuscript. The previous version is also available via Zenodo but should not be used for the current revision.