Additional file 1: Supplementary Table S1. Accession numbers, associated metadata, ST, BAPS sequence cluster, homologous recombination information, AMR and virulence genes and rep families of the 437 S. aureus genomes in this study. Supplementary Table S2. Functional classification of the unique genes (i.e., isolate-specific) detected in human and animal isolates according to eggnog. Supplementary Table S3. Genome-wide average nucleotide identity (ANI) values for every pair of S. aureus genomes. Supplementary Table S4. List of recombination events predicted by ClonalFrameML indicating the initial position and end position of each recombination event detected in the genomes as well as in the ancestor nodes. Supplementary Table S5. Recombination events inferred from the 437 genomes using fastGEAR. The results include information about the donor group, recipient group, start/end position of event, gene name, and a list of recipient genomes. Supplementary Table S6. Recombination events inferred from a subset of 228 genomes (114 human and 114 animals) using fastGEAR. The results include information about the donor group, recipient group, start/end position of event, gene name, and a list of recipient genomes.

Additional file 1: Supplementary Table S1. Accession numbers, associated metadata, ST, BAPS sequence cluster, homologous recombination information, AMR and virulence genes and rep families of the 437 S. aureus genomes in this study. Supplementary Table S2. Functional classification of the unique genes (i.e., isolate-specific) detected in human and animal isolates according to eggnog. Supplementary Table S3. Genome-wide average nucleotide identity (ANI) values for every pair of S. aureus genomes. Supplementary Table S4. List of recombination events predicted by ClonalFrameML indicating the initial position and end position of each recombination event detected in the genomes as well as in the ancestor nodes. Supplementary Table S5. Recombination events inferred from the 437 genomes using fastGEAR. The results include information about the donor group, recipient group, start/end position of event, gene name, and a list of recipient genomes. Supplementary Table S6. Recombination events inferred from a subset of 228 genomes (114 human and 114 animals) using fastGEAR. The results include information about the donor group, recipient group, start/end position of event, gene name, and a list of recipient genomes.

Supporting code for ‘The roles of antimicrobial resistance, phage diversity, isolation source, and selection in shaping the genomic architecture of Bacillus anthracis’ as published in Microbial Genomics.

Supporting code for ‘The roles of antimicrobial resistance, phage diversity, isolation source, and selection in shaping the genomic architecture of Bacillus anthracis’ as published in Microbial Genomics.

Bacillus anthracis, the causative agent of anthrax, is a considerable global health threat affecting wildlife, livestock, and the general public. In this study whole-genome sequence analysis of over 350 B. anthracis isolates was used to establish a new high-resolution global genotyping framework that is both biogeographically informative, and compatible with multiple genomic assays. The data presented in this study shed new light on the diverse global dissemination of this species and indicate that many lineages may be uniquely suited to the geographic regions in which they are found. In addition, we demonstrate that plasmid genomic structure for this species is largely consistent with chromosomal population structure, suggesting vertical inheritance in this bacterium has contributed to its evolutionary persistence. This classification methodology is the first based on population genomic structure for this species and has potential use for local and broader institutions seeking to understand both disease outbreak origins and recent introductions. In addition, we provide access to a newly developed genotyping script as well as the full whole genome sequence analyses output for this study, allowing future studies to rapidly employ and append their data in the context of this global collection. This framework may act as a powerful tool for public health agencies, wildlife disease laboratories, and researchers seeking to utilize and expand this classification scheme for further investigations into B. anthracis evolution.