Abstract
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.
Highlights
Bacillus anthracis is a Gram-positive, rod-shaped bacterium and worldwide clonal zoonotic pathogen, best known as the etiologic agent of anthrax
The data presented in this study demonstrate that the global B. anthracis population consists of 6 distinct primary clusters, and 18 clades that are geographically structured in most cases, with the exception of primary cluster 5 which exhibited both high genomic and geographic diversity
We demonstrate that the B. anthracis plasmids exhibit similar population structure to the core genome, suggesting that plasmid inheritance is vertical in the majority of cases
Summary
Bacillus anthracis is a Gram-positive, rod-shaped bacterium and worldwide clonal zoonotic pathogen, best known as the etiologic agent of anthrax. When examining the population genetic structure of this species in tandem with the sublineage classifications, results exhibited designations inconsistent with population genetic structure based on VNTR analysis in some instances, as well as a limited ability to discriminate isolates into lineages at the population level (Van Ert, Easterday, Huynh, et al, 2007) This framework has been incorporated into the canSNPer package for cladistic categorization and remains the current standard for B. anthracis classification across the globe (Lärkeryd et al, 2014; Van Ert, Easterday, Huynh, et al, 2007). We identified >14,500 chromosomal SNPs in the core genome, >580 SNPs in the pXO1 plasmid, and >320 SNPs in the pXO2 plasmid, all of which were used to construct comprehensive phylogenetic trees for each bacterial component We used this high-resolution WGS dataset to re-define the global systematics for B. anthracis using current methods for population genomic analysis, establishing a robust framework for primary cluster and clade designation based on hierarchical genomic structure. These results reveal the global biogeographic structure of B. anthracis lineages, but may act as a powerful tool for livestock and wildlife health surveillance, epidemiological studies, anti-terrorism investigations, and laboratory experiments involving B. anthracis and anthrax
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