A classification framework for Bacillus anthracis defined by global genomic structure

Abstract

Evolutionary Applications. 2020;13:935-944. | 935 wileyonlinelibrary.com/journal/eva | INTRODUC TI ONBacillus anthracis is a Gram-positive, rod-shaped bacterium and worldwide clonal zoonotic pathogen, best known as the etiologic agent of anthrax. Bacterial infections of B. anthracis are primarily relegated to wild and domestic herbivores, with occasional spillover to humans (Carlson et al., 2018(Carlson et al., , 2019De Vos, van Heerden, & Turner, 2018). B. anthracis has also garnered global attention as a bioterrorism weapon due to the highly resilient qualities of its endospores and their ability to be aerosolized for malicious purposes AbstractBacillus 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 highresolution 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. K E Y W O R D S Bacillus anthracis, bacterial pathogen, genotyping, global diversity, phylogenomics, population genomics, whole-genome sequencing S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section. How to cite this article: Bruce SA, Schiraldi NJ, Kamath PL, Easterday WR, Turner WC. A classification framework for Bacillus anthracis defined by global genomic structure. Evol Appl. 2020;13:935-944. https ://doi.

The roles of antimicrobial resistance, phage diversity, isolation source and selection in shaping the genomic architecture of Bacillus anthracis

“…The population genomic dataset used in these analyses was previously developed and published by Bruce et al . [27] consisting of 356 B. anthracis whole genomes collected from the NCBI sequence read archive ([27], File S1, available in the online version of this article).…”

“…However, the link between genomic architecture, and the scarcity of these genotypes remains largely unexamined. In addition, some of the individual clades identified are geographically specific, whereas others seem to be widely distributed, raising numerous questions about what factors are driving evolutionary success in this species [26–28]. Understanding the relationships among spatial variation, population stability, and genomic architectural variation is particularly important for B.…”

The roles of environmental variation and parasite survival in virulence–transmission relationships

“…There are, however, intriguing phenotypic differences among strains that could alter their ecological and evolutionary trajectories. The major clades differ in their fitness [182] and B. anthracis exhibits local adaptation, or differentiation, of strains in different parts of its range [184][185][186]. One of the variable-number tandem repeats (VNTRs) used to genotype B. anthracis (Ceb-Bams13), located in the bclA gene, has been linked to spore phenotype, where repeat length directly correlates with filament length on the exosporium surface [187,188].…”

Population genomics ofBacillus anthracisfrom an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity

“…The genomic diversity of B. anthracis has been well-described at a global scale. Isolates can be broadly divided into three major clades (A, B, C), of which A clade is the most widespread and globally dominant (5)(6)(7). Isolates from most B. anthracis lineages have been found across geographically widespread areas, often spanning multiple continents (7).…”

“…Isolates can be broadly divided into three major clades (A, B, C), of which A clade is the most widespread and globally dominant (5)(6)(7). Isolates from most B. anthracis lineages have been found across geographically widespread areas, often spanning multiple continents (7). While particular variants often predominate regionally, high lineage diversity has also been reported, including co-circulation of strains from multiple linages (8,9).…”