A classification framework forBacillus anthracisdefined by global genomic structure

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.

Genetic Diversity of Australian Bacillus anthracis Isolates Revealed by Multiple-Locus Variable-Number Tandem Repeat Analysis

“…Whole genome sequencing is a powerful alternative method to MLVA, with the versatility to look at disease outbreak origins, introductions, and routine surveillance to support epidemiological investigations. This technology is becoming standard practice for examining the genetic diversity of clonal bacterial species such as B. anthracis [ 32 , 33 ]. Rapid classification frameworks made available by researchers such as Bruce et al [ 32 ] offer a simplified and robust tool for the analysis of B. anthracis evolution and classification.…”

“…This technology is becoming standard practice for examining the genetic diversity of clonal bacterial species such as B. anthracis [ 32 , 33 ]. Rapid classification frameworks made available by researchers such as Bruce et al [ 32 ] offer a simplified and robust tool for the analysis of B. anthracis evolution and classification. Owing to the expansion of available genome sequence data and the comparison of B. anthracis strains worldwide [ 32 , 33 , 34 , 35 , 36 , 37 ], this approach offers greater insight into the global placement of the Australian strains and may provide a deeper understanding of the genomic diversity at a local level.…”

Population genomics of Bacillus anthracis from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity

“…The resulting phylogeny indicated that NCA isolates belong to the ancient A lineage. To further resolve the diversity among NCA isolates compared with other publicly available isolates from the same lineage, reads from eight additional isolates available from the Sequence Read Archive (SRA) from a study by Bruce et al [7] were accessed using Fastq-dump from the SRA-toolkit: all isolates (n=4) belonging to the 3.2 linage, and two arbitrarily selected isolates from each of the 3.1 and 3.3 lineages (Table S2). These were run through our SNP-calling pipeline as described above, resulting in a sequence alignment file free of -/N characters, which was used to infer a phylogeny in RAxML v8.2.11 [48] using a GTR (general time reversible) model of nucleotide substitution, and using the Ames Ancestor reference genome as an outgroup.…”

“…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 the 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].…”

Coalescence modeling of intrainfection Bacillus anthracis populations allows estimation of infection parameters in wild populations

“…An isolate was obtained from a blood swab from a zebra carcass containing the most common genotype in Etosha (genotype 6) according toBeyer et al (39). This isolate is from A.Br.003 (A.Br.Aust94) using Van Ert et al's(40) global classification, and group 5.4 using a new population genomic classification(41). The zebra carcass was found on 22 February 2010 (carcass ID: EB100224-01WT).…”