Comparative genomics of Bacillus anthracis from the wool industry highlights polymorphisms of lineage A.Br.Vollum

Sylviane Derzelle; Lisandra Aguilar-Bultet; Joachim Frey

doi:10.1016/j.meegid.2016.10.019

Comparative genomics of Bacillus anthracis from the wool industry highlights polymorphisms of lineage A.Br.Vollum

Infect Genet Evol. 2016 Dec:46:50-58. doi: 10.1016/j.meegid.2016.10.019. Epub 2016 Oct 25.

Authors

Sylviane Derzelle¹, Lisandra Aguilar-Bultet², Joachim Frey³

Affiliations

¹ Institute of Veterinary Bacteriology, Vetsuisse, University of Bern, Laenggasstrasse 122, 3001 Bern, Switzerland. Electronic address: sylviane.derzelle@lncr.org.
² Institute of Veterinary Bacteriology, Vetsuisse, University of Bern, Laenggasstrasse 122, 3001 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern CH-3012, Switzerland. Electronic address: lisandra.aguilar@vetsuisse.unibe.ch.
³ Institute of Veterinary Bacteriology, Vetsuisse, University of Bern, Laenggasstrasse 122, 3001 Bern, Switzerland. Electronic address: joachim.frey@vetsuisse.unibe.ch.

PMID: 27793731
DOI: 10.1016/j.meegid.2016.10.019

Abstract

Background: With the advent of affordable next-generation sequencing (NGS) technologies, major progress has been made in the understanding of the population structure and evolution of the B. anthracis species. Here we report the use of whole genome sequencing and computer-based comparative analyses to characterize six strains belonging to the A.Br.Vollum lineage. These strains were isolated in Switzerland, in 1981, during iterative cases of anthrax involving workers in a textile plant processing cashmere wool from the Indian subcontinent.

Results: We took advantage of the hundreds of currently available B. anthracis genomes in public databases, to investigate the genetic diversity existing within the A.Br.Vollum lineage and to position the six Swiss isolates into the worldwide B. anthracis phylogeny. Thirty additional genomes related to the A.Br.Vollum group were identified by whole-genome single nucleotide polymorphism (SNP) analysis, including two strains forming a new evolutionary branch at the basis of the A.Br.Vollum lineage. This new phylogenetic lineage (termed A.Br.H9401) splits off the branch leading to the A.Br.Vollum group soon after its divergence to the other lineages of the major A clade (i.e. 6 SNPs). The available dataset of A.Br.Vollum genomes were resolved into 2 distinct groups. Isolates from the Swiss wool processing facility clustered together with two strains from Pakistan and one strain of unknown origin isolated from yarn. They were clearly differentiated (69 SNPs) from the twenty-five other A.Br.Vollum strains located on the branch leading to the terminal reference strain A0488 of the lineage. Novel analytic assays specific to these new subgroups were developed for the purpose of rapid molecular epidemiology.

Conclusions: Whole genome SNP surveys greatly expand upon our knowledge on the sub-structure of the A.Br.Vollum lineage. Possible origin and route of spread of this lineage worldwide are discussed.

Keywords: Bacillus anthracis; Comparative genomics; High resolution melting; Phylogeny; Single nucleotide polymorphism; Whole genome sequencing.

MeSH terms

Animals
Anthrax / microbiology*
Bacillus anthracis / classification*
Bacillus anthracis / genetics*
Cattle
Cluster Analysis
Genome, Bacterial / genetics*
Genomics
Humans
India
Molecular Typing
Pakistan
Phylogeny
Polymorphism, Single Nucleotide / genetics*
Sequence Analysis, DNA
Textile Industry
Wool / microbiology*