Whole-genome sequencing investigation of animal-skin-drum-associated UK anthrax cases reveals evidence of mixed populations and relatedness to a US case

Abstract

There have been two anthrax cases affecting people that played and/or made animal-skin drums in the UK during the last 10 years, with single fatal occurrences in Scotland in 2006 and London in 2008. Investigations by the Health Protection Agency (now Public Health England) employing multi-locus-variable number tandem repeat analysis had previously linked the clinical cases to spores associated with animal skins and drums the patients had been in contact with. In this study, whole-genome sequencing of 23 Bacillus anthracis isolates harvested during the investigations was performed. High-quality draft assemblies of these genomes provided greater characterization of the B. anthracis strains present and placed them all upon a new branch of the global phylogeny. Although closely related, the clinical isolates from the two events, and another isolated from a drum-skin-associated case in New York in 2006, were distinct from each other. Multiple distinct genotypes were found during both investigations, implying either multiple contamination events or a single heterogeneous contamination. One environmental isolate from the Scottish incident was more closely related to London isolates than to the other Scottish isolates. As B. anthracis of this subgroup was present at both geographically and temporally distinct events, it may be more widespread at the source of contamination. All isolates were distinct from currently characterized West African strains, despite this being the likely origin of the drums and hides, therefore adding to our knowledge of B. anthracis diversity in the region.

A Bacillus anthracis Genome Sequence from the Sverdlovsk 1979 Autopsy Specimens

“…The deeper phylogenetic relationships ( Fig. 1A ) are consistent with those reported previously with a more limited number of genomes ( 16 – 18 , 20 – 24 ) as well as across different phylogenetic methods (maximum likelihood using the general time reversible [GTR] model of evolution and neighbor joining). There are three major clades, C being basal to the A and B clades ( Fig.…”

Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia

“…This is in agreement with the report by Kenefic et al demonstrating an introduction of WNA in the USA from Canada, and a progressive evolution from north to south. The West Africa clade from Guinea and Côte d’Ivoire [41] is branching out from lineage L2 at the same position as the WNA and Senegal-Gambia [42] clade. Apart from two Argentinian strains belonging to the L3_Pasteur II vaccine sublineage and one strain from the USA defining a recent split with a long branch within lineage L4, all the other A.Br.011/009 strains are from Italy and France.…”

Closed Genome Sequence Obtained Using Hybrid Nanopore/Illumina Assembly of a Bacillus anthracis Isolate from an Animal-Skin-Drum-Associated Anthrax Case in the United Kingdom

“…We previously characterized multiple isolates from two animal-skin-drum-associated anthrax cases in the United Kingdom, utilizing Illumina sequencing and a reference mapping-based approach to identify core genome single-nucleotide polymorphisms (SNPs). Phylogenetic analysis showed that these strains (along with another collected from a similar U.S. case [ 5 ]) formed a novel branch on the global B. anthracis phylogeny that was distinct from previously characterized West African strains, despite this being the likely origin of the contaminated animal skins ( 6 ). In order to produce a more complete reference sequence for this novel lineage, we used the Oxford Nanopore MinION genomic DNA sequencing kit (SQK-MAP006) on a MinION Mk1 device, with 1 μg of DNA (isolated as described previously) as input to produce 11,231 2D reads with a mean length of 7.5 kb; the predicted genome coverage depth was ∼16×.…”

“…In order to produce a more complete reference sequence for this novel lineage, we used the Oxford Nanopore MinION genomic DNA sequencing kit (SQK-MAP006) on a MinION Mk1 device, with 1 μg of DNA (isolated as described previously) as input to produce 11,231 2D reads with a mean length of 7.5 kb; the predicted genome coverage depth was ∼16×. Fasta sequences were extracted from FAST5 files using poRe ( 7 ) and used along with the existing Illumina data (∼50× read depth [ 6 ]) in a hybrid assembly using Unicycler ( 8 ). Assembly of the Illumina data alone using SPAdes ( 9 ) produced an assembly of 87 scaffolds, including a complete pX02 plasmid sequence but multicontig chromosomal and pX01 sequences (comprised of 82 and 4 contigs, respectively).…”