Genome-wide single nucleotide polymorphism typing method for identification of Bacillus anthracis species and strains among B. cereus group species.
As an issue of biosecurity, species-specific genetic markers have been well characterized. However, Bacillus anthracis strain-specific information is currently not sufficient for traceability to identify the origin of the strain. By using genome-wide screening using short read mapping, we identified strain-specific single nucleotide polymorphisms (SNPs) among B. anthracis strains including Japanese isolates, and we further developed a simplified 80-tag SNP typing method for the primary investigation of traceability. These 80-tag SNPs were selected from 2,965 SNPs on the chromosome and the pXO1 and pXO2 plasmids from a total of 19 B. anthracis strains, including the available genome sequences of 17 strains in the GenBank database and 2 Japanese isolates that were sequenced in this study. Phylogenetic analysis based on 80-tag SNP typing showed a higher resolution power to discriminate 12 Japanese isolates rather than the 25 loci identified by multiple-locus variable-number tandem-repeat analysis (MLVA). In addition, the 80-tag PCR testing enabled the discrimination of B. anthracis from other B. cereus group species, helping to identify whether a suspected sample originates from the intentional release of a bioterrorism agent or environmental contamination with a virulent agent. In conclusion, 80-tag SNP typing can be a rapid and sufficient test for the primary investigation of strain origin. Subsequent whole-genome sequencing will reveal apparent strain-specific genetic markers for traceability of strains following an anthrax outbreak.
Kuroda
Makoto
M
Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan. makokuro@nih.go.jp
Serizawa
Masakuni
M
Okutani
Akiko
A
Sekizuka
Tsuyoshi
T
Banno
Satomi
S
Inoue
Satoshi
S
D001408:Bacillus anthracis / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D001409:Bacillus cereus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D015373:Bacterial Typing Techniques / Q000379:methods*; D002876:Chromosomes, Bacterial; D004269:DNA, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D007564:Japan; D010802:Phylogeny; D010957:Plasmids; D016133:Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide
D004269:DNA, Bacterial