Single Nucleotide Polymorphism Typing ofBacillus anthracisfrom Sverdlovsk Tissue

Richard T Okinaka,Melinda Henrie,Kristins Lowery,Steven A Hofstadler,Paul J Jackson,Talima Pearson,Jodi Beaudry,James Schupp,Paul Keim,Leo Kenefic,Karen K Hill,Matthew Van Ert

doi:10.3201/eid1404.070984

Abstract

A small number of conserved canonical single nucleotide polymorphisms (canSNP) that define major phylogenetic branches for Bacillus anthracis were used to place a Sverdlovsk patient’s B. anthracis genotype into 1 of 12 subgroups. Reconstruction of the pagA gene also showed a unique SNP that defines a new lineage for B. anthracis.

Highlights

A small number of conserved canonical single nucleotide polymorphisms that define major phylogenetic branches for Bacillus anthracis were used to place a Sverdlovsk patient’s B. anthracis genotype into 1 of 12 subgroups
The distribution of the remaining 5 single nucleotide polymorphism (SNP) separated the 26 diverse isolates and the remaining Sverdlovsk samples into clusters that were consistent with diversity groups previously described by amplified fragment– length polymorphism (AFLP) analysis of a larger subset of
When all 1,033 isolates were evaluated against a panel of 13 canonical single nucleotide polymorphisms (canSNP), the results demonstrated that each B. anthracis isolate had 1 of only 12 different canSNP profiles

Summary

Sverdlovsk Tissue

A small number of conserved canonical single nucleotide polymorphisms (canSNP) that define major phylogenetic branches for Bacillus anthracis were used to place a Sverdlovsk patient’s B. anthracis genotype into 1 of 12 subgroups. Recent comparisons among 5 B. anthracis whole genome sequences uncovered ≈3,000 SNPs, and the rigorous examination of ≈1,000 of these SNPs across 27 diverse isolates demonstrated an extremely conserved clonal population structure for this species [7,8] These results led to a genotyping method that uses a small number of canonical SNPs (canSNPs) to replace the analysis of ≈1,000 SNPs and still precisely defines key positions and branch points within the B. anthracis tree [9]. The status of the new pagA 981 site was analyzed in a panel of isolates containing 89 diverse multiple-locus, variable-number, tandem-repeat analysis genotypes and an additional 154 A.Br.008/009 subgroup (Eurasian) isolates by using a custom made real-time PCR assay: TaqMan Minor Groove Binding probes and primers for SSNPs (Applied Biosystems) [14] These analyses indicate that the pagA 981 A–T transversion represents a rare SNP allele found in only 3 Eurasian isolates and the Sverdlovsk 7.RA93.15.15 sample.

Western North America

Conclusions