Strain-specific single-nucleotide polymorphism assays for the Bacillus anthracis Ames strain

Matthew N. Van Ert, W. Ryan Easterday, Tatum S. Simonson, Jana M. U'Ren, Talima R Pearson, Leo J. Kenefic, Joseph D. Busch, Lynn Y. Huynh, Megan Dukerich, Carla B. Trim, Jodi Beaudry, Amy Welty-Bernard, Timothy Read, Claire M. Fraser, Jacques Ravel, Paul S Keim

Research output: Contribution to journalArticle

88 Citations (Scopus)

Abstract

Highly precise diagnostics and forensic assays can be developed through a combination of evolutionary analysis and the exhaustive examination of genomic sequences. In Bacillus anthracis, whole-genome sequencing efforts revealed ca. 3,500 single-necleotide polymorphisms (SNPs) among eight different strains and evolutionary analysis provides the identification of canonical SNPs. We have previously shown that SNPs are highly evolutionarily stable, and the clonal nature of B. anthracis makes them ideal signatures for subtyping this pathogen. Here we identified SNPs that define the lineage of B. anthracis that contains the Ames strain, the strain used in the 2001 bioterrorist attacks in the United States. Sequencing and real-time PCR were used to validate these SNPs across B. anthracis strains, including (i) 88 globally and genetically diverse isolates; (ii) isolates that were shown to be genetic relatives of the Ames strain by multiple-locus variable number tandem repeat analysis (MLVA); and (iii) several different lab stocks of the Ames strain, including a clinical isolate from the 2001 letter attack. Six SNPs were found to be highly specific for the Ames strain; four on the chromosome, one on the pX01 plasmid, and one on the pX02 plasmid. All six SNPs differentiated the B. anthracis Ames strain from the 88 unique B. anthracis strains, while five of the six separated Ames from its close genetic relatives. The use of these SNPs coupled with real-time PCR allows specific and sensitive (<100 fg of template DNA) identification of the Ames strain. This evolutionary and genomics-based approach provides an effective means for the discovery of strain-specific SNPs in B. anthracis.

Original languageEnglish (US)
Pages (from-to)47-53
Number of pages7
JournalJournal of Clinical Microbiology
Volume45
Issue number1
DOIs
StatePublished - Jan 2007

Fingerprint

Bacillus anthracis
Single Nucleotide Polymorphism
Real-Time Polymerase Chain Reaction
Plasmids
Minisatellite Repeats
Genomics
Chromosomes
Genome
DNA

ASJC Scopus subject areas

  • Microbiology (medical)
  • Microbiology

Cite this

Strain-specific single-nucleotide polymorphism assays for the Bacillus anthracis Ames strain. / Van Ert, Matthew N.; Easterday, W. Ryan; Simonson, Tatum S.; U'Ren, Jana M.; Pearson, Talima R; Kenefic, Leo J.; Busch, Joseph D.; Huynh, Lynn Y.; Dukerich, Megan; Trim, Carla B.; Beaudry, Jodi; Welty-Bernard, Amy; Read, Timothy; Fraser, Claire M.; Ravel, Jacques; Keim, Paul S.

In: Journal of Clinical Microbiology, Vol. 45, No. 1, 01.2007, p. 47-53.

Research output: Contribution to journalArticle

Van Ert, MN, Easterday, WR, Simonson, TS, U'Ren, JM, Pearson, TR, Kenefic, LJ, Busch, JD, Huynh, LY, Dukerich, M, Trim, CB, Beaudry, J, Welty-Bernard, A, Read, T, Fraser, CM, Ravel, J & Keim, PS 2007, 'Strain-specific single-nucleotide polymorphism assays for the Bacillus anthracis Ames strain', Journal of Clinical Microbiology, vol. 45, no. 1, pp. 47-53. https://doi.org/10.1128/JCM.01233-06
Van Ert, Matthew N. ; Easterday, W. Ryan ; Simonson, Tatum S. ; U'Ren, Jana M. ; Pearson, Talima R ; Kenefic, Leo J. ; Busch, Joseph D. ; Huynh, Lynn Y. ; Dukerich, Megan ; Trim, Carla B. ; Beaudry, Jodi ; Welty-Bernard, Amy ; Read, Timothy ; Fraser, Claire M. ; Ravel, Jacques ; Keim, Paul S. / Strain-specific single-nucleotide polymorphism assays for the Bacillus anthracis Ames strain. In: Journal of Clinical Microbiology. 2007 ; Vol. 45, No. 1. pp. 47-53.
@article{063f33b656484306a6632d9f8d26200c,
title = "Strain-specific single-nucleotide polymorphism assays for the Bacillus anthracis Ames strain",
abstract = "Highly precise diagnostics and forensic assays can be developed through a combination of evolutionary analysis and the exhaustive examination of genomic sequences. In Bacillus anthracis, whole-genome sequencing efforts revealed ca. 3,500 single-necleotide polymorphisms (SNPs) among eight different strains and evolutionary analysis provides the identification of canonical SNPs. We have previously shown that SNPs are highly evolutionarily stable, and the clonal nature of B. anthracis makes them ideal signatures for subtyping this pathogen. Here we identified SNPs that define the lineage of B. anthracis that contains the Ames strain, the strain used in the 2001 bioterrorist attacks in the United States. Sequencing and real-time PCR were used to validate these SNPs across B. anthracis strains, including (i) 88 globally and genetically diverse isolates; (ii) isolates that were shown to be genetic relatives of the Ames strain by multiple-locus variable number tandem repeat analysis (MLVA); and (iii) several different lab stocks of the Ames strain, including a clinical isolate from the 2001 letter attack. Six SNPs were found to be highly specific for the Ames strain; four on the chromosome, one on the pX01 plasmid, and one on the pX02 plasmid. All six SNPs differentiated the B. anthracis Ames strain from the 88 unique B. anthracis strains, while five of the six separated Ames from its close genetic relatives. The use of these SNPs coupled with real-time PCR allows specific and sensitive (<100 fg of template DNA) identification of the Ames strain. This evolutionary and genomics-based approach provides an effective means for the discovery of strain-specific SNPs in B. anthracis.",
author = "{Van Ert}, {Matthew N.} and Easterday, {W. Ryan} and Simonson, {Tatum S.} and U'Ren, {Jana M.} and Pearson, {Talima R} and Kenefic, {Leo J.} and Busch, {Joseph D.} and Huynh, {Lynn Y.} and Megan Dukerich and Trim, {Carla B.} and Jodi Beaudry and Amy Welty-Bernard and Timothy Read and Fraser, {Claire M.} and Jacques Ravel and Keim, {Paul S}",
year = "2007",
month = "1",
doi = "10.1128/JCM.01233-06",
language = "English (US)",
volume = "45",
pages = "47--53",
journal = "Journal of Clinical Microbiology",
issn = "0095-1137",
publisher = "American Society for Microbiology",
number = "1",

}

TY - JOUR

T1 - Strain-specific single-nucleotide polymorphism assays for the Bacillus anthracis Ames strain

AU - Van Ert, Matthew N.

AU - Easterday, W. Ryan

AU - Simonson, Tatum S.

AU - U'Ren, Jana M.

AU - Pearson, Talima R

AU - Kenefic, Leo J.

AU - Busch, Joseph D.

AU - Huynh, Lynn Y.

AU - Dukerich, Megan

AU - Trim, Carla B.

AU - Beaudry, Jodi

AU - Welty-Bernard, Amy

AU - Read, Timothy

AU - Fraser, Claire M.

AU - Ravel, Jacques

AU - Keim, Paul S

PY - 2007/1

Y1 - 2007/1

N2 - Highly precise diagnostics and forensic assays can be developed through a combination of evolutionary analysis and the exhaustive examination of genomic sequences. In Bacillus anthracis, whole-genome sequencing efforts revealed ca. 3,500 single-necleotide polymorphisms (SNPs) among eight different strains and evolutionary analysis provides the identification of canonical SNPs. We have previously shown that SNPs are highly evolutionarily stable, and the clonal nature of B. anthracis makes them ideal signatures for subtyping this pathogen. Here we identified SNPs that define the lineage of B. anthracis that contains the Ames strain, the strain used in the 2001 bioterrorist attacks in the United States. Sequencing and real-time PCR were used to validate these SNPs across B. anthracis strains, including (i) 88 globally and genetically diverse isolates; (ii) isolates that were shown to be genetic relatives of the Ames strain by multiple-locus variable number tandem repeat analysis (MLVA); and (iii) several different lab stocks of the Ames strain, including a clinical isolate from the 2001 letter attack. Six SNPs were found to be highly specific for the Ames strain; four on the chromosome, one on the pX01 plasmid, and one on the pX02 plasmid. All six SNPs differentiated the B. anthracis Ames strain from the 88 unique B. anthracis strains, while five of the six separated Ames from its close genetic relatives. The use of these SNPs coupled with real-time PCR allows specific and sensitive (<100 fg of template DNA) identification of the Ames strain. This evolutionary and genomics-based approach provides an effective means for the discovery of strain-specific SNPs in B. anthracis.

AB - Highly precise diagnostics and forensic assays can be developed through a combination of evolutionary analysis and the exhaustive examination of genomic sequences. In Bacillus anthracis, whole-genome sequencing efforts revealed ca. 3,500 single-necleotide polymorphisms (SNPs) among eight different strains and evolutionary analysis provides the identification of canonical SNPs. We have previously shown that SNPs are highly evolutionarily stable, and the clonal nature of B. anthracis makes them ideal signatures for subtyping this pathogen. Here we identified SNPs that define the lineage of B. anthracis that contains the Ames strain, the strain used in the 2001 bioterrorist attacks in the United States. Sequencing and real-time PCR were used to validate these SNPs across B. anthracis strains, including (i) 88 globally and genetically diverse isolates; (ii) isolates that were shown to be genetic relatives of the Ames strain by multiple-locus variable number tandem repeat analysis (MLVA); and (iii) several different lab stocks of the Ames strain, including a clinical isolate from the 2001 letter attack. Six SNPs were found to be highly specific for the Ames strain; four on the chromosome, one on the pX01 plasmid, and one on the pX02 plasmid. All six SNPs differentiated the B. anthracis Ames strain from the 88 unique B. anthracis strains, while five of the six separated Ames from its close genetic relatives. The use of these SNPs coupled with real-time PCR allows specific and sensitive (<100 fg of template DNA) identification of the Ames strain. This evolutionary and genomics-based approach provides an effective means for the discovery of strain-specific SNPs in B. anthracis.

UR - http://www.scopus.com/inward/record.url?scp=33846185879&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33846185879&partnerID=8YFLogxK

U2 - 10.1128/JCM.01233-06

DO - 10.1128/JCM.01233-06

M3 - Article

VL - 45

SP - 47

EP - 53

JO - Journal of Clinical Microbiology

JF - Journal of Clinical Microbiology

SN - 0095-1137

IS - 1

ER -