Anthrax molecular epidemiology and forensics

Using the appropriate marker for different evolutionary scales

Paul S Keim, Matthew N. Van Ert, Talima R Pearson, Amy J. Vogler, Lynn Y. Huynh, David M Wagner

Research output: Contribution to journalArticle

224 Citations (Scopus)

Abstract

Precise identification of Bacillus anthracis isolates has aided forensic and epidemiological analyses of natural anthrax cases, bioterrorism acts and industrial scale accidents by state-sponsored bioweapons programs. Because there is little molecular variation among B. anthracis isolates, identifying and using rare variation is crucial for precise strain identification. We think that mutation is the primary diversifying force in a clonal, recently emerged pathogen, such as B. anthracis, since mutation rate is correlated with diversity on a per locus basis. While single nucleotide polymorphisms (SNPs) are rare, their detection is facilitated by whole genome discovery approaches. As highly stable phylogenetic markers, SNPs are useful for identifying long branches or key phylogenetic positions. Selection of single, diagnostic "Canonical SNPs" (canSNPs) for these phylogenetic positions allows for efficient and defining assays. We have taken a nested hierarchal strategy for subtyping B. anthracis, which is consistent with traditional diagnostics and applicable to a wide range of pathogens. Progressive hierarchical resolving assays using nucleic acids (PHRANA) uses a progression of diagnostic genomic loci that are initially highly stable but with low resolution and, ultimately, very unstable but with high resolution. This approach mitigates the need for data weighting and provides both a deeply rooted phylogenetic hypothesis and high resolution discrimination among closely related isolates.

Original languageEnglish (US)
Pages (from-to)205-213
Number of pages9
JournalInfection, Genetics and Evolution
Volume4
Issue number3
DOIs
StatePublished - Sep 2004

Fingerprint

anthrax
Bacillus anthracis
Anthrax
molecular epidemiology
Molecular Epidemiology
epidemiology
single nucleotide polymorphism
Single Nucleotide Polymorphism
phylogenetics
polymorphism
phylogeny
mutation
pathogen
assay
bioterrorism
Occupational Accidents
Bioterrorism
loci
pathogens
nucleic acid

Keywords

  • Anthrax
  • Bacillus anthracis
  • Bioterrorism
  • Canonical SNPs
  • canSNPs
  • Microbial forensics
  • MLVA
  • PHRANA
  • SNPs
  • SNR

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Microbiology
  • Infectious Diseases

Cite this

Anthrax molecular epidemiology and forensics : Using the appropriate marker for different evolutionary scales. / Keim, Paul S; Van Ert, Matthew N.; Pearson, Talima R; Vogler, Amy J.; Huynh, Lynn Y.; Wagner, David M.

In: Infection, Genetics and Evolution, Vol. 4, No. 3, 09.2004, p. 205-213.

Research output: Contribution to journalArticle

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