Bacillus anthracis, commonly referred toas anthrax, has been a tough microbe tocrack genetically because its strainsexhibit minimal variation worldwide. Buta new bacterial typing system developedby researchers at the Northern ArizonaUniversity (NAU), the TranslationalGenomics Research Institute (TGen) andThe Institute for Genomic Research(TIGR) has enabled them to detectminute variations among several anthraxisolates and holds potential for similardiscoveries in other pathogens.

Evolutionary historyAnthrax does not appear to accumulatemutations at a high rate and most of themutations that that occur are stable. Asa result, genetic fingerprinting has failedto fully identify the group’s phylogenicdiversity [1]. ‘Most strains differ bybetween 400 and not even 100nucleotides out of 5 million,’ saysJacques Ravel, an Assistant Investigatorin Microbial Genomics at TIGR(http://www.tigr.org). ‘You just can’taccess this diversity using [conventional]typing systems.’

Paul Keim, Cowden Endowed Chair inMicrobiology at NAU (http://www.nau.edu) and Director of the PathogenGenomics Division at TGen(http://www.tgen.org), recently led thedevelopment of a novel identificationapproach that was able to define theevolution of anthrax with remarkableaccuracy [2]. ‘We went through andpicked out very different strains ofBacillus anthracis to sequence theirwhole genome,’ he explains. SNPs, thesingle nucleotide polymorphisms ordifferences among strains, wereidentified and characterized.

It turns out that anthrax has threemajor phylogenic lineages: the A branch

is the most successful and accounts for85% of all cases worldwide; the B1 andB2 branches account for ~15% of thetotal; and the C branch, which hasevolved very slowly, is rare [2].

New detection modelThe researchers mapped 990 of about3,500 SNPs that were identified fromfive anthrax strain sequences [2]. By‘canonizing’ redundant SNPs, essentiallychoosing one SNP to represent thosethat provide the same diagnosticinformation, the significant differenceswere summarized in 24 SNPs, says Keim.His laboratory has since used thisinformation to develop diagnostic assaysthat can differentiate between twostrains of anthrax at the singlenucleotide level. ‘The SNPs that we used to determine the evolution ofanthrax fit right into a diagnosticstrategy,’ Keim says.

This has obvious implications forforensics, says Philip Hanna, AssistantProfessor of Microbiology andImmunology at the University ofMichigan Medical School (http://www.med.umich.edu/medschool/). ‘They canuse these SNPs to track strains andpinpoint them to other strainsthroughout the world.’ Those involvedin anthrax decontamination efforts alsowill be able ‘to detect what strain it isvery quickly,’ says Ravel.

Further studies underway with plaguesuggest the same approach will workwith it and other pathogens that posebioterrorism or public health risks.‘You’re developing tools for the forensicstoolkit that could play an important rolein [determining] how cholera travelsaround the world,’ suggests JennieHunter-Cevera, President of theUniversity of Maryland Biotechnology

Institute (http://www.umbi.umd.edu/).Ultimately, this could lead those workingin clinical microbiology and infectiousdiseases to develop ‘prophylacticapproaches, new class of antibiotics andperhaps even better vaccines’, she adds.

Drug discoveryThese findings are good news for thoseworking to develop an anthrax vaccine.‘It shows quite strongly that one strainmay not be worse than another incausing disease,’ says Hanna. ‘They lookvery similar and the differences aremainly at the point of these SNPs thatdon’t really change the way the buginteracts with its environment, itsmetabolism or its pathogenesis.’

References1 Keim, P. et al. (2000) Multiple-locus variable-

number tandem repeat analysis revealsgenetic relationships within Bacillusanthracis. J. Bacteriol. 182, 2928–2936

2 Pearson, T. et al. (2004) Phylogeneticdiscovery bias in Bacillus anthracis using singlenucleotide polymorphisms from wholegenome sequencing. Proc. Nat. Acad. Sci.U. S. A. DOI: 10.1073/pnas.0403844101 (Epub ahead of print; http://www.pnas.org)

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Using SNPs to decode anthraxVida Foubister, v_foubister@yahoo.com

Bacillis anthracis visible as white colonieson a petri dish with other bacteria.Image courtesy of P. Keim of theNorthern Arizona University and theTranslational Genomics ResearchInstitute (http://www.tgen.org).