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Journal of Bacteriology, April 2009, p. 2474-2484, Vol. 191, No. 8
0021-9193/09/$08.00+0 doi:10.1128/JB.01786-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
Phylogeography of Francisella tularensis: Global Expansion of a Highly Fit Clone
,
Amy J. Vogler,1
Dawn Birdsell,1
Lance B. Price,2
Jolene R. Bowers,2
Stephen M. Beckstrom-Sternberg,1,2
Raymond K. Auerbach,1,
James S. Beckstrom-Sternberg,1
Anders Johansson,3
Ashley Clare,1
Jordan L. Buchhagen,1
Jeannine M. Petersen,4
Talima Pearson,1
Josée Vaissaire,5
Michael P. Dempsey,6
Paul Foxall,7
David M. Engelthaler,2
David M. Wagner,1 and
Paul Keim1,2*
Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona 86011-4073,1 Translational Genomics Research Institute, Phoenix, Arizona 85004,2 Department of Clinical Microbiology, Infectious Diseases and Bacteriology, Umeå University, SE 901 85 Umeå, and Division of CBRN Defence and Security, Swedish Defence Research Agency, SE 901 82 Umeå, Sweden,3 Centers for Disease Control and Prevention, Fort Collins, Colorado 80521,4 Agence Française de Sécurité Sanitaire des Aliments, Laboratoire d'Etudes et de Recherches en Pathologie Animale et Zoonoses, 94700 Maison-Alfort, France,5 Division of Microbiology, Armed Forces Institute of Pathology, Washington, D.C. 20306,6 Affymetrix, Inc., Santa Clara, California 950517
Received 19 December 2008/ Accepted 10 February 2009
Francisella tularensis contains several highly pathogenic subspecies, including Francisella tularensis subsp. holarctica, whose distribution is circumpolar in the northern hemisphere. The phylogeography of these subspecies and their subclades was examined using whole-genome single nucleotide polymorphism (SNP) analysis, high-density microarray SNP genotyping, and real-time-PCR-based canonical SNP (canSNP) assays. Almost 30,000 SNPs were identified among 13 whole genomes for phylogenetic analysis. We selected 1,655 SNPs to genotype 95 isolates on a high-density microarray platform. Finally, 23 clade- and subclade-specific canSNPs were identified and used to genotype 496 isolates to establish global geographic genetic patterns. We confirm previous findings concerning the four subspecies and two Francisella tularensis subsp. tularensis subpopulations and identify additional structure within these groups. We identify 11 subclades within F. tularensis subsp. holarctica, including a new, genetically distinct subclade that appears intermediate between Japanese F. tularensis subsp. holarctica isolates and the common F. tularensis subsp. holarctica isolates associated with the radiation event (the B radiation) wherein this subspecies spread throughout the northern hemisphere. Phylogenetic analyses suggest a North American origin for this B-radiation clade and multiple dispersal events between North America and Eurasia. These findings indicate a complex transmission history for F. tularensis subsp. holarctica.
* Corresponding author. Mailing address: Center for Microbial Genetics and Genomics, Northern Arizona University, P.O. Box 4073, Flagstaff, AZ 86011. Phone: (928) 523-1078. Fax: (928) 523-4015. E-mail: Paul.Keim{at}nau.edu
Published ahead of print on 27 February 2009.
Supplemental material for this article may be found at http://jb.asm.org/.
Present address: Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT.
Journal of Bacteriology, April 2009, p. 2474-2484, Vol. 191, No. 8
0021-9193/09/$08.00+0 doi:10.1128/JB.01786-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
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