title: Phylogeography of Francisella tularensis: global expansion of a highly fit clone.
abstract: 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.
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, P.O. Box 4073, Flagstaff, AZ 86011, USA.
authors.forename: Amy J
authors.initials: AJ
authors.lastname: Vogler
authors.forename: Dawn
authors.initials: D
authors.lastname: Birdsell
authors.forename: Lance B
authors.initials: LB
authors.lastname: Price
authors.forename: Jolene R
authors.initials: JR
authors.lastname: Bowers
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Beckstrom-Sternberg
authors.forename: Raymond K
authors.initials: RK
authors.lastname: Auerbach
authors.forename: James S
authors.initials: JS
authors.lastname: Beckstrom-Sternberg
authors.forename: Anders
authors.initials: A
authors.lastname: Johansson
authors.forename: Ashley
authors.initials: A
authors.lastname: Clare
authors.forename: Jordan L
authors.initials: JL
authors.lastname: Buchhagen
authors.forename: Jeannine M
authors.initials: JM
authors.lastname: Petersen
authors.forename: Talima
authors.initials: T
authors.lastname: Pearson
authors.forename: Josée
authors.initials: J
authors.lastname: Vaissaire
authors.forename: Michael P
authors.initials: MP
authors.lastname: Dempsey
authors.forename: Paul
authors.initials: P
authors.lastname: Foxall
authors.forename: David M
authors.initials: DM
authors.lastname: Engelthaler
authors.forename: David M
authors.initials: DM
authors.lastname: Wagner
authors.forename: Paul
authors.initials: P
authors.lastname: Keim
mesh_terms: D001208:Asia / Q000453:epidemiology; D015373:Bacterial Typing Techniques; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000235:genetics*; D005060:Europe / Q000453:epidemiology; D005604:Francisella tularensis / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D016680:Genome, Bacterial; D005838:Genotype; D005843:Geography; D046228:Microarray Analysis / Q000379:methods; D017720:Molecular Epidemiology; D009656:North America / Q000453:epidemiology; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D014406:Tularemia / Q000453:epidemiology* / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial