Phylogeography of Francisella tularensis: global expansion of a highly fit clone.
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.
Vogler
Amy J
AJ
Center for Microbial Genetics and Genomics, Northern Arizona University, P.O. Box 4073, Flagstaff, AZ 86011, USA.
Birdsell
Dawn
D
Price
Lance B
LB
Bowers
Jolene R
JR
Beckstrom-Sternberg
Stephen M
SM
Auerbach
Raymond K
RK
Beckstrom-Sternberg
James S
JS
Johansson
Anders
A
Clare
Ashley
A
Buchhagen
Jordan L
JL
Petersen
Jeannine M
JM
Pearson
Talima
T
Vaissaire
Josée
J
Dempsey
Michael P
MP
Foxall
Paul
P
Engelthaler
David M
DM
Wagner
David M
DM
Keim
Paul
P
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*
D004269:DNA, Bacterial