Vogler Amy J, Birdsell Dawn, Price Lance B, Bowers Jolene R, Beckstrom-Sternberg Stephen M, Auerbach Raymond K, Beckstrom-Sternberg James S, Johansson Anders, Clare Ashley, Buchhagen Jordan L, Petersen Jeannine M, Pearson Talima, Vaissaire Josée, Dempsey Michael P, Foxall Paul, Engelthaler David M, Wagner David M, Keim Paul
Center for Microbial Genetics and Genomics, Northern Arizona University, P.O. Box 4073, Flagstaff, AZ 86011, USA.
J Bacteriol. 2009 Apr;191(8):2474-84. doi: 10.1128/JB.01786-08. Epub 2009 Feb 27.
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.
土拉弗朗西斯菌包含几个高致病性亚种，包括土拉弗朗西斯菌全北区亚种，其分布于北半球的环极地区。利用全基因组单核苷酸多态性（SNP）分析、高密度微阵列SNP基因分型和基于实时PCR的标准SNP（canSNP）检测方法，对这些亚种及其亚分支的系统地理学进行了研究。在用于系统发育分析的13个全基因组中鉴定出近30000个SNP。我们选择了1655个SNP，在高密度微阵列平台上对95个分离株进行基因分型。最后，鉴定出23个分支和亚分支特异性canSNP，并用于对496个分离株进行基因分型，以建立全球地理遗传模式。我们证实了之前关于四个亚种和两个土拉弗朗西斯菌土拉亚种亚群的研究结果，并在这些群体中发现了更多的结构。我们在土拉弗朗西斯菌全北区亚种中鉴定出11个亚分支，包括一个新的、遗传上不同的亚分支，它似乎介于日本土拉弗朗西斯菌全北区亚种分离株和与辐射事件（B辐射）相关的常见土拉弗朗西斯菌全北区亚种分离株之间，在该辐射事件中，该亚种传播到了整个北半球。系统发育分析表明，这个B辐射分支起源于北美，并且在北美和欧亚大陆之间发生了多次扩散事件。这些发现表明土拉弗朗西斯菌全北区亚种具有复杂的传播历史。
