High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery.
High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery.
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DOI：
10.1186/1471-2164-15-288
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发表时间：
2014-04-16
期刊：
影响因子：
4.4
通讯作者：
Derzelle S
中科院分区：
文献类型：
--
作者：
Girault G;Blouin Y;Vergnaud G;Derzelle S
单核苷酸多态性（SNPs）是对单态病原体（如炭疽杆菌）进行亚型分型的理想标记。在这里，我们报告了使用新一代测序技术来调查法国炭疽芽孢杆菌的历史，地理和遗传多样性。对全国60年来分离的122株菌株进行了全基因组测序，并进行了比较分析，重点是SNPs发现，以区分菌株的区域亚群。共有1581个染色体SNP精确地建立了法国菌株之间存在的系统发育关系。观察到法国存在的三个canSNP亚系（即B.Br.CNEVA、A.Br.011/009和A.Br.001/002）内的系统地理学模式。其中一个更显着的发现是在A.Br.011/009亚组中鉴定出了各种基因型，这些基因型在法国不同地区持续存在。定义A.Br.011/009附属法国菌株的560个SNP将跨欧亚亚群分成六个不同的分支，没有任何中间节点。不同的分支机构，与一些地理集群，得到解决。定义主要B.Br CNEVA亚系的345个SNP聚类了三个主要的地理分支，阿尔卑斯山、比利牛斯山和中央山脉，其中一个小的索恩-卢瓦尔亚群嵌套在后一组内。属于次要A.Br.001/002组的法国菌株的特征在于226个SNP。最近从杜布斯省收集的所有分离株都密切相关。从全基因组序列中识别SNP有助于高分辨率菌株追踪，并提供疫情调查所需的鉴别水平。因此，选择了代表主要的法国特定地理集群的8个诊断SNP，并开发成高分辨率熔解SNP判别分析。本工作建立了B最准确的系统发育重建方法之一。一个国家的炭疽菌种群结构。已经创建了122个法国菌株的广泛的下一代测序（NGS）数据集，该数据集允许鉴定用于快速确定在法国发现的任何菌株的地理起源的新型诊断SNP。
Single nucleotide polymorphisms (SNPs) are ideal signatures for subtyping monomorphic pathogens such as Bacillus anthracis. Here we report the use of next-generation sequencing technology to investigate the historical, geographic and genetic diversity of Bacillus anthracis in France. 122 strains isolated over a 60-years period throughout the country were whole-genome sequenced and comparative analyses were carried out with a focus on SNPs discovery to discriminate regional sub-groups of strains. A total of 1581 chromosomal SNPs precisely establish the phylogenetic relationships existing between the French strains. Phylogeography patterns within the three canSNP sub-lineages present in France (i.e. B.Br.CNEVA, A.Br.011/009 and A.Br.001/002) were observed. One of the more remarkable findings was the identification of a variety of genotypes within the A.Br.011/009 sub-group that are persisting in the different regions of France. The 560 SNPs defining the A.Br.011/009- affiliated French strains split the Trans-Eurasian sub-group into six distinct branches without any intermediate nodes. Distinct sub-branches, with some geographic clustering, were resolved. The 345 SNPs defining the major B.Br CNEVA sub-lineage clustered three main phylogeographic clades, the Alps, the Pyrenees, and the Massif Central, with a small Saône-et-Loire sub-cluster nested within the latter group. The French strains affiliated to the minor A.Br.001/002 group were characterized by 226 SNPs. All recent isolates collected from the Doubs department were closely related. Identification of SNPs from whole-genome sequences facilitates high-resolution strain tracking and provides the level of discrimination required for outbreak investigations. Eight diagnostic SNPs, representative of the main French-specific phylogeographic clusters, were therefore selected and developed into high-resolution melting SNP discriminative assays. This work has established one of the most accurate phylogenetic reconstruction of B. anthracis population structure in a country. An extensive next-generation sequencing (NGS) dataset of 122 French strains have been created that allowed the identification of novel diagnostic SNPs useful to rapidly determine the geographic origin of any strain found in France.
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影响因子：
9.4
作者：
Derzelle, S.;Laroche, S.;Madani, N.
通讯作者：
Madani, N.
影响因子：
5
作者：
Vaissaire, J;Mock, M;Levy, M
通讯作者：
Levy, M
炭疽芽孢杆菌的全球遗传种群结构。
影响因子：
3.7
作者：
Van Ert, Matthew N.;Easterday, W. Ryan;Huynh, Lynn Y.;Okinaka, Richard T.;Hugh-Jones, Martin E.;Ravel, Jacques;Zanecki, Shaylan R.;Pearson, Talima;Simonson, Tatum S.;U'Ren, Jana M.;Kachur, Sergey M.;Leadem-Dougherty, Rebecca R.;Rhoton, Shane D.;Zinser, Guenevier;Farlow, Jason;Coker, Pamala R.;Smith, Kimothy L.;Wang, Bingxiang;Kenefic, Leo J.;Fraser-Liggett, Claire M.;Wagner, David M.;Keim, Paul
通讯作者：
Keim, Paul
影响因子：
9.4
作者：
Van Ert, Matthew N.;Easterday, W. Ryan;Keim, Paul
通讯作者：
Keim, Paul
影响因子：
4.2
作者：
Simonson TS;Okinaka RT;Wang B;Easterday WR;Huynh L;U'Ren JM;Dukerich M;Zanecki SR;Kenefic LJ;Beaudry J;Schupp JM;Pearson T;Wagner DM;Hoffmaster A;Ravel J;Keim P
通讯作者：
Keim P