Data from: High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery

Background: 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 50-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.Results: 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. Conclusions: 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.背景：单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）是炭疽芽孢杆菌（Bacillus anthracis）等单态性病原体分型的理想分子标识。本研究利用下一代测序（next-generation sequencing, NGS）技术，探究法国境内炭疽芽孢杆菌的历史、地理与遗传多样性特征。研究纳入了50年间在法国全境分离的122株菌株，对其完成全基因组测序，并开展比较基因组分析，重点聚焦SNPs的发掘以区分菌株的区域亚群。结果：总计1581个染色体SNPs精准解析了法国菌株间的系统发育关系。研究观察到法国境内存在的3个canSNP亚谱系（即B.Br.CNEVA、A.Br.011/009与A.Br.001/002）的系统地理分布模式。其中一项核心发现为：在A.Br.011/009亚群中鉴定出多种持续存在于法国不同区域的基因型。定义A.Br.011/009关联法国菌株的560个SNPs，将跨欧亚亚群划分为6个独立分支，且无中间过渡节点。研究进一步解析出多个具备一定地理聚集特征的亚分支。定义主要B.Br CNEVA亚谱系的345个SNPs，将其划分为3个主要的系统地理演化支：阿尔卑斯山、比利牛斯山与中央高原，其中还嵌套有一个隶属于中央高原支的小型索恩-卢瓦尔省（Saône-et-Loire）亚支。隶属于次要亚群A.Br.001/002的法国菌株，可通过226个SNPs完成分型。所有从杜省（Doubs department）采集的近期分离株亲缘关系极为密切。基于全基因组序列鉴定的SNPs可实现高分辨率的菌株溯源，且具备暴发调查所需的精准区分度。据此，研究筛选出8个可代表法国主要特有系统地理演化簇的诊断性SNPs，并开发了高分辨率熔解曲线SNP分型检测方法。结论：本研究构建了全球范围内精度顶尖的单国境内炭疽芽孢杆菌种群结构系统发育重建成果之一。研究生成了包含122株法国菌株的大型下一代测序数据集，借此鉴定出新型诊断性SNPs，可用于快速确定法国境内分离的任意菌株的地理来源。