Whole-Genome-Based Mycobacterium tuberculosis Surveillance: a Standardized, Portable, and Expandable Approach
Whole-Genome-Based Mycobacterium tuberculosis Surveillance: a Standardized, Portable, and Expandable Approach
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DOI：
10.1128/jcm.00567-14
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发表时间：
2014-07-01
影响因子：
9.4
通讯作者：
Niemann, Stefan
中科院分区：
文献类型：
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作者：
Kohl, Thomas A.;Diel, Roland;Niemann, Stefan
全基因组测序(WGS)可以有效地追踪结核分枝杆菌复合体(MTBC)(结核病病原体)的传播。然而，它很难标准化，因此还不能用于实验室间的前瞻性监测。为了使其得到广泛的应用，迫切需要数据标准化和存储在易于扩展的数据库中的解决方案。为了解决这个问题，我们使用Ridom SeqSphere(+)软件开发了一种用于临床MTBC分离株的核心基因组多位点序列分型(CgMLST)方案，该方案将全基因组范围的单核苷酸多态(SNP)多样性转移到一个标准化、可移植且计算不密集的等位基因编号系统中。为了测试其性能，我们对德国联邦汉堡(2001至2010年间通报的一次纵向疫情)中具有相同IS6110 DNA指纹和SPOG型模式的26个分离株进行了WGS分析。CgMLST方法(3,041个基因)区分了26个菌株，其分辨率与基于SNP的WGS分型方法相当(一个由22个相同或密切相关的主要簇和4个异常分离株组成的簇，至少有97个不同的SNP或63个等位基因变异)。得到的树状拓扑高度一致，并以相似的方式将两种情况下的分离物分组。我们的数据表明，基于SNP和cgMLST的WGS分析有助于对纵向MTBC疫情的高分辨率区分。CgMLST允许对WGS基因分型数据进行有意义的流行病学解释。它为流行病学调查提供了标准化的WGS基因分型，例如在区域公共卫生办公室一级，并通过一个综合预警系统为全球结核病监测创建了可上网的数据库。
Whole-genome sequencing (WGS) allows for effective tracing of Mycobacterium tuberculosis complex (MTBC) (tuberculosis pathogens) transmission. However, it is difficult to standardize and, therefore, is not yet employed for interlaboratory prospective surveillance. To allow its widespread application, solutions for data standardization and storage in an easily expandable database are urgently needed. To address this question, we developed a core genome multilocus sequence typing (cgMLST) scheme for clinical MTBC isolates using the Ridom SeqSphere(+) software, which transfers the genome-wide single nucleotide polymorphism (SNP) diversity into an allele numbering system that is standardized, portable, and not computationally intensive. To test its performance, we performed WGS analysis of 26 isolates with identical IS6110 DNA fingerprints and spoligotyping patterns from a longitudinal outbreak in the federal state of Hamburg, Germany (notified between 2001 and 2010). The cgMLST approach (3,041 genes) discriminated the 26 strains with a resolution comparable to that of SNP-based WGS typing (one major cluster of 22 identical or closely related and four outlier isolates with at least 97 distinct SNPs or 63 allelic variants). Resulting tree topologies are highly congruent and grouped the isolates in both cases analogously. Our data show that SNP-and cgMLSTbased WGS analyses facilitate high-resolution discrimination of longitudinal MTBC outbreaks. cgMLST allows for a meaningful epidemiological interpretation of the WGS genotyping data. It enables standardized WGS genotyping for epidemiological investigations, e. g., on the regional public health office level, and the creation of web-accessible databases for global TB surveillance with an integrated early warning system.