Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria
Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria
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DOI：
10.1128/jcm.06094-11
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发表时间：
2012-04-01
影响因子：
9.4
通讯作者：
Lund, Ole
中科院分区：
文献类型：
--
作者：
Larsen, Mette V.;Cosentino, Salvatore;Lund, Ole
准确的菌株鉴定对任何从事细菌工作的人来说都是至关重要的。对许多物种来说，多位点序列分型(MLST)被认为是分型的“黄金标准”，但它传统上是以昂贵和耗时的方式进行的。随着全基因组测序(WGS)的成本持续下降，科学家和常规诊断实验室越来越容易获得全基因组测序。目前，成本低于传统的MLST。新的挑战将是如何从大量数据中提取相关信息，以便能够在一段时间内和实验室之间进行比较。理想情况下，此信息还应允许与历史数据进行比较。我们开发了一种基于WGS数据的基于Web的66种细菌的MLST方法。作为输入，该方法使用从四个测序平台或预组装的基因组中读取的短序列。每月从MLST数据库下载更新，并使用基于BLAST的排名方法找到指定MLST方案的最佳匹配MLST等位基因。然后，序列类型由所识别的等位基因组合来确定。该方法在覆盖56个MLST方案的336个分离物的预组装基因组上进行了测试，在覆盖10个方案的387个分离物的短序列读取上进行了测试，并在29个通过传统方法确定了序列类型的分离物的短序列读取的小测试集上进行了测试。本文介绍的方法使研究人员能够根据WGS数据确定其分离物的序列类型。该方法可在www.cbs.dtu.dk/services/mlst上公开获得。
Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56 MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types of their isolates on the basis of WGS data. This method is publicly available at www.cbs.dtu.dk/services/MLST.