MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples.
MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples.
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DOI：
10.1093/nar/gkw837
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发表时间：
2017-01-25
影响因子：
14.9
通讯作者：
Segata N
中科院分区：
文献类型：
--
作者：
Zolfo M;Tett A;Jousson O;Donati C;Segata N
微生物群落的宏基因组学表征有可能成为鉴定人体样本中病原体的工具。然而，需要能够从宏基因组数据中提取菌株水平分型信息的软件工具。低通量分子分型模式，如多位点序列分型（MLST）仍然被广泛使用，并提供了丰富的菌株水平的信息，目前没有利用宏基因组方法。我们介绍MetaMLST，一个软件工具，从宏基因组数据中重建微生物群落中存在的微生物的MLST基因座。在合成的和掺入的真实的宏基因组上进行测试，该管道能够在低至1×的覆盖率下以>98.5%的准确度重建MLST序列。在真实的样本上，管道显示出比基于组装的方法更高的灵敏度，并且证明它在识别流行病爆发以及肠道，皮肤和胃肠道微生物组样本中的菌株方面是成功的。
Metagenomic characterization of microbial communities has the potential to become a tool to identify pathogens in human samples. However, software tools able to extract strain-level typing information from metagenomic data are needed. Low-throughput molecular typing schema such as Multilocus Sequence Typing (MLST) are still widely used and provide a wealth of strain-level information that is currently not exploited by metagenomic methods. We introduce MetaMLST, a software tool that reconstructs the MLST loci of microorganisms present in microbial communities from metagenomic data. Tested on synthetic and spiked-in real metagenomes, the pipeline was able to reconstruct the MLST sequences with >98.5% accuracy at coverages as low as 1×. On real samples, the pipeline showed higher sensitivity than assembly-based approaches and it proved successful in identifying strains in epidemic outbreaks as well as in intestinal, skin and gastrointestinal microbiome samples.