An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes
An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes
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DOI：
10.3389/fmicb.2017.02351
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发表时间：
2017-11-29
影响因子：
5.2
通讯作者：
Hendriksen, Rene S.
中科院分区：
文献类型：
--
作者：
Henri, Clementine;Leekitcharoenphon, Pimlapas;Hendriksen, Rene S.
背景/目的：全基因组测序（WGS）已被证明是一个强大的分型工具，食源性致病菌，如L。单核细胞增多症基因组规模分析对国家监测、疫情检测或源头追踪的好处已在很大程度上得到证明。然而，基因组数据可以利用许多不同的生物信息学方法，如单核苷酸多态性（SNP）、核心基因组多位点序列分型（cgMLST）、全基因组多位点序列分型（wgMLST）或核心基因组（cgMLPPST）或泛基因组（wgMLPPST）上的多位点预测蛋白质序列分型（MLPPST）。目前，很少有这些不同的分析方法的比较研究。我们的目的是评估和比较不同的基因组方法，可以实施，以集群分离的单核细胞增生李斯特菌。食物来源的单核细胞增多症基因组代表了Anses集合的遗传多样性。然后使用强大的统计analysis.Results：传统的分型方法和基因组方法之间的向后可比性，揭示了一个近乎完美的一致性的树木进行比较。强调了在调用SNP时选择适当参考的重要性，尽管菌株之间的距离保持相同。分析还表明，wgMLST和cgMLST之间的系统发育树的拓扑结构非常相似。SNP与cgMLST或SNP与wgMLST方法的比较表明，SNP基因树的拓扑结构在统计学上相似，聚类结果基本一致。单核细胞增多症考虑到这两种方法在参考实验室中的实施方式各不相同，可比聚类是一个重要的观察结果。
Background/objectives: Whole genome sequencing (WGS) has proven to be a powerful subtyping tool for foodborne pathogenic bacteria like L. monocytogenes. The interests of genome-scale analysis for national surveillance, outbreak detection or source tracking has been largely documented. The genomic data however can be exploited with many different bioinformatics methods like single nucleotide polymorphism (SNP), core-genome multi locus sequence typing (cgMLST), whole-genome multi locus sequence typing (wgMLST) or multi locus predicted protein sequence typing (MLPPST) on either core-genome (cgMLPPST) or pan genome (wgMLPPST). Currently, there are little comparisons studies of these different analytical approaches. Our objective was to assess and compare different genomic methods that can be implemented in order to cluster isolates of L monocytogenes.Methods: The clustering methods were evaluated on a collection of 207 L. monocytogenes genomes of food origin representative of the genetic diversity of the Anses collection. The trees were then compared using robust statistical analyses.Results: The backward comparability between conventional typing methods and genomic methods revealed a near-perfect concordance. The importance of selecting a proper reference when calling SNPs was highlighted, although distances between strains remained identical. The analysis also revealed that the topology of the phylogenetic trees between wgMLST and cgMLST were remarkably similar. The comparison between SNP and cgMLST or SNP and wgMLST approaches showed that the topologies of phylogenic trees were statistically similar with an almost equivalent clustering.Conclusion: Our study revealed high concordance between wgMLST, cgMLST, and SNP approaches which are all suitable for typing of L. monocytogenes. The comparable clustering is an important observation considering that the two approaches have been variously implemented among reference laboratories.