Improved Subtyping of Staphylococcus aureus Clonal Complex 8 Strains Based on Whole-Genome Phylogenetic Analysis.
Improved Subtyping of Staphylococcus aureus Clonal Complex 8 Strains Based on Whole-Genome Phylogenetic Analysis.
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DOI：
10.1128/msphere.00464-17
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发表时间：
2018-05
期刊：
影响因子：
4.8
通讯作者：
Limbago BM
中科院分区：
文献类型：
--
作者：
Bowers JR;Driebe EM;Albrecht V;McDougal LK;Granade M;Roe CC;Lemmer D;Rasheed JK;Engelthaler DM;Keim P;Limbago BM
金黄色葡萄球菌是世界范围内社区和卫生保健环境中的主要人类病原体。金黄色葡萄球菌菌株的监测对于我们了解其传播和通知感染预防和控制非常重要。围绕金黄色葡萄球菌最流行的谱系之一克隆复合物8（CC 8）的菌株命名的混乱，以及目前用于分型金黄色葡萄球菌的工具的不精确性，使得监测和来源追踪变得困难，有时甚至是误导。在这项研究中，我们澄清了CC 8菌株名称，并提出了一个新的分型方案，CC 8分离株，是快速和易于使用。这种分型方案基于相对稳定的基因组标记，我们证明了其优于传统分型技术。该方案有可能大大改善金黄色葡萄球菌的流行病学调查。克隆复合物8（CC 8）中的金黄色葡萄球菌菌株，包括USA 300、USA 500和伊比利亚克隆，是美国卫生保健机构内外的流行病原体。随着CC 8菌株的进化和多样化，用于对CC 8菌株进行分型的方法变得过时，并且全基因组测序已经表明，一些菌株类型落入CC 8内的多个亚系。在这项研究中，我们试图澄清CC 8的菌株命名法，使用甲氧西林耐药金黄色葡萄球菌（MRSA）和甲氧西林敏感金黄色葡萄球菌（MSSA）基因组，基于全基因组序列遗传学对主要菌株类型进行分类。我们发现，几十年前的分离株的西班牙和伊比利亚的克隆组成了最基本的分支的主要CC 8谱系和CC 8的至少一个成功的谱系，主要由MSSA，分歧之前，其他知名的菌株类型USA 500和USA 300。我们还表明，USA 500型包括两个分支分开的先前描述的“加拿大流行性MRSA”菌株CMRSA 9，一个分支含有USA 500也包含USA 300分支，和USA 300 -0114菌株类型不是一个单系群。此外，我们提出了一种快速，简单的CC 8菌株分型方案，使用实时PCR检测，靶向来自我们的CC 8基因组的单核苷酸多态性（SNP），并显示使用更稳定的基因组标记的显着优势，基于传统的金黄色葡萄球菌分型技术的进化谱系。这种更准确和更容易获得的金黄色葡萄球菌分型系统可以改善监测，并更好地为这种非常重要的病原体的流行病学提供信息。重要性金黄色葡萄球菌是世界范围内社区和卫生保健环境中的主要人类病原体。金黄色葡萄球菌菌株的监测对于我们了解其传播和通知感染预防和控制非常重要。围绕金黄色葡萄球菌最流行的谱系之一克隆复合物8（CC 8）的菌株命名的混乱，以及目前用于分型金黄色葡萄球菌的工具的不精确性，使得监测和来源追踪变得困难，有时甚至是误导。在这项研究中，我们澄清了CC 8菌株名称，并提出了一个新的分型方案，CC 8分离株，是快速和易于使用。这种分型方案基于相对稳定的基因组标记，我们证明了其优于传统分型技术。该方案有可能大大改善金黄色葡萄球菌的流行病学调查。
Staphylococcus aureus is a major human pathogen worldwide in both community and health care settings. Surveillance for S. aureus strains is important to our understanding of their spread and to informing infection prevention and control. Confusion surrounding the strain nomenclature of one of the most prevalent lineages of S. aureus, clonal complex 8 (CC8), and the imprecision of current tools for typing S. aureus make surveillance and source tracing difficult and sometimes misleading. In this study, we clarify the CC8 strain designations and propose a new typing scheme for CC8 isolates that is rapid and easy to use. This typing scheme is based on relatively stable genomic markers, and we demonstrate its superiority over traditional typing techniques. This scheme has the potential to greatly improve epidemiological investigations of S. aureus. Strains of Staphylococcus aureus in clonal complex 8 (CC8), including USA300, USA500, and the Iberian clone, are prevalent pathogens in the United States, both inside and outside health care settings. Methods for typing CC8 strains are becoming obsolete as the strains evolve and diversify, and whole-genome sequencing has shown that some strain types fall into multiple sublineages within CC8. In this study, we attempt to clarify the strain nomenclature of CC8, classifying the major strain types based on whole-genome sequence phylogenetics using both methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) genomes. We show that isolates of the Archaic and Iberian clones from decades ago make up the most basal clade of the main CC8 lineages and that at least one successful lineage of CC8, made up mostly of MSSA, diverged before the other well-known strain types USA500 and USA300. We also show that the USA500 type includes two clades separated by the previously described “Canadian epidemic MRSA” strain CMRSA9, that one clade containing USA500 also contains the USA300 clade, and that the USA300-0114 strain type is not a monophyletic group. Additionally, we present a rapid, simple CC8 strain-typing scheme using real-time PCR assays that target single nucleotide polymorphisms (SNPs) derived from our CC8 phylogeny and show the significant benefit of using more stable genomic markers based on evolutionary lineages over traditional S. aureus typing techniques. This more accurate and accessible S. aureus typing system may improve surveillance and better inform the epidemiology of this very important pathogen. IMPORTANCE Staphylococcus aureus is a major human pathogen worldwide in both community and health care settings. Surveillance for S. aureus strains is important to our understanding of their spread and to informing infection prevention and control. Confusion surrounding the strain nomenclature of one of the most prevalent lineages of S. aureus, clonal complex 8 (CC8), and the imprecision of current tools for typing S. aureus make surveillance and source tracing difficult and sometimes misleading. In this study, we clarify the CC8 strain designations and propose a new typing scheme for CC8 isolates that is rapid and easy to use. This typing scheme is based on relatively stable genomic markers, and we demonstrate its superiority over traditional typing techniques. This scheme has the potential to greatly improve epidemiological investigations of S. aureus.