Rapid and robust phylotyping of spa t003, a dominant MRSA clone in Luxembourg and other European countries.
Rapid and robust phylotyping of spa t003, a dominant MRSA clone in Luxembourg and other European countries.
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DOI：
10.1186/1471-2334-13-339
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发表时间：
2013-07-23
影响因子：
3.7
通讯作者：
Even J
中科院分区：
文献类型：
--
作者：
Engelthaler DM;Kelley E;Driebe EM;Bowers J;Eberhard CF;Trujillo J;Decruyenaere F;Schupp JM;Mossong J;Keim P;Even J
spa分型是欧洲耐甲氧西林金黄色葡萄球菌（MRSA）的常见基因分型工具。鉴于优势克隆的高流行率，SPA分型被证明在区分爆发分离株与背景分离株的能力方面是有限的。需要采用新的分子工具来改善占优势的本地MRSA菌株的亚型分型（例如，SPA型T003）。通过对来自卢森堡的40个MRSA全基因组进行序列分析，将系统发生关键或典型SNP（can-SNP）确定为亚型分型靶点。实时PCR检测是围绕目标SNP设计的，并使用240个先前亚型和流行病学特征的卢森堡MRSA分离株的储存库进行验证，其中包括153个社区和医院分离株，69个来自长期护理（LTC）设施的分离株和21个前瞻性分析的MRSA分离株。还通过全基因组SNP分型（WGST）分析了选定的分离株，以与SNP测定和其他分型技术进行比较。开发并验证了14种实时PCR检测方法，包括两种用于确定spa t003或t008是否存在的检测方法。其他12个检测试剂盒成功提供了t003亚型内的高度分辨率。LTC设施分离株的WGST分析提供了比其他分型工具更高的分辨率，识别出指示LTC设施内正在进行的传播的簇。基于canSNP的PCR测定可用于局部水平的MRSA分型，特别是在存在一个或多个显性克隆的情况下。这里设计的检测方法可以很容易地适用于研究西欧其他地区的t003 MRSA菌株。WGST提供了比其他打字方法更好的分辨率。
spa typing is a common genotyping tool for methicillin-resistant Staphylococcus aureus (MRSA) in Europe. Given the high prevalence of dominant clones, spa-typing is proving to be limited in its ability to distinguish outbreak isolates from background isolates. New molecular tools need to be employed to improve subtyping of dominant local MRSA strains (e.g., spa type t003). Phylogenetically critical, or canonical, SNPs (can-SNPs) were identified as subtyping targets through sequence analysis of 40 MRSA whole genomes from Luxembourg. Real-time PCR assays were designed around target SNPs and validated using a repository of 240 previously sub-typed and epidemiologically characterized Luxembourg MRSA isolates, including 153 community and hospital isolates, 69 isolates from long term care (LTC) facilities, and 21 prospectively analyzed MRSA isolates. Selected isolates were also analyzed by whole genome SNP typing (WGST) for comparison to the SNP assays and other subtyping techniques. Fourteen real-time PCR assays were developed and validated, including two assays to determine presence of spa t003 or t008. The other twelve assays successfully provided a high degree of resolution within the t003 subtype. WGST analysis of the LTC facility isolates provided greater resolution than other subtyping tools, identifying clusters indicative of ongoing transmission within LTC facilities. canSNP-based PCR assays are useful for local level MRSA phylotyping, especially in the presence of one or more dominant clones. The assays designed here can be easily adapted for investigating t003 MRSA strains in other regions in Western Europe. WGST provides substantially better resolution than other typing methods.