Replicon sequence typing of IncF plasmids carrying virulence and resistance determinants
Replicon sequence typing of IncF plasmids carrying virulence and resistance determinants
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DOI：
10.1093/jac/dkq347
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发表时间：
2010-12-01
影响因子：
5.2
通讯作者：
Carattoli, Alessandra
中科院分区：
文献类型：
--
作者：
Villa, Laura;Garcia-Fernandez, Aurora;Carattoli, Alessandra
临床肠杆菌中常见的INCF质粒与相关的耐药基因和毒力基因的传播有关。这些质粒的大小通常是不同的，携带多个复制子，技术上的困难会影响限制性片段长度多态性分析对相关质粒的比对和检测。我们设计了一种基于序列的快速分型方案，将该质粒家族的成员归入同质组，比较现有的INCF复制子序列，确定不同的INCF复制子等位基因的组合是这些质粒支架的区分特征。建立了一种基于PCR扩增和INCF复制子序列分型的INCF分型方法。利用该分型系统对不同来源和不同地理来源的菌株中携带抗性和/或毒力基因的INCF质粒进行了检测，设计了一种复制子序列分型(RST)方案来区分INCF质粒变异体。在收集的INCF质粒上进行测试，结果表明，该系统不仅可以区分携带相同抗性基因(即Bla(CTX-M-15)基因)的质粒，而且可以识别与之密切相关的毒力质粒(即IncFIme质粒)。基于PCR的复制子分型(PBRT)体系也得到了更新，加入了新的引物对，以识别沙门氏菌、克雷伯氏菌和耶尔森氏菌的INCF质粒.根据同质组的系统发育关系，RST识别INCF质粒并对其进行亚类分类的能力有助于分析它们在自然界的分布和发现它们的进化起源.
IncF plasmids are frequently encountered in clinical enterobacterial strains associated with the dissemination of relevant antimicrobial resistance and virulence genes. These plasmids are usually heterogeneous in size and carry multiple replicons, and technical difficulties can impair the comparison and detection of related plasmids by restriction fragment length polymorphism analysis. We devised a rapid sequence-based typing scheme to categorize the members of this plasmid family into homogeneous groups.We compared the available IncF replicon sequences, identifying the combination of the different IncF replicon alleles as the discriminating characteristic of these plasmid scaffolds. An IncF typing method based on PCR amplification and sequence typing of the IncF replicons was devised. A collection of IncF plasmids carrying resistance and/or virulence genes, identified in strains from different sources and geographical origins, was tested with this typing system.We devised a replicon sequence typing (RST) scheme discriminating IncF plasmid variants. This system was tested on the collection of IncF plasmids, demonstrating that it was useful for the discrimination of plasmids carrying the same resistance gene (i.e. the bla(CTX-M-15) gene), but also recognized strictly related virulence plasmids (i.e. IncFIme plasmids). The PCR-based replicon typing (PBRT) system was also updated by including new primer pairs to allow the identification of the Salmonella, Klebsiella and Yersinia IncF plasmids.The ability to recognize and sub-categorize IncF plasmids by RST in homogeneous groups on the basis of their phylogenetic relatedness can be helpful in analysing their distribution in nature and discovering their evolutionary origin.