In recent years, numerous outbreaks of multidrug‐resistant Pseudomonas aeruginosa have been reported across the world. Once an outbreak occurs, besides routinely testing isolates for susceptibility to antimicrobials, it is required to check their virulence genotypes and clonality profiles. Replacing pulsed‐field gel electrophoresis DNA fingerprinting are faster, easier‐to‐use, and less expensive polymerase chain reaction (PCR)‐based methods for characterizing hospital isolates. P. aeruginosa possesses a mosaic genome structure and a highly conserved core genome displaying low sequence diversity and a highly variable accessory genome that communicates with other Pseudomonas species via horizontal gene transfer. Multiple‐locus variable‐number tandem‐repeat analysis and multilocus sequence typing methods allow for phylogenetic analysis of isolates by PCR amplification of target genes with the support of Internet‐based services. The target genes located in the core genome regions usually contain low‐frequency mutations, allowing the resulting phylogenetic trees to infer evolutionary processes. The multiplex PCR‐based open reading frame typing (POT) method, integron PCR, and exoenzyme genotyping can determine a genotype by PCR amplifying a specific insertion gene in the accessory genome region using a single or a multiple primer set. Thus, analyzing P. aeruginosa isolates for their clonality, virulence factors, and resistance characteristics is achievable by combining the clonality evaluation of the core genome based on multiple‐locus targeting methods with other methods that can identify specific virulence and antimicrobial genes. Software packages such as eBURST, R, and Dendroscope, which are powerful tools for phylogenetic analyses, enable researchers and clinicians to visualize clonality associations in clinical isolates.

中文翻译：

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临床高危铜绿假单胞菌菌株的分子流行病学：实用概述。

近年来，全世界已报道了多起具有多重耐药性的铜绿假单胞菌的暴发。一旦发生暴发，除了要常规检测分离株对抗菌药物的敏感性外，还需要检查其毒力基因型和克隆性。取代脉冲场凝胶电泳DNA指纹图谱可更快，更易于使用且更便宜，基于聚合酶链反应（PCR）的方法可用于鉴定医院分离株。铜绿假单胞菌具有镶嵌基因组结构和高度保守的核心基因组，显示出较低的序列多样性以及与其他假单胞菌通讯的高度可变的辅助基因组物种通过水平基因转移。多位点可变数串联重复分析和多位点序列分型方法允许在基于Internet的服务的支持下，通过PCR扩增靶基因，对分离株进行系统发育分析。位于核心基因组区域的目标基因通常包含低频突变，从而使最终的系统发育树能够推断进化过程。基于多重PCR的开放阅读框分型（POT）方法，整合子PCR和外切酶基因分型可以使用单个或多个引物组通过PCR扩增辅助基因组区域中的特定插入基因来确定基因型。因此，分析铜绿假单胞菌通过将基于多位点靶向方法的核心基因组的克隆性评估与其他可识别特定毒力和抗菌素基因的方法相结合，可以实现分离株的克隆性，毒力因子和耐药特性。eBURST，R和Dendroscope等软件包是系统发育分析的强大工具，使研究人员和临床医生可以直观地看到临床分离株中的克隆性关联。