High-resolution analysis by whole genome sequencing of an international lineage (ST-111) of Pseudomonas aeruginosa associated with metallo-carbapenemases in the United Kingdom. Pseudomonas study

Whole genome sequencing (WGS) was carried out on 87 isolates of ST-111 of Pseudomonas aeruginosa collected between 2005 and 2014 from 65 patients and 12 environmental isolates from 24 hospital laboratories across the United Kingdom on an Illumina HiSeq. Most isolates (73) carried VIM-2, but others carried IMP (IMP-1 or IMP-13) (5) or NDM-1 (1); one isolate had VIM-2 and IMP-18 and 7 carried no metallo-beta-lactamase (MBL) gene. Single nucleotide polymorphism analysis divided the isolates into distinct clusters, with the NDM-1 isolate an outlier and the IMP isolates and 6 MBL-negative isolates clustering separately from the main set of 72 VIM-2 isolates. Within the VIM-2 set, there were at least 3 distinct clusters, including a tightly clustered set of isolates from 3 hospital laboratories consistent with an outbreak from a single introduction that was quickly brought under control and a much broader set dominated by isolates from a long-running outbreak in a London hospital, also including isolates from 7 other hospital laboratories in London and South East England, likely seeded from an environmental source, requiring different control measures. Bayesian Evolutionary Analysis indicated all the isolates shared a common ancestor dating back some 50 years (1960s), with the main VIM-2 set separating approximately 20 to 30 years ago. Accessory gene profiling revealed blocks of genes associated with particular clusters, with some having high similarity (≥95 %) to bacteriophage genes. WGS of international lineages such as ST-111 that are widely found provides the necessary resolution to inform epidemiological investigations and intervention policies.

本研究对2005年至2014年间采集自英国24家医院实验室的65名患者来源的87株铜绿假单胞菌（Pseudomonas aeruginosa）ST-111型菌株，以及12株环境分离株，采用Illumina HiSeq平台完成全基因组测序（Whole Genome Sequencing, WGS）。其中73株携带VIM-2型金属β-内酰胺酶（metallo-beta-lactamase, MBL）基因，其余菌株分别携带IMP型（IMP-1或IMP-13）基因（共5株）或NDM-1型基因（1株）；另有1株同时携带VIM-2与IMP-18基因，剩余7株未携带任何MBL基因。单核苷酸多态性（Single Nucleotide Polymorphism, SNP）分析将所有分离株划分为多个独立聚类簇：携带NDM-1基因的菌株为独立外群，携带IMP型基因的菌株与6株MBL阴性菌株单独聚类，与由72株VIM-2型菌株构成的主要聚类组相互分离。在VIM-2型菌株的主要聚类组内，至少存在3个独立聚类簇：其中一组为来自3家医院实验室的紧密聚集菌株，对应一次经单次感染引入后迅速得到控制的暴发疫情；另一组规模更为庞大，主要由伦敦某医院长期暴发疫情的分离株主导，同时包含伦敦及英格兰东南部另外7家医院实验室的分离株，该组大概率起源于某环境污染源，需采取差异化的防控措施。贝叶斯进化分析（Bayesian Evolutionary Analysis）显示，所有分离株共享一个可追溯至约50年前（20世纪60年代）的共同祖先，而主要的VIM-2型菌株聚类组则于约20至30年前分化形成。附属基因谱分析显示，不同聚类簇携带特征性基因模块，其中部分模块与噬菌体（bacteriophage）基因的相似度≥95%。对广泛传播的国际流行谱系（如ST-111）开展全基因组测序，可为流行病学调查与干预策略制定提供必要的分型分辨率支撑。