SRA

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.