Isolation of an Extensively Drug-Resistant Pseudomonas aeruginosa exoS(+)/O4 Strain Belonging to the “High-Risk” Clone ST654 and Coproducer of NDM-1 and the Novel VIM-80

The aim of this study was to investigate the genomic features of an extensively drug-resistant (XDR) Pseudomonas aeruginosa isolate (P-469) emerging in Chile. Antibiotic susceptibility was determined by disk diffusion and “colistin agar” test. Whole-genome sequencing (WGS) was performed by the Illumina NextSeq 2000 platform, and epidemiologically and clinically relevant data (i.e., sequence-type, serotype, mobile genetic elements, virulome, resistome, plasmidome, prophages, and CRISPR-Cas systems) were retrieved using multiple bioinformatic tools. The P-469 strain displayed an XDR profile, remaining susceptible to colistin. Genomic analysis revealed that this isolate belonged to the “high-risk” clone ST654 (CC654), serotype O4, and genotype exoS(+). Strikingly, two CRISPR-Cas systems, five intact prophages sequences, and a broad resistome that included bla(NDM-1) and the novel bla(VIM-80) carbapenemase genes were predicted. Our results revealed the genomic characteristics of P. aeruginosa belonging to the high-risk clone ST654/O4 coproducing NDM-1 and VIM-80 in Chile, supporting that genomic surveillance is necessary to track the emergence and spread of epidemiologically successful WHO’s critical priority pathogens in order to prevent their rapid dissemination.