Genomic and Phylogenomic Characterization of Carbapenem-resistant Pseudomonas aeruginosa ‘High-risk’ Clone O4/ExoS+/ST654 Circulating in Chilean Hospitals

Abstract

Introduction: Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a serious threat to public health. Globally, carbapenemases-producing CRPA isolates mainly belong to ‘high-risk’ clones; however, the molecular epidemiology of CRPA isolates circulating in Chile are scarce, where this pathogen is the main aetiological agent of ventilator-associated pneumonia. Objectives: To characterize the phylogenomics and molecular features of ST654 CRPA isolates collected in Chile between 2016 and 2022. Methods: Eighty-nine CRPA isolates collected in different Chilean hospitals from clinical specimens between 2005 and 2022 were analysed. Antibiotic susceptibility tests and carbapenemases production were carried out on the CRPA ST654 isolates. Also, they were subjected to whole-genome sequencing, from which in silico analyses were performed. Results: Thirty-four strains (38.2%) belonged to the ST654 high-risk clone, being the most predominant lineage of the collection. Most of these isolates belonged to a subclade including KPC producers that also clustered with strains from Argentina and the United States, whereas few VIM and NDM co-producers clustered in two different smaller subclades. The isolates exhibited a broad resistome encompassing genes mediating resistance to several other clinically relevant drugs. Additionally, all the 34 ST654 isolates were ExoS+ as a virulence factor and associated to the O4-serotype. Conclusions: Our report represents the most comprehensive phylogenomic study of a CRPA high-risk clone ST654 to date. Our analyses suggest that this lineage is undergoing a divergent evolutionary path in Chile, because most of the isolates were KPC producers and were O4 serotype, differing from previous descriptions, which underline the relevance of performing molecular surveillance on this pathogen.

Keywords

• Carbapenem-resistant Pseudomonas aeruginosa
• Carbapenemases
• Molecular epidemiology
• ST654
• ‘High-risk’ clones