Resistome, virulome and phage defense systems of a hypervirulent XDR Pseudomonas aeruginosa ST357

Introduction: We aimed to perform a comprehensive genomic and phenotypic characterization of Pseudomonas aeruginosa clinical isolate ID-047/23, focusing on its resistance mechanisms, virulence factors, and defense systems against mobile genetic elements (MGEs). Materials and methods: The study utilized phenotypic antimicrobial susceptibility testing and high-throughput genomic sequencing to identify the sequence type (ST), resistome, virulome, and presence of MGEs and defense systems. Results: Lineage and Resistance: Isolate ID-047/23 was identified as the high-risk clone ST357 with an extensively drug-resistant (XDR) profile, susceptible only to polymyxin B. Genomic analysis revealed a complex resistome featuring the carbapenemase gene blaNDM-1 (within a Tn125 transposon) and the extended-spectrum β-lactamase (ESBL) gene blaVEB-1. This represents a unique co-occurrence for this lineage in Brazil. In terms of virulence and persistence, the isolate carries a hypervirulent genotype (exoU+/exoS-), Type III and VI secretion systems, and biofilm determinants (pel, psl). Pathogenicity is further enhanced by the integration of Pseudomonas aeruginosa pathogenicity island 1 (PAPI-1) and Pseudomonas aeruginosa pathogenicity island 2 (PAPI-2). The detection of active Type I-F clustered regularly interspaced short palindromic repeats (CRISPR) and associated proteins (Cas) (CRISPR-Cas) and restriction-modification (R-M) systems indicates a robust, multi-layered defense against foreign DNA. Conclusions: Isolate ID-047/23 is a highly adaptable and virulent XDR clone. The presence of sophisticated anti-phage defense systems suggests significant barriers to developing phage-based therapies. These findings underscore the urgent need for enhanced surveillance and the development of alternative therapeutic strategies to manage high-risk P. aeruginosa clones.