Chromosomal bla NDM-1 embedded within mosaic genomic islands in Pseudomonas aeruginosa ST235 co-producing VIM-2 or KPC-2

Abstract

ABSTRACT Chromosomal integration of carbapenemase genes in Pseudomonas aeruginosa remains rare and poorly characterized. We report the genomic resolution of two extensively drug-resistant (XDR) Pseudomonas aeruginosa ST235 clinical isolates from Southern Brazil co-producing multiple carbapenemases. Hybrid Illumina-Nanopore sequencing revealed the rare chromosomal integration of bla NDM-1 within large mosaic genomic islands in both strains. Additionally, CCBH33512 harbored a chromosomal tandem duplication of bla VIM-2 , while CCBH33606 carried a 149-kb IncU-type plasmid bearing bla KPC-2 . These atypical architectures demonstrate structural adaptations that favor the stable persistence of extreme resistance determinants in clinical settings. IMPORTANCE The persistent threat of Pseudomonas aeruginosa lies in its structural adaptability. By sequencing extensively resistant clinical isolates, we revealed that extreme resistance genes are embedded within massive, complex genomic islands. These major structural rearrangements permanently lock resistance traits into the bacterial chromosome. Understanding this architectural evolution is vital, as it highlights how hospital pathogens use complex genetic strategies to ensure stable, long-term survival against last-resort antibiotics.