Genomic diversity and adaptive resistance mechanisms in <i>Pseudomonas aeruginosa</i> from bronchiectasis

<i>Pseudomonas aeruginosa</i> is a predominant colonizer of airways in non-cystic fibrosis bronchiectasis (NCFB), yet its adaptive mechanisms remain poorly understood. This study investigates the genetic characteristics, virulence variation, and resistance mechanisms of 66 <i>P</i>. <i>aeruginosa</i> isolates derived from NCFB patients. Whole-genome sequencing revealed extensive genetic diversity, encompassing 53 sequence types and a predominance of the O6 serotype (30/66, 45.5%). Phylogenetic analysis indicated that most NCFB isolates were acquired independently, with limited evidence of transmission. Extensive loss-of-function mutations were identified, with <i>mucA</i> mutations present in 90.6% (29/32) of mucoid and 67.6% (23/34) of non-mucoid isolates. Most <i>mucA</i> mutations were frameshift variants, predominantly at codon 144 (Ala144fs), indicating the selective advantage of this site in driving alginate overproduction during chronic airway infection. Virulence gene profiling demonstrated a highly conserved core repertoire but considerable variability in type VI secretion and pyoverdine systems. Notably, mucoid isolates exhibited significantly higher cefiderocol MICs compared to non-mucoid isolates (<i>P</i> = 0.0073), along with enhanced biofilm formation (<i>P</i> < 0.0001) but reduced virulence in the <i>Galleria mellonella</i> infection model. Mechanistic studies revealed that cefiderocol resistance in mucoid <i>P. aeruginosa</i> was driven by synergistic interactions between alginate overproduction and mutations in iron-uptake regulatory genes, particularly Gly132 frameshift in <i>pirR</i>. Disruption of alginate biosynthesis (Δ<i>algD</i>) and complementation of <i>pirR</i> in mucoid strains markedly restored cefiderocol susceptibility. These findings highlight the remarkable genomic diversity and adaptive resistance mechanisms of <i>P. aeruginosa</i> in NCFB, providing important insights into its persistence and therapeutic challenges in chronic airway infection.IMPORTANCEUnderstanding the adaptive mechanisms of <i>Pseudomonas aeruginosa</i> in non-cystic fibrosis bronchiectasis (NCFB) is critical for improving treatment strategies. This study reveals substantial genomic diversity and highlights alginate overproduction as a key feature of chronic adaptation. Notably, we uncover a novel resistance mechanism involving synergistic interactions between alginate production and mutations in iron-uptake regulators, particularly <i>pirR</i>. These findings underscore the complex evolutionary pressures shaping <i>P. aeruginosa</i> persistence in NCFB and provide valuable insights into its resistance and virulence balance, offering potential targets for more effective therapeutic interventions.