Genomic diversity and adaptive resistance mechanisms in Pseudomonas aeruginosa from bronchiectasis

ABSTRACT Pseudomonas aeruginosa 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 P . aeruginosa 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 mucA mutations present in 90.6% (29/32) of mucoid and 67.6% (23/34) of non-mucoid isolates. Most mucA 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 ( P = 0.0073), along with enhanced biofilm formation ( P < 0.0001) but reduced virulence in the Galleria mellonella infection model. Mechanistic studies revealed that cefiderocol resistance in mucoid P. aeruginosa was driven by synergistic interactions between alginate overproduction and mutations in iron-uptake regulatory genes, particularly Gly132 frameshift in pirR . Disruption of alginate biosynthesis (Δ algD ) and complementation of pirR in mucoid strains markedly restored cefiderocol susceptibility. These findings highlight the remarkable genomic diversity and adaptive resistance mechanisms of P. aeruginosa in NCFB, providing important insights into its persistence and therapeutic challenges in chronic airway infection. IMPORTANCE Understanding the adaptive mechanisms of Pseudomonas aeruginosa 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 pirR . These findings underscore the complex evolutionary pressures shaping P. aeruginosa persistence in NCFB and provide valuable insights into its resistance and virulence balance, offering potential targets for more effective therapeutic interventions.