Genomic and phenotypic adaptation of imipenem-resistant Pseudomonas aeruginosa during chronic infection in a COPD patient

ABSTRACT Pseudomonas aeruginosa airway colonization and infection are major drivers of chronic obstructive pulmonary disease (COPD) acute exacerbations, yet its adaptive evolution in the COPD airway remains poorly understood. Here, six serial P. aeruginosa strains were isolated over a 5-month interval from a single COPD patient: two initial isolates (SCPa03-1 and SCPa03-2) from one sputum sample and four subsequent isolates (SCPa12-1, SCPa12-2, SCPa12-3, and SCPa12-4) from another. Of them, SCPa03-1, SCPa12-1, and SCPa12-2 exhibited a non-mucoid phenotype, while SCPa03-2, SCPa12-3, and SCPa12-4 were mucoid. All isolates were resistant to most β -lactam antibiotics, including imipenem, but susceptible to amikacin and gentamicin. Notably, three mucoid strains were susceptible to meropenem. Genomic and phylogenetic analysis revealed that all isolates were clonally related, belonged to ST274, and were closely related to the globally prevalent high-risk ST274 clone. Sequence analysis and qRT-PCR suggested that their imipenem resistance may be associated with ampC overexpression and oprD mutations, while reduced ciprofloxacin susceptibility likely stemmed from gyrA / gyrB mutations and acquisition of crpP -harboring ICEs. Despite a shared mucA frameshift mutation, secondary mutations in prc (SCPa03-1) and algU (SCPa12-1, SCPa12-2) likely accounted for the non-mucoid phenotype. Relative to PAO1, all isolates showed reduced growth, diminished pyoverdine, attenuated Galleria mellonella virulence, and increased pyocyanin. Besides, three mucoid strains exhibited slower growth, reduced serum resistance, and attenuated virulence compared with non-mucoid counterparts, suggesting adaptive trade-off during host adaptation. Four late-stage isolates showed enhanced pyoverdine production and improved growth under iron limitation, indicating progressive airway adaptation to the iron-restricted airway niche. IMPORTANCE Pseudomonas aeruginosa is a leading cause of chronic airway infection and poses a severe clinical threat when it develops carbapenem resistance. While the adaptive evolution of P. aeruginosa has been well characterized in cystic fibrosis, its evolutionary patterns during chronic infection in patients with chronic obstructive pulmonary disease (COPD) remain poorly understood. Here, we analyzed six imipenem-resistant P. aeruginosa isolates sequentially recovered from a single COPD patient. Integrated genomic and phenotypic analyses demonstrated that the high-risk clone ST274 diversified extensively within the host, with genetic variations strongly associated with enhanced airway persistence. These findings advance our understanding of how carbapenem-resistant P. aeruginosa adapts during chronic COPD infection and provide new insights into resistance evolution and adaptive strategies that may inform the control of drug-resistant chronic respiratory infections.