Mechanisms of and risk factors for in vivo evolution of carbapenem resistance in Pseudomonas aeruginosa causing lower respiratory tract infections

Objectives To elucidate the molecular mechanisms and epidemiological risk factors driving the in vivo evolution from carbapenem susceptible Pseudomonas aeruginosa (CSPA) to carbapenem resistant PA (CRPA). Methods We conducted a retrospective cohort study among inpatients with PA lower respiratory tract infections (PA LRTIs) in a tertiary care teaching hospital in 2021-2023. Consecutive inpatients with CSPA LRTIs first and then with CRPA LRTIs during hospitalization were enrolled. For each pair of CSPA and CRPA isolates recovered from the inpatients, whole genome sequencing followed by comparative genomic analysis was performed to identify phylogenetics, resistance and virulence determinants. One inpatient was matched with 3 controls who remained CSPA LRTIs by sex, age, ward, and admission date. Conditional logistic regression modeling was used to determine risk factors for in vivo carbapenem resistance evolution. Results A total of 30 inpatients were included. In 25 of the 30 patients, phylogenetic and cgSNP analysis confirmed that the CRPA isolate evolved directly from the ancestral CSPA isolate within host with a median evolution lag time 25 days (range: 3-138 days). CRPA isolates showed low resistance to colistin (0.00%) and aminoglycosides (3.33-16.67%). Mutations were common in evolved CRPA isolates, with the most common mutations observed in oprD (15/25, 60.00%), vgrG (13/25, 52.00%), and ccoN1 (11/25, 44.00%). Only one CRPA isolate acquired carbapenemase gene bla VIM-2 . Notably, virulence gene profiles of great clinical concern remained stable throughout the evolutionary process. Quantity of meropenem use during the evolution lag time [adjusted odds ratio (aOR) 1.72, 95% confidence interval (95%CI) 1.19-2.48, P =0.004)] was the only independent risk factor for in vivo carbapenem resistance evolution. Conclusions In vivo evolution of carbapenem resistance in PA LRTIs is a rapid process primarily driven by meropenem selection pressure through chromosomal mutations without compromise of virulence. These findings highlight the urgent need for optimized carbapenem stewardship to prevent the emergence of carbapenem resistance during PA LRTIs treatment.