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 (LRTIs) in a tertiary care teaching hospital from 2021 to 2023. Consecutive inpatients who initially had CSPA LRTIs and then had 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. Each inpatient was matched with three control patients who continued to have 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 core-genome single nucleotide polymorphism analysis confirmed that the CRPA isolate evolved directly from the ancestral CSPA isolate within the host, with a median evolution lag time of 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 the carbapenemase gene blaVIM-2. Notably, virulence gene profiles of great clinical concern remained stable throughout the evolutionary process. The quantity of meropenem use during the evolution lag time [adjusted odds ratio (aOR), 1.72, 95% confidence interval (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 compromising virulence. These findings highlight the urgent need for optimized carbapenem stewardship to prevent the emergence of carbapenem resistance during PA LRTI treatment.