Dynamics of Adaptive Microevolution of Hypermutable Pseudomonas aeruginosa during Chronic Pulmonary Infection in Patients with Cystic Fibrosis

Abstract

BACKGROUND: In patients with cystic fibrosis (CF), the emergence of hypermutable Pseudomonas aeruginosa drives the selection of P. aeruginosa variants that are efficiently adapted to the inflamed lungs of these patients. OBJECTIVE: To provide a detailed survey of adaptive changes in the physiology of P. aeruginosa during chronic lung infection in patients with CF. METHODS: We performed a comparative proteome and transcriptome analysis of sequential, isogenic isolates recovered over a period of 3-5 years from 3 selected patients with CF. The isolates analyzed included both those with high mutation rates and defects in their methyl-directed mismatch repair system (hereafter, "mutators") and those without such changes (hereafter, "nonmutators"). RESULTS: In addition to attenuation of virulence, the P. aeruginosa adaptation process predominantly affects metabolic pathways. In mutator isolates recovered from patients with end-stage CF lung disease, we observed increases in the transcripts of genes or proteins involved in the metabolism of fatty acids and amino acids and the generation of energy. Of particular interest is the increased expression of genes involved in the following pathways and processes: (1) the anaerobic arginine-deiminase pathway, (2) anaerobic respiration (e.g., nitrate-uptake protein OprF, azurin, and cytochrome c551 peroxidase), (3) microaerobic respiration (e.g., cytochrome oxidase cbb3), and (4) the tricarboxylic acid cycle and glyoxylate shunt. Strikingly, increased transcription of the anaerobic regulator gene anr correlates with the up-regulation of ANR-dependent genes. CONCLUSIONS: These changes indicate an adaptive shift toward constitutive expression of genes required for growth under the nutritional and microaerobic conditions created by suppurative secretions in the lungs of patients with CF. In addition, these results provide important clues about the persistence strategies used by P. aeruginosa during progressive CF lung disease.