Genomic and phenotypic comparison of environmental and patient-derived isolates of Pseudomonas aeruginosa suggest that antimicrobial resistance is rare within the environment

Abstract

Patient-derived isolates of the opportunistic pathogen <i>Pseudomonas aeruginosa</i> are frequently resistant to antibiotics due to the presence of sequence variants in resistance-associated genes. However, the frequency of antibiotic resistance and of resistance-associated sequence variants in environmental isolates of <i>P. aeruginosa</i> has not been well studied. Antimicrobial susceptibility testing (ciprofloxacin, ceftazidime, meropenem, tobramycin) of environmental (<i>n</i>=50) and cystic fibrosis (<i>n</i>=42) <i>P. aeruginosa</i> isolates was carried out. Following whole genome sequencing of all isolates, 25 resistance-associated genes were analysed for the presence of likely function-altering sequence variants. Environmental isolates were susceptible to all antibiotics with one exception, whereas patient-derived isolates had significant frequencies of resistance to each antibiotic and a greater number of likely resistance-associated genetic variants. These findings indicate that the natural environment does not act as a reservoir of antibiotic-resistant <i>P. aeruginosa,</i> supporting a model in which antibiotic susceptible environmental bacteria infect patients and develop resistance during infection.