Genomic dissection of nosocomial multiclonal-outbreak by carbapenem-resistant Pseudomonas aeruginosa strains in a tertiary children’s hospital in Japan

Abstract

Objective: Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is an important antimicrobial-resistant bacterial pathogen. We observed an increase in the detection rate of CRPA isolates at a tertiary children’s hospital in Japan. We suspected an outbreak of a clonal CRPA strain and conducted a genetic study to elucidate the resistance mechanism and possible spread of CRPA strains. Methods: For 25 CRPA isolates, antimicrobial susceptibilities to eight antibiotics that are generally used for P. aeruginosa infection were tested. Whole genomes of the isolates were sequenced via next-generation sequencing analysis and subjected to comparative lineage analysis, AMR gene profiling, and Bayesian inference of transmission routes. Results: The genomes of the strains were not monoclonal but comprised multiple lineages with various sequence types. The CRPA isolates had a dysfunctional oprD gene, which is an importer of carbapenem; however, specific nucleotide mutations varied by lineage. Furthermore, administration of antimicrobials against CRPA, such as piperacillin, ceftazidime, and aztreonam, was immediately followed by resistance to these antimicrobials, and in these cases, some unique single nucleotide variants in lasR were identified. Conclusions: Molecular epidemiological data have revealed a multilineage outbreak of P. aeruginosa strains that independently developed carbapenem resistance. This emphasises the rapid evolution of antimicrobial resistance in P. aeruginosa in response to the antimicrobial doses administered to patients who are hospitalised.

Keywords

• Pseudomonas aeruginosa
• Nosocomial infection
• Antimicrobial resistance
• Whole genome sequencing
• Bayesian inference