blaGES-producing ST654 comprises a quarter of all carbapenem-resistant Pseudomonas aeruginosa in blood isolates from 15 hospitals

Abstract

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) are of major clinical concern. We analyzed 85 P. aeruginosa blood isolates non-susceptible to carbapenems collected during 2021-2023 from 15 medical centers in Israel. We aimed to determine the prevalence of high-risk clones, examine clonality, test antibiotic susceptibility, and assess the presence of acquired resistance genes, including carbapenemases. Whole-genome sequencing was performed using Illumina sequencing technology. Susceptibly was determined using the broth microdilution method. In the entire sample, 43.5% were high-risk clones. A main clade (27.1% of isolates) found in multiple hospitals comprised 19 isolates belonging to the high-risk ST654 clone and four closely related isolates. The isolates in this main clade harbored a broad set of resistance genes, including GES-type genes, and 91% had a mutated outer membrane protein (OprD). Isolates in the main clade were uniformly tobramycin (TOB) resistant and 83% were ceftolozane/tazobactam resistant. In the entire sample, we found high resistance to most antipseudomonal agents, including new beta-lactam/beta-lactamase inhibitor combinations. No uniform susceptibility to an antipseudomonal agent was found. Carbapenemases were carried by 9.4% of isolates (5.9% bla_GES-5 and 3.5% bla_NDM-1) and oprD was mutated in 67% of isolates. Thus, the epidemiology of CRPA is explained by a combination of clonal expansion of a dominant high-risk clade and sporadic occurrence of mutated strains. Our findings highlight the importance of susceptibility testing using a wide panel of antibiotics when CRPA is detected. Prevention measures tracking and controlling emerging high-risk clades and clones are crucial to limit the spread of CRPA.

Keywords: Pseudomonas aeruginosa; antimicrobial resistance; carbapenemase; surveillance; whole-genome sequencing.

Fig 1

Heat map presenting the phenotype and the genotype of the sample: presence/absence of antibiotic resistance genes (i.e., ARG pattern), ST type, phylogenetic tree clade, and phenotypic resistance. The yellow square outlines the main clade of 23 isolates. The tree clade column represents the division of tree clades according to the phylogenetic tree of the entire sample from Fig. S1. ARG, antibiotic resistance genes; ST, sequencing type; AZT, aztreonam; C/T, ceftolozane/tazobactam; COL, colistin; P/T4, piperacillin/tazobactam; IMI, imipenem; IMR, imipenem/relebactam; FEP, cefepime; CAZ, ceftazidime; CZA, ceftazidime/avibactam; AMI, amikacin; FOS+, fosfomycin+glucose-6-phosphate; MEM, meropenem; TOB, tobramycin; MEV, meropenem/vaborbactam; GEN, gentamicin; CIP, ciprofloxacin.

Fig 2

Phylogenetic tree of the main clade of 23 carbapenem-resistant P. aeruginosa isolates and controls.

Fig 3

Phenotypic resistance profile of 85 carbapenem-non-susceptible P. aeruginosa isolates. The numbers above each column represent the percentage of isolates that were resistant. R, resistant; I, intermediate; S, susceptible.

Fig 4

Prevalence of resistance genes among 85 carbapenem-non-susceptible P. aeruginosa isolates.