Dynamic evolution of imipenem/relebactam resistance in a KPC-producing Klebsiella pneumoniae from a single patient during ceftazidime/avibactam-based treatments

Abstract

Objectives The novel carbapenem/β-lactamase inhibitor combination imipenem/cilastatin/relebactam has been developed for the treatment of infections due to carbapenemase-producing Enterobacteriaceae (CPE). Herein, we describe the in vivo evolution of imipenem/cilastatin/relebactam resistance in longitudinal intra-patient Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae (KPC-Kp) strains isolated from a patient following ceftazidime/avibactam-based treatments. Methods WGS analysis was performed on KPC-Kp strains isolated at different times and during antimicrobial treatments from the same patient. Genome assemblies were performed using a hybrid approach using Illumina iSeq 100 and Minion Oxford Nanopore platforms. Subpopulation analysis and allele frequency determination was performed by mapping Illumina reads to blaKPC. Results During antimicrobial treatment, resistance to ceftazidime/avibactam was observed following 16 days of antimicrobial therapy. WGS results showed that all KPC-Kp exhibited a low SNP rate of divergence, belonged to ST512 and shared similar antimicrobial resistance and porin gene patterns. Genetic analysis demonstrated that the first ceftazidime/avibactam-resistant KPC-Kp strain harboured a blaKPC-53 gene in a Tn4401 transposon moved from IncFII(K) to a 43 kb IncX3 plasmid, while a imipenem/cilastatin/relebactam-resistant strain exhibited two copies of the Tn4401 transposon in IncFII(K) and IncX3 plasmids, resulting in an increased blaKPC copy number. Of note, frequency analysis demonstrated that imipenem/cilastatin/relebactam-resistant KPC-Kp consisted of mixed subpopulations harbouring blaKPC-40 and blaKPC-53 alleles. Conclusions Our results show the in vivo evolution of genetic rearrangement conferring resistance to imipenem/relebactam in a patient with KPC-Kp infection and treated with different ceftazidime/avibactam-based treatments. The rapid development of mutations and the high adaptability of its genome highlight the potential threat of KPC-Kp.

Impact ofompk36genotype and KPC subtype on thein vitroactivity of ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam against KPC-producingK. pneumoniaeclinical isolates

“…Thus, isolates harbouring a GD duplication may not demonstrate outright resistance to imipenem/relebactam unless other mechanisms, such as an increased bla KPC copy number are present. 26 , 27 …”

“…Most notably, we did not study KPC-3-producing isolates that harboured GD duplications; however, comparable findings for KPC-3 have been reported previously. 26 , 27 , 29 We also did not fully characterize ompK36 mutations that were classified as ‘other’ mutations. Although ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam MICs were generally not impacted unless GD duplication or IS 5 mutations were present, it does not preclude the possibility that other loss-of-function mutations in ompK36 may manifest in a similar impact on these agents.…”

In vivo adaptive antimicrobial resistance in Klebsiella pneumoniae during antibiotic therapy

“…More attention should be paid to the resistance of these types of antimicrobials. Besides, it is nerve-wracking to find that the antimicrobial resistance in K. pneumoniae is changing rapidly in response to in vivo microenvironmental stress during antimicrobial therapy ( MacKenzie et al, 1997 ; Gaibani et al, 2022 ).…”

Comparison of Broth Microdilution, Disk Diffusion and Strip Test Methods for Cefiderocol Antimicrobial Susceptibility Testing on KPC-Producing Klebsiella pneumoniae

“…However, none of the new combinations of βL-βLICs are stable against metallo-β-lactamases [ 5 ]. At the same time, emerging resistance against these novel drug combinations has been recently reported [ 6 , 7 ].…”