Genomic and molecular characterisation of a KPC-producing Klebsiella pneumoniae clinical isolate resistant to meropenem-vaborbactam, imipenem-relebactam, and ceftazidime-avibactam
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Published version
Author(s)
Type
Journal Article
Abstract
Background
Resistance to carbapenems and third-generation cephalosporins is increasing in Klebsiella pneumoniae
globally, restricting therapeutic options. The β-lactam/β-lactamase inhibitor combinations are widely
used to circumvent β-lactamase-mediated resistance. In 2021, an unusual K. pneumoniae clinical isolate, KpMVR1, was recovered from a hospitalised patient in England, exhibiting resistance to meropenem-vaborbactam, imipenem-relebactam, and ceftazidime-avibactam. To investigate this phenomenon, we characterised the genome and antimicrobial susceptibility of KpMVR1 alongside two clonally related isolates susceptible to all three β-lactam/β-lactamase inhibitor combinations: KpMVS1, collected from the same patient 42 days earlier, and KpMVS2, from another patient in the same hospital.
Methods
Illumina and MinION whole-genome sequencing were conducted for these three isolates, followed by
hybrid genome assembly. Annotated genome assemblies were compared to identify genetic variation.
Mutagenesis experiments were performed to verify predicted functional alterations.
Results
All isolates belonged to clone ST8134 and carried blaKPC-2 alleles (KpMVR1: blaKPC-157; KpMVS1
and KpMVS2: blaKPC-2) in plasmids predicted to be conjugative. Insertion sequence ISEc68 caused a
frameshift mutation in KpMVR1’s ompK36 gene, reducing susceptibility to meropenem-vaborbactam
and imipenem-relebactam. KPC-157 demonstrated decreased hydrolysis of imipenem and ceftazidime
when compared with KPC-2. KpMVR1 also encoded a disrupted transcriptional repressor MarR and
a destabilising mutation in AcrB, a component of the AcrAB-TolC multidrug efflux pump. An intact,
iron-transporting fec operon was identified on a novel IncFII(pKP91)/IncFIB(K) plasmid unique to KpMVS2, possibly accounting for the cefiderocol resistance observed in this isolate.
Conclusions
KpMVR1 carried multiple resistance-associated genetic alterations and likely developed its resistance
profile through within-patient evolution. This study highlights the importance of routine screening for
resistant pathogens in vulnerable patients to guide antimicrobial chemotherapy and the need to
characterise underlying resistance mechanisms to assess the risk of onward dissemination.
Resistance to carbapenems and third-generation cephalosporins is increasing in Klebsiella pneumoniae
globally, restricting therapeutic options. The β-lactam/β-lactamase inhibitor combinations are widely
used to circumvent β-lactamase-mediated resistance. In 2021, an unusual K. pneumoniae clinical isolate, KpMVR1, was recovered from a hospitalised patient in England, exhibiting resistance to meropenem-vaborbactam, imipenem-relebactam, and ceftazidime-avibactam. To investigate this phenomenon, we characterised the genome and antimicrobial susceptibility of KpMVR1 alongside two clonally related isolates susceptible to all three β-lactam/β-lactamase inhibitor combinations: KpMVS1, collected from the same patient 42 days earlier, and KpMVS2, from another patient in the same hospital.
Methods
Illumina and MinION whole-genome sequencing were conducted for these three isolates, followed by
hybrid genome assembly. Annotated genome assemblies were compared to identify genetic variation.
Mutagenesis experiments were performed to verify predicted functional alterations.
Results
All isolates belonged to clone ST8134 and carried blaKPC-2 alleles (KpMVR1: blaKPC-157; KpMVS1
and KpMVS2: blaKPC-2) in plasmids predicted to be conjugative. Insertion sequence ISEc68 caused a
frameshift mutation in KpMVR1’s ompK36 gene, reducing susceptibility to meropenem-vaborbactam
and imipenem-relebactam. KPC-157 demonstrated decreased hydrolysis of imipenem and ceftazidime
when compared with KPC-2. KpMVR1 also encoded a disrupted transcriptional repressor MarR and
a destabilising mutation in AcrB, a component of the AcrAB-TolC multidrug efflux pump. An intact,
iron-transporting fec operon was identified on a novel IncFII(pKP91)/IncFIB(K) plasmid unique to KpMVS2, possibly accounting for the cefiderocol resistance observed in this isolate.
Conclusions
KpMVR1 carried multiple resistance-associated genetic alterations and likely developed its resistance
profile through within-patient evolution. This study highlights the importance of routine screening for
resistant pathogens in vulnerable patients to guide antimicrobial chemotherapy and the need to
characterise underlying resistance mechanisms to assess the risk of onward dissemination.
Date Issued
2026-12-01
Date Acceptance
2026-03-30
Citation
BMC Genomic Data, 2026, 27 (1)
ISSN
2730-6844
Publisher
BMC
Journal / Book Title
BMC Genomic Data
Volume
27
Issue
1
Copyright Statement
© The Author(s) 2026. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
License URL
Identifier
10.1186/s12863-026-01421-x
Subjects
Klebsiella pneumoniae
Antimicrobial resistance
Carbapenem resistance
β-Lactamase inhibitors
KPC-157
OmpK36
Insertion sequences
Hybrid genome assembly
Comparative genomics
Mutagenesis experiments
Publication Status
Published
Article Number
ARTN 37
Date Publish Online
2026-05-09