Whole-genome sequencing characterisation of a new KPC-245 variant-carrying Klebsiella pneumoniae strain isolated from a transplanted patient and resistant to ceftazidime/avibactam, meropenem/vaborbactam and imipenem/relebactam
Claudia Vaiana, Roberta Vazzana, Salvatore Castelbuono, Andrea Cona, Alessandra Mularoni, Rita Minucci, Francesco Monaco, Daniele Di Carlo, Pier Giulio Conaldi, Alessia Gallo, Nicola Cuscino
Abstract
• Klebsiella pneumoniae carbapenemase-carrying K. pneumoniae represents a significant threat to human health worldwide. • Whole-genome sequencing is a useful approach for understanding severe multidrug-resistant phenotypes. • A new bla KPC variant was identified that is potentially responsible for resistance to all new β-lactams/β-lactamase inhibitors tested as well as cefiderocol in a clinical isolate. In recent decades, the increasing prevalence of multidrug-resistant Klebsiella pneumoniae carbapenemase (KPC)-carrying K. pneumoniae (KPC-Kp) has become a worldwide public concern. Herein, we characterised a ceftazidime/avibactam (CAZ/AVI), meropenem/vaborbactam (MER/VAB) and imipenem/relebactam (IMI/REL)-resistant KPC-Kp strain isolated from a critically ill transplant patient. Antimicrobial susceptibility testing and whole-genome sequencing (WGS) were conducted to characterise the strain at phenotypic and genotypic levels. Genomic DNA was sequenced using the Illumina platform. Bioinformatic analyses were used to investigate the genome sequences both for resistance and virulence features, and for the characterisation of plasmids. Phenotypic characterisation revealed that the KPC-Kp isolate was highly resistant to a wide range of antibiotics, including all β-lactam/β-lactamase inhibitor combinations such as CAZ/AVI, MER/VAB, IMI/REL and cefiderocol. WGS analysis showed that the isolate, belonging to the rare lineage ST661, contained several resistance and virulence genes. Among the resistance genes, we identified a new KPC variant within the mobile genetic element Tn4401—KPC-245—characterised by the insertion of nine amino acids (RAPNKDDYT) at position 263 as well as an amino acid change within the protein sequence, E274D, compared with KPC-3. Interestingly, the presence of mutations only in the bla KPC gene and not in other β-lactamase coding genes strongly points to the role of KPC-245 in β-lactam/β-lactamase inhibitor combinations and cefiderocol resistance. In our study, by using WGS analysis on a clinical isolate, we identified a new bla KPC variant within the Tn4401 transposon. Our results confirm the importance of continuous surveillance of multidrug-resistant K. pneumoniae in the clinical context.