High-Molecular-Weight Plasmids Carrying Carbapenemase Genes blaNDM-1, blaKPC-2, and blaOXA-48 Coexisting in Clinical Klebsiella pneumoniae Strains of ST39

Abstract

Background: Klebsiella pneumoniae, a member of the ESKAPE group of bacterial pathogens, has developed multi-antimicrobial resistance (AMR), including resistance to carbapenems, which has increased alarmingly due to the acquisition of carbapenemase genes located on specific plasmids. Methods: Four clinical K. pneumoniae isolates were collected from four patients of a neuro-intensive care unit in Moscow, Russia, during the point prevalence survey. The AMR phenotype was estimated using the Vitec-2 instrument, and whole genome sequencing (WGS) was done using Illumina and Nanopore technologies. Results: All strains were resistant to beta-lactams, nitrofurans, fluoroquinolones, sulfonamides, aminoglycosides, and tetracyclines. WGS analysis revealed that all strains were closely related to K. pneumoniae ST39, capsular type K-23, with 99.99% chromosome identity. The novelty of the study is the description of the strains carrying simultaneously three large plasmids of the IncHI1B, IncC, and IncFIB groups carrying the carbapenemase genes of three types, blaOXA-48, blaNDM-1, and blaKPC-2, respectively. The first of them, highly identical in all strains, was a hybrid plasmid that combined two regions of the resistance genes (blaOXA-48 and blaTEM-1 + blaCTX-M-15 + blaOXA-1 + catB + qnrS1 + int1) and a region of the virulence genes (iucABCD, iutA, terC, and rmpA2::IS110). Conclusion: The spread of K. pneumoniae strains carrying multiple plasmids conferring resistance even to last-resort antibiotics is of great clinical concern.

Genomic characterization of a WHO critical priority isolate Enterobacter kobei ST2070 harboring OXA-10, KPC-2, and CTX-M-12 recovered from a water irrigation channel in Ecuador

“…The isolate UTA41 co-harbor the OXA-10-type class D β-lactamase and the KPC-2-type class A β-lactamase. This co-carriage was observed on different studies of Klebsiella pneumoniae from clinical origin on Sweden, Taiwan, and Russia [ [34] , [35] , [36] ]. KPC-2 has become the most clinically important carbapenemases enzyme due to its prevalence in enteric bacteria from human, animal and environmental origin [ [37] , [38] , [39] ].…”

Detection of Klebsiella pneumoniae Carbapenem Resistance Genes by qPCR: Choosing the Right Method for Total DNA Extraction

“…Since the DNA is usually isolated from patient samples like rectal swabs or stool, which contain only a limited number of the bacteria of interest, the chosen DNA extraction method should be very efficient. In addition, carbapenem resistance genes are often encoded on medium to large low-copy plasmids [19,20,50,51], but can also be found on the bacterial chromosome [18]. Besides that, species-specific genes used as targets, like khe in the case of K. pneumoniae, are also located on the bacterial chromosome.…”

Genetic Characterization of Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates in a Tertiary Hospital in Greece, 2018–2022

“…The present study also included the recently reported four ST39 isolates carrying both bla KPC-2 and bla VIM-1 [ 21 ]. Recently, Kuzina et al highlighted the concurrent isolation of bla NDM-1 , bla KPC-2 , and bla OXA-48 in ST39 CRKP isolates [ 49 ]. Three CRKP isolates (12.5%) were assigned to ST323; sporadic cases of ST323 CRKP have been previously reported in Greece and other European countries [ 50 , 51 ].…”