Characterization of blaKPC-2 and blaNDM-1 Plasmids of a K. pneumoniae ST11 Outbreak Clone

Abstract

The most common resistance mechanism to carbapenems is the production of carbapenemases. In 2021, the Pan American Health Organization warned of the emergence and increase in new carbapenemase combinations in Enterobacterales in Latin America. In this study, we characterized four Klebsiella pneumoniae isolates harboring blaKPC and blaNDM from an outbreak during the COVID-19 pandemic in a Brazilian hospital. We assessed their plasmids’ transference ability, fitness effects, and relative copy number in different hosts. The K. pneumoniae BHKPC93 and BHKPC104 strains were selected for whole genome sequencing (WGS) based on their pulsed-field gel electrophoresis profile. The WGS revealed that both isolates belong to ST11, and 20 resistance genes were identified in each isolate, including blaKPC-2 and blaNDM-1. The blaKPC gene was present on a ~56 Kbp IncN plasmid and the blaNDM-1 gene on a ~102 Kbp IncC plasmid, along with five other resistance genes. Although the blaNDM plasmid contained genes for conjugational transfer, only the blaKPC plasmid conjugated to E. coli J53, without apparent fitness effects. The minimum inhibitory concentrations (MICs) of meropenem/imipenem against BHKPC93 and BHKPC104 were 128/64 and 256/128 mg/L, respectively. Although the meropenem and imipenem MICs against E. coli J53 transconjugants carrying the blaKPC gene were 2 mg/L, this was a substantial increment in the MIC relative to the original J53 strain. The blaKPC plasmid copy number was higher in K. pneumoniae BHKPC93 and BHKPC104 than in E. coli and higher than that of the blaNDM plasmids. In conclusion, two ST11 K. pneumoniae isolates that were part of a hospital outbreak co-harbored blaKPC-2 and blaNDM-1. The blaKPC-harboring IncN plasmid has been circulating in this hospital since at least 2015, and its high copy number might have contributed to the conjugative transfer of this particular plasmid to an E. coli host. The observation that the blaKPC-containing plasmid had a lower copy number in this E. coli strain may explain why this plasmid did not confer phenotypic resistance against meropenem and imipenem.

Unveiling the genome of a high-risk pandrug-resistant Klebsiella pneumoniae emerging in the Brazilian Amazon Region, 2022

“…Although less prevalent than the carbapenemase-coding bla KPC-2 gene, several studies demonstrated the occurrence of bla NDM-1 among clinical K. pneumoniae in Brazil, (17) including the ST11 lineage, where this gene was found in the context of an IncC plasmid. (18) Interestingly, the bla NDM-1 occurrence in Brazil was not restricted to clinical settings since it had already been found in environmental K. pneumoniae isolates recovered from both surface waters, (19) and wastewater treatment plants (WWTPs). (20) Most of the genes composing the resistome were flanked or in the vicinity of insertion sequences and plasmid-related genes, the exception was the tetD, fosA5, and bla SHV-11 , which were chromosomally encoded.…”

Characterisation of a Novel Hybrid IncFIIpHN7A8:IncR:IncN Plasmid Co-Harboring blaNDM-5 and blaKPC-2 from a Clinical ST11 Carbapenem-Resistant Klebsiella pneumoniae Strain

“… 37 Although we could not measure the fitness cost of this plasmid, we suspected that the loss of horizontal transfer ability was a manifestation of fitness cost. Furthermore, although there have been many reports on the concurrence of the bla NDM -plasmid and bla KPC -plasmid in the same K. pneumoniae isolate, 9 , 16 , 38 the same plasmid co-harboring bla NDM and bla KPC in K. pneumoniae has not yet been reported. However, with the widespread use of ceftazidime/avibactam and frequent combined with carbapenems in clinical practice, plasmids co-carrying these two critical carbapenemase genes might gradually gain a selection advantage during continuous evolution.…”