Novel Megaplasmid Driving NDM-1-Mediated Carbapenem Resistance in Klebsiella pneumoniae ST1588 in South America

Abstract

Carbapenem-resistant Enterobacterales (CRE) is a critical public health problem in South America, where the prevalence of NDM metallo-betalactamases has increased substantially in recent years. In this study, we used whole genome sequencing to characterize a multidrug-resistant (MDR) Klebsiella pneumoniae (UCO-361 strain) clinical isolate from a teaching hospital in Chile. Using long-read (Nanopore) and short-read (Illumina) sequence data, we identified a novel un-typeable megaplasmid (314,976 kb, pNDM-1_UCO-361) carrying the bla_NDM-1 carbapenem resistance gene within a Tn3000 transposon. Strikingly, conjugal transfer of pNDM-1_UCO-361 plasmid only occurs at low temperatures with a high frequency of 4.3 × 10^-6 transconjugants/receptors at 27 °C. UCO-361 belonged to the ST1588 clone, previously identified in Latin America, and harbored aminoglycoside, extended-spectrum β-lactamases (ESBLs), carbapenem, and quinolone-resistance determinants. These findings suggest that bla_NDM-1-bearing megaplasmids can be adapted to carriage by some K. pneumoniae lineages, whereas its conjugation at low temperatures could contribute to rapid dissemination at the human-environmental interface.

Keywords: Klebsiella pneumoniae; NDM-1; carbapenem-resistant Enterobacterales; carbapenemases; plasmid transfer.

Figure 1

Circular representation of plasmid harboring bla_NDM-1 in K. pneumoniae UCO-361. (A) General representation of genes encoded by pNDM-1_UCO361 showing coding sequences (CDS) in black, mobile-genetic elements in green, antibiotic-resistance genes in red and plasmid replication/conjugation proteins in blue. The genetic context of bla_NDM-1 is highlighted inside the red box. (B) Linear view of Tn3000 containing the bla_NDM-1 gene. Figures were created with Proksee (Proksee.ca).