KlcAHS genes are ubiquitous in clinical, blaKPC-2-positive, Klebsiella pneumoniae isolates

Profiling the landscape of carbapenem resistance and hypervirulence in Klebsiella pneumoniae: A global epidemiological analysis of the plasmidome

The emergence and spread of carbapenem resistance (CR) and hypervirulence (hv) in Klebsiella pneumoniae represent a growing global health threat. Plasmids play an important role in the dissemination of these traits; however, the plasmidome of draft genomes of a large number of K. pneumoniae has not been analyzed so far. To recover K. pneumoniae plasmids, OMAP-KP was developed, achieving a recall rate of 85.27 % for plasmids exceeding 10,000 bp in length from draft genomes. From a global collection of 69,969 K. pneumoniae genomes, we identified 226,110 plasmids, providing the most comprehensive profiling of the K. pneumoniae plasmidome to date. The study recovered 12,790 KPC-encoding plasmids, 6214 NDM-encoding plasmids, and 6843 hv plasmids. Plasmid KPC PC_392 was found to be associated with ST11 K. pneumoniae in China, featuring the klcA within the genetic context around blaKPC. NDM plasmids exhibited a widespread distribution, and stabilization began before 2015. There was an increased prevalence of blaNDM-5 with the qnrS1 gene compared to blaNDM-1 after 2020. The frequent convergence of CR and hv plasmid pairs was observed in different STs: hv PC_499 with KPC PC_362 (ST11) and OXA PC_7078 (ST15), and hv PC_394 with OXA PC_7078 (ST2096) and OXA PC_804 (ST383), suggesting clone transmission of K. pneumoniae carrying CR-hv plasmid pairs. Alarmingly, PC_394 can encode both hv loci and CR genes, with an increasing prevalence detected from the public database from North America and Europe & Central Asia after 2019, which might result from the change of isolation or treatment strategy, or potentially from the ongoing spread of plasmids that have not been detected in other areas. This observed pattern coincides with the period of the COVID-19 pandemic needs further investigation. This study highlights the potential to integrate plasmid-level analysis into genome surveillance projects. The plasmidome reference and identification approach can track the emergence and convergence of CR and hv PCs in the evolution and transmission of K. pneumoniae, paving the way for more effective interventions to protect public health.

Functional comparison of anti-restriction and anti-methylation activities of ArdA, KlcA, and KlcAHS from Klebsiella pneumoniae

Anti-restriction proteins are typically encoded by plasmids, conjugative transposons, or phages to improve their chances of entering a new bacterial host with a type I DNA restriction and modification (RM) system. The invading DNA is normally destroyed by the RM system. The anti-restriction proteins ArdA, KlcA, and their homologues are usually encoded on plasmid of carbapenemase-resistant Klebsiella pneumoniae. We found that the plasmid sequence and restriction proteins affected horizontal gene transfer, and confirmed the anti-restriction and anti-methylation activities of ArdA and KlcA during transformation and transduction. Among the three anti-restriction proteins, ArdA shows stronger anti-restriction and anti-methylation effects, and KlcAHS was weaker. KlcA shows anti-methylation only during transformation. Understanding the molecular mechanism underlying the clinical dissemination of K. pneumoniae and other clinically resistant strains from the perspective of restrictive and anti-restrictive systems will provide basic theoretical support for the prevention and control of multidrug-resistant bacteria, and new strategies for delaying or even controlling the clinical dissemination of resistant strains in the future.

Towards a better understanding of antimicrobial resistance dissemination: what can be learnt from studying model conjugative plasmids?

Bacteria can evolve rapidly by acquiring new traits such as virulence, metabolic properties, and most importantly, antimicrobial resistance, through horizontal gene transfer (HGT). Multidrug resistance in bacteria, especially in Gram-negative organisms, has become a global public health threat often through the spread of mobile genetic elements. Conjugation represents a major form of HGT and involves the transfer of DNA from a donor bacterium to a recipient by direct contact. Conjugative plasmids, a major vehicle for the dissemination of antimicrobial resistance, are selfish elements capable of mediating their own transmission through conjugation. To spread to and survive in a new bacterial host, conjugative plasmids have evolved mechanisms to circumvent both host defense systems and compete with co-resident plasmids. Such mechanisms have mostly been studied in model plasmids such as the F plasmid, rather than in conjugative plasmids that confer antimicrobial resistance (AMR) in important human pathogens. A better understanding of these mechanisms is crucial for predicting the flow of antimicrobial resistance-conferring conjugative plasmids among bacterial populations and guiding the rational design of strategies to halt the spread of antimicrobial resistance. Here, we review mechanisms employed by conjugative plasmids that promote their transmission and establishment in Gram-negative bacteria, by following the life cycle of conjugative plasmids.

Plasmid diversity among genetically related Klebsiella pneumoniae blaKPC-2 and blaKPC-3 isolates collected in the Dutch national surveillance

Carbapenemase-producing Klebsiella pneumoniae emerged as a nosocomial pathogen causing morbidity and mortality in patients. For infection prevention it is important to track the spread of K. pneumoniae and its plasmids between patients. Therefore, the major aim was to recapitulate the contents and diversity of the plasmids of genetically related K. pneumoniae strains harboring the beta-lactamase gene bla_KPC-2 or bla_KPC-3 to determine their dissemination in the Netherlands and the former Dutch Caribbean islands from 2014 to 2019. Next-generation sequencing was combined with long-read third-generation sequencing to reconstruct 22 plasmids. wgMLST revealed five genetic clusters comprised of K. pneumoniae bla_KPC-2 isolates and four clusters consisted of bla_KPC-3 isolates. KpnCluster-019 bla_KPC-2 isolates were found both in the Netherlands and the Caribbean islands, while bla_KPC-3 cluster isolates only in the Netherlands. Each K. pneumoniae bla_KPC-2 or bla_KPC-3 cluster was characterized by a distinct resistome and plasmidome. However, the large and medium plasmids contained a variety of antibiotic resistance genes, conjugation machinery, cation transport systems, transposons, toxin/antitoxins, insertion sequences and prophage-related elements. The small plasmids carried genes implicated in virulence. Thus, implementing long-read plasmid sequencing analysis for K. pneumoniae surveillance provided important insights in the transmission of a KpnCluster-019 bla_KPC-2 strain between the Netherlands and the Caribbean.