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

Abstract

Carbapenemase-producing Klebsiella pneumoniae emerged over the past decades as an important pathogen causing morbidity and mortality in hospitalized patients. For infection prevention and control, it is important to track the spread of bacterial strains in humans including the plasmids they contain. However, little is known concerning the plasmid repertoire among K. pneumoniae strains. Therefore, the major aim was to recapitulate the size, contents and diversity of the plasmids of genetically related K. pneumoniae strains harboring the beta-lactamase gene blaKPC-2 or blaKPC-3 to determine their dissemination in the Netherlands and the former Dutch Caribbean islands from 2014-2019. Next-generation sequencing was combined with long-read third-generation sequencing to reconstruct 18 plasmids of K. pneumoniae. wgMLST revealed five genetic clusters (termed KpnClusters) comprised of K. pneumoniae blaKPC-2 isolates and four clusters consisted of blaKPC-3 isolates. Each cluster was characterized by a distinct resistome and plasmidome. KpnCluster-019 blaKPC-2 isolates were found both in the Netherlands and the Caribbean islands. K. pneumoniae blaKPC-3 isolates were found in the collection of the Netherlands. The 18 plasmids were mostly unrelated and varied between K. pneumoniae blaKPC-2 and blaKPC-3 clusters. However, the large and medium sized plasmids contained a variety of antibiotic resistance genes, transposons, insertion sequence elements, conjugal transfer systems, cation transport systems, toxin/antitoxin systems, and prophage-related sequence 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 success and understanding of transmission of a KpnCluster-019 blaKPC-2 strain between the Netherlands and the Caribbean. ImportanceCarbapenemase-producing Klebsiella pneumoniae has spread globally and is of great concern for debilitated patients. K. pneumoniae is notorious for spreading antimicrobial resistance genes by plasmids among Enterobacterales. Combining short and long read sequencing enables reconstruction of plasmids containing antibiotic resistance genes, conjugation machinery, transposons, toxins and/or virulence determinants and thereby enhancing international pathogen surveillance.