Biology subjects

Witteveen, S.

Publications and source records attributed to Witteveen, S..

2 recordsLinked to original sources

bioRxiv2020

blaOXA-48-like genome architecture among carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the Netherlands

Carbapenem-hydrolyzing enzymes belonging to the OXA-48-like group are encoded by blaOXA-48-like alleles and are abundant among Enterobacterales in the Netherlands. Therefore, the objective was to investigate the characteristics, gene content, and diversity of the blaOXA-48-like carrying plasmids and chromosomes of Escherichia coli and Klebsiella pneumoniae collected in the Dutch national surveillance from 2014-2019 in comparison with genome sequences retrieved from 29 countries. By combining short-read and long-read sequencing, 47 and 132 complete blaOXA-48-like plasmids were reconstructed for E. coli and K. pneumoniae, respectively. Distinct plasmid groups designated as pOXA-48, pOXA-181, and pOXA-232 were identified in the Netherlands and varied in size, % G+C, presence of antibiotic resistance genes, replicons and gene content. The pOXA-48 plasmids were variable, while pOXA-181 and pOXA-232 plasmids were conserved. A group of non-related pOXA-48 plasmids contained different resistance genes, non-IncL type replicons or carried no replicons. K. pneumoniae isolates carrying blaOXA-48 or blaOXA-232 were mostly resistant, while E. coli blaOXA-48, blaOXA-181 and chromosomal blaOXA-48 or blaOXA-244 isolates were mostly sensitive for meropenem. Analysis of chromosomally localized blaOXA-48-like alleles revealed that these were flanked by a direct repeat (DR) upstream of IS1R, which were found at multiple locations in the chromosome of distinct genetic backgrounds. In conclusion, the overall blaOXA-48-like plasmid population in the Netherlands is conserved and similar to that reported for other countries, although a highly diverse blaOXA-48-like plasmid subgroup was present. Chromosomally encoded blaOXA-48-like alleles are from distinct genetic backgrounds and occurs at variable positions containing the DR, thereby indicating multiple independent transpositions. ImportanceOXA-48-type of carbapenem hydrolyzing enzymes encoded by blaOXA-48-like genes from transmissible plasmids or chromosomes of Escherichia coli and Klebsiella pneumoniae have spread world-wide and are of concern. Dissecting the blaOXA-48-like genome architecture at the molecular level by combining short-read and long-read sequencing will lead to understanding trends in the plasmid reservoir of E. coli and K. pneumoniae in the Netherlands and may enhance future international pathogen surveillance.

microbiology↗

bioRxiv2020

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

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.

microbiology↗