Molecular characteristics of carbapenemase-producing Enterobacterales in the Netherlands; results of the 2014–2018 national laboratory surveillance

Abstract

Objectives: Carbapenem resistance mediated by mobile genetic elements has emerged worldwide and has become a major public health threat. To gain insight into the molecular epidemiology of carbapenem resistance in The Netherlands, Dutch medical microbiology laboratories are requested to submit suspected carbapenemase-producing Enterobacterales (CPE) to the National Institute for Public Health and the Environment as part of a national surveillance system. Methods: Meropenem MICs and species identification were confirmed by E-test and MALDI-TOF and carbapenemase production was assessed by the Carbapenem Inactivation Method. Of all submitted CPE, one species/carbapenemase gene combination per person per year was subjected to next-generation sequencing (NGS). Results: In total, 1838 unique isolates were received between 2014 and 2018, of which 892 were unique CPE isolates with NGS data available. The predominant CPE species were Klebsiella pneumoniae (n ¼ 388, 43%), Escherichia coli (n ¼ 264, 30%) and Enterobacter cloacae complex (n ¼ 116, 13%). Various carbapenemase alleles of the same carbapenemase gene resulted in different susceptibilities to meropenem and this effect varied between species. Analyses of NGS data showed variation of prevalence of carbapenemase alleles over time with bla OXA-48 being predominant (38%, 336/892), followed by bla NDM-1 (16%, 145/892). For the first time in the Netherlands, bla OXA-181 , bla OXA-232 and bla VIM-4 were detected. The genetic background of K. pneumoniae and E. coli isolates was highly diverse. Conclusions: The CPE population in the Netherlands is diverse, suggesting multiple introductions. The predominant carbapenemase alleles are bla OXA-48 and bla NDM-1. There was a clear association between species, carbapenemase allele and susceptibility to meropenem.

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

“…Lastly, the plasmids of KpnCluster-019 isolates contained also unique plasmid content, including a distinct transposon signature, two toxin-antitoxin systems and a ceaC colicin which possibly contribute to the success in survival, niche adaptation or transmission of this strain. The K. pneumoniae bla KPC-3 isolates had higher MICs for meropenem than the K. pneumoniae bla KPC-2 isolates, which is in line with a previous study 21 . The KPC-2 enzyme differs in a single amino acid substitution (Histidine 272 to Tyrosine) from KPC-3.…”

“…The K. pneumoniae bla KPC-3 isolates had higher MICs for meropenem than the K. pneumoniae bla KPC-2 isolates, which is in line with a previous study 21 . The KPC-2 enzyme differs in a single amino acid substitution (Histidine 272 to Tyrosine) from KPC-3.…”

“…The NGS data of the K. pneumoniae isolates were used for classical MLST and wgMLST analyses using the in-house wgMLST scheme in SeqSphere software version 6.0.2 (Ridom GmbH, Münster, Germany). The in-house K. pneumoniae wgMLST scheme was comprised of 4978 genes (3471 core-genome and 1507 accessory-genome targets) using K. pneumoniae MGH 78,578 (NC_009648.1) as a reference genome 21 . For classical MLST, the existing scheme was used and cluster nomenclature were depicted in Table 1 34 .…”

“…bla KPC -type K. pneumoniae represent the third largest group (17.5%) of the K. pneumoniae isolates collected in the Dutch National CPE Surveillance Program after the bla OXA-48 -type (48.5%) and bla NDM-1 -type (24.3%) K. pneumoniae . While the prevalence of carbapenemase-producing K. pneumoniae and associated infections in the Netherlands is relatively low, the establishment of genomic surveillance of K. pneumoniae using TGS is of high importance 20 , 21 . It provides for insights in the transmission of specific strains containing plasmids with AMR genes and/or virulence determinants.…”

blaOXA-48-like genome architecture among carbapenemase-producingEscherichia coliandKlebsiella pneumoniaein the Netherlands

“…Enterobacter cloacae complex (13%) (4). Carbapenemases are classified in Ambler classes A (i.e., KPCtypes), B (i.e., IMP-, NDM-and VIM-types), and D (OXA β-lactamases) type of carbapenem antibiotic degrading enzymes (5).…”