Illumina short-read and MinION long-read WGS to characterize the molecular epidemiology of an NDM-1 <i>Serratia marcescens</i> outbreak in Romania


Phan, HTT, Stoesser, N, Maciuca, IE, Toma, F, Szekely, E, Flonta, M, Hubbard, ATM, Pankhurst, L, Do, T, Peto, TEA et al (show 3 more authors) (2018) Illumina short-read and MinION long-read WGS to characterize the molecular epidemiology of an NDM-1 <i>Serratia marcescens</i> outbreak in Romania. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 73 (3). pp. 672-679.

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Abstract

<h4>Background and objectives</h4>Serratia marcescens is an emerging nosocomial pathogen, and the carbapenemase blaNDM has been reported in several surveys in Romania. We aimed to investigate the molecular epidemiology of S. marcescens in two Romanian hospitals over 2010-15, including a neonatal NDM-1 S. marcescens outbreak.<h4>Methods</h4>Isolates were sequenced using Illumina technology together with carbapenem-non-susceptible NDM-1-positive and NDM-1-negative Klebsiella pneumoniae and Enterobacter cloacae to provide genomic context. A subset was sequenced with MinION to fully resolve NDM-1 plasmid structures. Resistance genes, plasmid replicons and ISs were identified in silico for all isolates; an annotated phylogeny was reconstructed for S. marcescens. Fully resolved study NDM-1 plasmid sequences were compared with the most closely related publicly available NDM-1 plasmid reference.<h4>Results</h4>44/45 isolates were successfully sequenced (S. marcescens, n = 33; K. pneumoniae, n = 7; E. cloacae, n = 4); 10 with MinION. The S. marcescens phylogeny demonstrated several discrete clusters of NDM-1-positive and -negative isolates. All NDM-1-positive isolates across species harboured a pKOX_NDM1-like plasmid; more detailed comparisons of the plasmid structures demonstrated a number of differences, but highlighted the largely conserved plasmid backbones across species and hospital sites.<h4>Conclusions</h4>The molecular epidemiology is most consistent with the importation of a pKOX_NDM1-like plasmid into Romania and its dissemination amongst K. pneumoniae/E. cloacae and subsequently S. marcescens across hospitals. The data suggested multiple acquisitions of this plasmid by S. marcescens in the two hospitals studied; transmission events within centres, including a large outbreak on the Targu Mures neonatal unit; and sharing of the pKOX_NDM1-like plasmid between species within outbreaks.

Item Type: Article
Uncontrolled Keywords: Feces, Humans, Enterobacteriaceae, Klebsiella pneumoniae, Serratia marcescens, Enterobacteriaceae Infections, Klebsiella Infections, Serratia Infections, beta-Lactamases, DNA, Bacterial, Sequence Analysis, DNA, Disease Outbreaks, Gene Transfer, Horizontal, Genome, Bacterial, Plasmids, Hospitals, Romania, Whole Genome Sequencing
Depositing User: Symplectic Admin
Date Deposited: 15 May 2019 09:14
Last Modified: 13 Feb 2024 15:18
DOI: 10.1093/jac/dkx456
Open Access URL: https://doi.org/10.1093/jac/dkx456
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3041413
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