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Genomic Dynamics of Species and Mobile Genetic Elements in a Prolonged blaIMP-4-associated Carbapenemase Outbreak in an Australian Hospital

Kizny Gordon, A; Phan, HTT; Lipworth, S; Cheong, E; Gottlieb, T; George, S; Peto, T; ... Stoesser, N; + view all (2020) Genomic Dynamics of Species and Mobile Genetic Elements in a Prolonged blaIMP-4-associated Carbapenemase Outbreak in an Australian Hospital. Journal of Antimicrobial Chemotherapy , 75 (4) pp. 873-882. 10.1093/jac/dkz526. Green open access

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Abstract

Background: Hospital outbreaks of carbapenemase-producing organisms, such as blaIMP-4-containing organisms, are an increasing threat to patient safety. Objectives: To investigate the genomic dynamics of a 10 year (2006–15) outbreak of blaIMP-4-containing organisms in a burns unit in a hospital in Sydney, Australia. Methods: All carbapenem-non-susceptible or MDR clinical isolates (2006–15) and a random selection of equivalent or ESBL-producing environmental isolates (2012–15) were sequenced [short-read (Illumina), long-read (Oxford Nanopore Technology)]. Sequence data were used to assess genetic relatedness of isolates (Mash; mapping and recombination-adjusted phylogenies), perform in silico typing (MLST, resistance genes and plasmid replicons) and reconstruct a subset of blaIMP plasmids for comparative plasmid genomics. Results: A total of 46/58 clinical and 67/96 environmental isolates contained blaIMP-4. All blaIMP-4-positive organisms contained five or more other resistance genes. Enterobacter cloacae was the predominant organism, with 12 other species mainly found in either the environment or patients, some persisting despite several cleaning methods. On phylogenetic analysis there were three genetic clusters of E. cloacae containing both clinical and environmental isolates, and an additional four clusters restricted to either reservoir. blaIMP-4 was mostly found as part of a cassette array (blaIMP-4-qacG2-aacA4-catB3) in a class 1 integron within a previously described IncM2 plasmid (pEl1573), with almost complete conservation of this cassette across the species over the 10 years. Several other plasmids were also implicated, including an IncF plasmid backbone not previously widely described in association with blaIMP-4. Conclusions: Genetic backgrounds disseminating blaIMP-4 can persist, diversify and evolve amongst both human and environmental reservoirs during a prolonged outbreak despite intensive prevention efforts.

Type: Article
Title: Genomic Dynamics of Species and Mobile Genetic Elements in a Prolonged blaIMP-4-associated Carbapenemase Outbreak in an Australian Hospital
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/jac/dkz526
Publisher version: https://doi.org/10.1093/jac/dkz526
Language: English
Additional information: © The Author(s) 2020. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
UCL classification: UCL
UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Inst of Clinical Trials and Methodology
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Inst of Clinical Trials and Methodology > MRC Clinical Trials Unit at UCL
URI: https://discovery.ucl.ac.uk/id/eprint/10088052
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