Integrated analysis of patient networks and plasmid genomes reveals a regional, multi-species outbreak of carbapenemase-producing Enterobacterales carrying both blaIMP and mcr-9 genes.


Wan, Yu ORCID: 0000-0002-8354-7647, Myall, Ashleigh C ORCID: 0000-0001-6202-0662, Boonyasiri, Adhiratha ORCID: 0000-0001-6549-9621, Bolt, Frances, Ledda, Alice ORCID: 0000-0002-2387-3774, Mookerjee, Siddharth, Weiße, Andrea Y ORCID: 0000-0001-7786-8252, Getino, Maria ORCID: 0000-0002-2937-3420, Turton, Jane F ORCID: 0000-0001-5652-6472, Abbas, Hala et al (show 18 more authors) (2024) Integrated analysis of patient networks and plasmid genomes reveals a regional, multi-species outbreak of carbapenemase-producing Enterobacterales carrying both blaIMP and mcr-9 genes. The Journal of infectious diseases, 230 (1). jiae019-. ISSN 0022-1899, 1537-6613

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Abstract

<h4>Background</h4>Carbapenemase-producing Enterobacterales (CPE) are challenging in healthcare, with resistance to multiple classes of antibiotics. This study describes the emergence of IMP-encoding CPE amongst diverse Enterobacterales species between 2016 and 2019 across a London regional network.<h4>Methods</h4>We performed a network analysis of patient pathways, using electronic health records, to identify contacts between IMP-encoding CPE positive patients. Genomes of IMP-encoding CPE isolates were overlayed with patient contacts to imply potential transmission events.<h4>Results</h4>Genomic analysis of 84 Enterobacterales isolates revealed diverse species (predominantly Klebsiella spp, Enterobacter spp, E. coli); 86% (72/84) harboured an IncHI2 plasmid carrying blaIMP and colistin resistance gene mcr-9 (68/72). Phylogenetic analysis of IncHI2 plasmids identified three lineages showing significant association with patient contacts and movements between four hospital sites and across medical specialities, which was missed on initial investigations.<h4>Conclusions</h4>Combined, our patient network and plasmid analyses demonstrate an interspecies, plasmid-mediated outbreak of blaIMPCPE, which remained unidentified during standard investigations. With DNA sequencing and multi-modal data incorporation, the outbreak investigation approach proposed here provides a framework for real-time identification of key factors causing pathogen spread. Plasmid-level outbreak analysis reveals that resistance spread may be wider than suspected, allowing more interventions to stop transmission within hospital networks.

Item Type: Article
Uncontrolled Keywords: IMP carbapenemase, carbapenem-resistant Enterobacterales, horizontal gene transfer, patient pathways, spatiotemporal network
Depositing User: Symplectic Admin
Date Deposited: 03 Sep 2024 08:25
Last Modified: 08 Dec 2024 03:00
DOI: 10.1093/infdis/jiae019
Open Access URL: https://doi.org/10.1093/infdis/jiae019
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URI: https://livrepository.liverpool.ac.uk/id/eprint/3184212
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