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Dissemination of carbapenemase-producing Enterobacterales in Ireland from 2012 to 2017: a retrospective genomic surveillance study.

Accepted version
Peer-reviewed

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Type

Article

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Authors

Hadjirin, Nazreen F 
van Tonder, Andries J 
Blane, Beth 
Lees, John A 
Kumar, Narender 

Abstract

The spread of carbapenemase-producing Enterobacterales (CPE) is of major public health concern. The transmission dynamics of CPE in hospitals, particularly at the national level, are not well understood. Here, we describe a retrospective nationwide genomic surveillance study of CPE in Ireland between 2012 and 2017. We sequenced 746 national surveillance CPE samples obtained between 2012 and 2017. After clustering the sequences, we used thresholds based on pairwise SNPs, and reported within-host diversity along with epidemiological data to infer recent putative transmissions. All clusters in circulating clones, derived from high-resolution phylogenies, of a species (Klebsiella pneumoniae, Escherichia coli, Klebsiella oxytoca, Enterobacter cloacae, Enterobacter hormaechei and Citrobacter freundii) were individually examined for evidence of transmission. Antimicrobial resistance trends over time were also assessed. We identified 352 putative transmission events in six species including widespread and frequent transmissions in three species. We detected putative outbreaks in 4/6 species with three hospitals experiencing prolonged outbreaks. The bla OXA-48 gene was the main cause of carbapenem resistance in Ireland in almost all species. An expansion in the number of sequence types carrying bla OXA-48 was an additional cause of the increasing prevalence of carbapenemase-producing K. pneumoniae and E. coli.

Description

Keywords

Ireland national survey, SNP-based phylogeny, carbapenemase-producing Enterobacterales (CPE), hospital transmission, whole genome analysis, Escherichia coli, Ireland, Retrospective Studies, Klebsiella pneumoniae, Genomics

Journal Title

Microb Genom

Conference Name

Journal ISSN

2057-5858
2057-5858

Volume Title

Publisher

Microbiology Society
Sponsorship
Wellcome Trust (098600/Z/12/Z)
National Institute for Health and Care Research (HICF-T5-342)
We are grateful to the library construction, sequencing and Pathogen Informatics teams at the Wellcome Trust Sanger Institute for assistance with Illumina sequencing. This publication presents independent research supported by the Health Innovation Challenge Fund (WT098600, HICF-T5-342), a parallel funding partnership between the Department of Health and Wellcome Trust. The views expressed in this publication are those of the author(s) and not necessarily those of the Department of Health or Wellcome Trust. C.L. is a Wellcome Trust Sir Henry Postdoctoral Fellow (110243/Z/15/Z). S.J.P. is a National Institute for Health Research (NIHR) Senior Investigator. JAL acknowledges funding from the MRC Centre for Global Infectious Disease Analysis (MR/R015600/1), jointly funded by the UK Medical Research Council (MRC) and the UK Foreign, Commonwealth & Development Office (FCDO), under the MRC/FCDO Concordat agreement and is also part of the EDCTP2 programme supported by the European Union. Finally we would also like to thank Dr Sebastian Bruchmann for providing the K. pneumoniae reference genomes.