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. 2024 Dec 20;23(1):108.
doi: 10.1186/s12941-024-00762-8.

Tracing the transmission of carbapenem-resistant Enterobacterales at the patient: ward environmental nexus

Linzy Elton  1 , Alan Williams  2 , Shanom Ali  3   4 , Jelena Heaphy  5 , Vicky Pang  5 , Liam Commins  5 , Conor O'Brien  5 , Özge Yetiş  3   4 , Estelle Caine  4 , Imogen Ward  4 , Monika Muzslay  4 , Samuel Yui  4 , Kush Karia  4 , Ellinor Shore  2   4 , Sylvia Rofael  3   6 , Damien J F Mack  5 , Timothy D McHugh  3 , Emmanuel Q Wey  3   7
Affiliations

Tracing the transmission of carbapenem-resistant Enterobacterales at the patient: ward environmental nexus

Linzy Elton et al. Ann Clin Microbiol Antimicrob. .

Abstract

Introduction: Colonisation and infection with Carbapenem-resistant Enterobacterales (CRE) in healthcare settings poses significant risks, especially for vulnerable patients. Genomic analysis can be used to trace transmission routes, supporting antimicrobial stewardship and informing infection control strategies. Here we used genomic analysis to track the movement and transmission of CREs within clinical and environmental samples.

Methods: 25 isolates were cultured from clinical patient samples or swabs, that tested positive for OXA-48-like variants using the NG-Test® CARBA-5 test and whole genome sequenced (WGS) using Oxford Nanopore Technologies (ONT). 158 swabs and 52 wastewater samples were collected from the ward environment. 60 isolates (matching clinical isolate genera; Klebsiella, Enterobacter, Citrobacter and Escherichia) were isolated from the environmental samples using selective agar. Metagenomic sequencing was undertaken on 36 environmental wastewater and swab samples.

Results: 21/25 (84%) clinical isolates had > 1 blaOXA gene and 19/25 (76%) harboured > 1 blaNDM gene. Enterobacterales were most commonly isolated from environmental wastewater samples 27/52 (51.9%), then stick swabs 5/43 (11.6%) and sponge swabs 5/115 (4.3%). 11/60 (18%) environmental isolates harboured > 1 blaOXA gene and 1.9% (1/60) harboured blaNDM-1. blaOXA genes were found in 2/36 (5.5%) metagenomic environmental samples.

Conclusions: Potential for putative patient-patient and patient-ward transmission was shown. Metagenomic sampling needs optimization to improve sensitivity.

Keywords: Antimicrobial resistance; CRE; Carbapenem-resistant Enterobacterales; Environment; Hospital; Metagenomics; NDM; OXA48; Oxford Nanopore; Plasmids; Transmission.

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Conflict of interest statement

Declarations. Ethical approval and consent to participate: This diagnostic service evaluation was undertaken at the request of the Division of Nursing in support of the Infection Prevention and Control team as part of enhanced standard of care practices for IPC outbreak investigation, in accordance with the Declaration of Helsinki. This project is under HRA approval for ELCID and registered with Health Services London. IRAS project ID: 283,831, National HRA REC reference: 20/HRA/4928, Local REC: RFL R&D ref: 134,895, HSL Project number: 1529. Consent for publications: Not applicable. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Dendograms for species sequenced in this study
Fig. 1
Fig. 1
Dendograms for species sequenced in this study
See this image and copyright information in PMC

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