Tracing the transmission of carbapenem-resistantEnterobacteralesat the patient:ward environmental nexus

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.

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. Metagenomic sequencing was undertaken on 36 environmental wastewater and swab samples.

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 at >1 blaOXA gene and 1.9% (1/60) harboured blaNDM-1. blaOXA genes were found in 2/36 (5.5%) metagenomic environmental samples.

Potential for putative patient-patient and patient-ward transmission was shown. ONT sequencing can expedite clinical decisions whilst awaiting reference laboratory results, providing economic and patient care benefits. Metagenomic sampling needs optimization to improve sensitivity. Competing Interest Statement The authors have declared no competing interest. Funding Statement This research was funded by the Royal Free London NHS Foundation Trust Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: 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. This project is under HRA approval for ELCID and registered with Health Services London. IRAS project ID: 283831, National HRA REC reference: 20/HRA/4928, Local REC: RFL R&D ref: 134895, HSL Project number: 1529 I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Data Availability All data produced in the present work are contained in the manuscript or available online under ENA bioproject number PRJEB76684. For patient and ward metadata, please contact the authors. Abbreviations - AMR - Antimicrobial resistance - AST - Antibiotic sensitivity test - CRE - Carbapenem-resistant Enterobacterales - DWT - Drain waste trap - HCAI - Healthcare associated infection - HWB - Hand wash basin - IPC - Infection prevention and control - MDRO - Multi-drug resistant organism - NDM - New Delhi metallo-beta lactamase - ONT - Oxford Nanopore Technologies - RDT - Rapid diagnostic test - SD - Standard deviation - WoW - Workstation on wheels