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

Abstract

Structured summaryIntroductionColonisation 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.Methods25 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.Results21/25 (84%) clinical isolates had >1blaOXAgene and 19/25 (76%) harboured >1blaNDMgene. 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 >1blaOXAgene and 1.9% (1/60) harbouredblaNDM-1.blaOXAgenes were found in 2/36 (5.5%) metagenomic environmental samples.DiscussionPotential 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.