Spatiotemporal and genomic analysis of carbapenem resistance elements in Enterobacterales from hospital inpatients and natural water ecosystems of an Irish city

• DOI: 10.1128/spectrum.00904-24
• Publication Date: 2024-11-27T14:00:43Z
• Authors: Mark Maguire; Carlos Serna; Natalia Montero S...; Aneta Kovarova; Louise O’Connor; Niamh Cahill; Brigid Hooban; Niall DeLappe; Wendy Brennan; Genevieve Devane; Martin Cormican; Dearbháile Morris; Simone C. Coughlan; Georgios Miliotis; Bruno Gonzalez-Zorn; Liam P. Burke
• Keywords: 0301 basic medicine; plasmids; 03 medical and health sciences; antibiotic resistance; Enterobacterales; environmental microbiology; transposons; carbapenems; Microbiology; QR1-502; Research Article

ABSTRACT Carbapenemase-producing Enterobacterales (CPE) is a diverse group of often multidrug-resistant organisms. Surveillance and control infections are complicated due to the inter-species spread carbapenemase-encoding genes (CEGs) on mobile genetic elements (MGEs), including plasmids transposons. Due wastewater discharges, urban water ecosystems represent known reservoir CPE. However, dynamics carbapenemase-bearing MGE dissemination between in humans environmental waters poorly understood. We carried out whole-genome sequencing, combining short- long-sequencing reads enable complete characterization CPE isolated from patients, wastewaters, natural 2018 2020 Galway, Ireland. Isolates were selected based their carriage Class A bla KPC-2 ( n = 6), B NDM-5 12), D OXA-48 21) CEGs. CEGs plasmid-borne all but two isolates. was associated with 64 kb IncL plasmid (62%), broad range isolates both niches. Conversely, usually larger more variable multireplicon IncF Klebsiella pneumoniae Escherichia coli , respectively. In every isolate, each CEG surrounded by gene-specific common environment which constituted part, or all, transposable element that present bacterial chromosome. Transposons Tn 1999 4401 respectively, while IS 26 bound composite transposons, containing class 1 integron. IMPORTANCE Since 2018, Irish National Carbapenemase-Producing Reference Laboratory Service at University Hospital Galway has performed sequencing suspected confirmed clinical specimens as well patient screening Understanding gene encoding (MGE) flux human reservoirs important for One Health surveillance these priority employed hybrid assembly approaches improved resolution genomic surveillance, typing, characterization. analyzed collection 17) 22) found across multiple species different ecological The conjugation ability frequency subset demonstrated be affected presence absence necessary size. characterize several play local carbapenemase genes. This may facilitate future detection laboratory.