Genomic Epidemiology of ESBL- and Carbapenemase-Producing Enterobacterales in a Spanish Hospital: Exploring the Clinical–Environmental Interface

Abstract

Antimicrobial resistance (AMR), particularly due to extended-spectrum β-lactamases (ESBLs) and carbapenemases (CPs), poses a critical threat to global health. This study aimed to characterize the molecular epidemiology, resistance profiles, and genomic features of ESBL- and CP-producing Escherichia coli and Klebsiella pneumonaie (ESBL/CP-Ec/Kp) isolates from a Spanish hospital (2020–2024) and explore links to environmental reservoirs like white storks foraging at a nearby landfill. A total of 121 clinical Ec/Kp isolates (55 ESBL-Ec, 1 CP-Ec, 35 ESBL-Kp, 17 CP-Kp, 13 ESBL+CP-Kp) underwent phenotypic testing, PCR, and whole-genome sequencing (WGS). Analyses included phylogenomics (cgMLST), detection of AMR genes, plasmid typing, and comparative genomics. Among ESBL-Ec, blaCTX-M-15 was the most prevalent (60.0%), and one CP-Ec carrying blaNDM-5 was identified. WGS of 44 selected ESBL/CP-Ec isolates revealed a variety of AMR genes, and 56.8% of isolates carried class one integrons (56.8%). IncF-type plasmids predominated, and 84.1% of isolates were assigned as ExPEC/UPEC. The lineage ST131 dominated (75%), with IncF-blaCTX-M-15-carrying plasmids. Among the 18 ESBL/CP-Kp isolates sequenced, the lineage ST307 was the most frequent (44.4%), followed by ST15 and ST11, carrying a diversity of AMR determinants and plasmids (IncFIB(K), IncL, ColpVC). Virulence included ybt loci in ICEKp; hypervirulence genes were absent. Genomic analysis of 62 clinical isolates (44 Ec, 18 Kp) showed close phylogenetic links to stork-derived strains, with ST131-Ec and ST307-Kp from humans and birds differing just by ≤22 and ≤10 ADs, respectively, with a conserved plasmid content (i.e., IncL-blaOXA-48, IncFIB(K)-blaCTX-M-15). High-risk ESBL/CP-Ec/Kp clones persist across clinical and environmental contexts. WGS-based surveillance is key for understanding AMR spread and guiding interventions. Results support a One Health approach to combat AMR through cross-sector collaboration.