National genomic surveillance of carbapenemase-producing Escherichia coli isolates in Slovenia, January 1st–December 31st 2023

Introduction The incidence of carbapenemase-producing (CP) Escherichia coli has increased worldwide, with the first reports in Europe dating back to the early 2000s. As part of the European Genomic Reference Laboratory Capacity Building (EURGen-RefLabCap) project, Slovenia conducted its first national genomic surveillance study of CP– E. coli . The aim was to characterize CP– E. coli isolates recovered from Slovenian patients between 1 January and 31 December 2023 using whole-genome sequencing (WGS), providing a national snapshot of the population structure and circulating strains. Methods WGS was performed using short-read sequencing. Bioinformatic analyses included identification of antimicrobial resistance (AMR) determinants, multilocus sequence typing (MLST), phylogroup typing, core genome multilocus sequence typing (cgMLST), assessment of genetic relatedness, and plasmid reconstruction using MOB-suite. Results A total of 108 CP– E. coli isolates (108 patients) were included. Most isolates originated from surveillance samples (89.8%), 30.6% were detected more than 48 h after hospital admission. OXA-48-like carbapenemases predominated (70.4%), followed by metallo-β-lactamases (29.6%), with OXA-48 (44.4%), OXA-244 (22.2%), and VIM-1 (18.5%) being the most common enzymes. Despite carbapenemase production, 69.4% of isolates remained phenotypically susceptible to carbapenems. WGS revealed substantial genetic diversity, with 67 sequence types (STs) identified among 108 isolates. The most common lineages were ST10 (13.9%), ST38 (12.0%), ST5295 (9.3%), and ST69 (6.5%). Phylogroup A was the most prevalent, followed by D, B2, and B1. cgMLST analysis identified six transmission clusters comprising 26 isolates (24.1%), the remaining isolates were sporadic. Plasmid analysis based on short-read sequencing demonstrated extensive horizontal dissemination of carbapenemase genes, with blaOXA-48 predominantly associated with IncL/M plasmids and blaVIM-1 with IncA plasmids. Closely related plasmids were detected across multiple genetically distinct STs, indicating widespread plasmid-mediated transmission. Discussion CP– E. coli in Slovenia is characterized by a rising burden, high genetic diversity, and a predominance of OXA-48-like carbapenemases. While limited clonal transmission was observed, the widespread distribution of closely related carbapenemase-carrying plasmids across diverse sequence types indicates that horizontal plasmid transfer is the principal driver of dissemination. These findings highlight the value of the national genomic surveillance for monitoring both clonal spread and plasmid-mediated transmission of carbapenem resistance.