Exploring the presence, genomic traits, and pathogenic potential of extended-spectrum β-lactamase Escherichia coli in freshwater, wastewater, and hospital effluents

Abstract

Aims The purpose of this work was to study extended-spectrum β-lactamase-producing E. coli (ESBL-EC) in freshwaters, hospital effluents and wastewaters during two sampling campaigns in 2021. Methods and results Water sampling was performed in 24 stations of the Ourthe watershed in Belgium. A total of 644 ESBL (n = 642) and AmpC (n = 2) E. coli strains were isolated. Disk-diffusion assays were performed following the EUCAST's recommendations. All strains were tested for the presence of blaCTX-M-1, blaCTX-M-2 and blaCTX-M-9 gene's group by PCR. Genes belonging to blaCTX-M-1 and blaCTX-M-9 groups were detected respectively in 73.6% and 14.9% of the strains. No blaCTX-M-2 group's gene was found. A subset of strains (n = 40) was selected for whole genome sequencing. E. coli serotype O18: H7 ST 1463 was predominant (n = 14) in the sequenced strains and showed pathogenicity in the Galleria mellonella larvae model. β-lactamase genes identified were blaCTX-M (n = 21), with blaCTX-M-15 mostly represented (n = 15), as well as blaTEM (n = 11), blaOXA (n = 7) and blaSHV (n = 9) and carbapenemase (CP) genes were observed in several strains—blaKPC-3 (n = 19), blaNDM-1 (n = 1), blaVIM-1 (n = 2) and blaOXA-244 (n = 2)—even from freshwaters. Conclusions ESBL-EC are widely distributed in the aquatic environment in Belgium and contain a variety of ESBL and CP genes.