Occurrence and Genomic Characterization of ESBL-, AmpC-, and Carbapenemase-Producing Escherichia coli and Klebsiella pneumoniae Isolated from Surface Water in Southern Italy, 2023–2024

Antimicrobial resistance (AMR) is recognised as a major global public health threat, with the environment increasingly acknowledged as a key reservoir and dissemination pathway for resistant bacteria and resistance genes. In this study, 148 surface water samples were collected between 2023 and 2024 from six rivers and three canals discharging wastewater into two lake waters in Southern Italy to assess the occurrence and genomic features of extended-spectrum β-lactamase (ESBL)-, AmpC-, and carbapenemase-producing Escherichia coli and Klebsiella pneumoniae. Relevant isolates were obtained using selective culturing, and tested for antimicrobial susceptibility by broth microdilution. Major β-lactam resistance genes were detected by real-time PCR. Whole-genome sequencing (WGS) was performed on presumptive carbapenemase-producing isolates. ESBL- and/or carbapenemase-producing Enterobacterales were detected in 67.6% of samples, yielding a total of 176 non-duplicate isolates. The most prevalent gene was blaCTX-M, detected in 79.3% of positive isolates (96/121), while carbapenemase genes were detected in 20.6% (25/121) of isolates, mainly blaOXA-48 and blaVIM. WGS analysis of carbapenemase PCR-positive isolates revealed occurrence of clinically relevant high-risk clones, such as K. pneumoniae ST512/ST307 carrying blaKPC-3 and E. coli ST10 harbouring blaOXA-244. These findings highlight a potential risk to public health and underscore the importance of integrating environmental compartments into One Health surveillance frameworks for AMR.