Comprehensive Regional Study of ESBL Escherichia coli: Genomic Insights into Antimicrobial Resistance and Inter-Source Dissemination of ESBL Genes

Lisa Di Marcantonio^1*Sofia Chiatamone Ranieri²Michela Toro¹Alice Marchegiano¹Francesca Cito¹Nadia Sulli¹Ilaria Del Matto¹Valeria Di Lollo¹Alessandra Alessiani¹Giovanni Foschi¹Ilenia Platone²Massimiliano Paoletti¹Nicola D’Alterio¹Giuliano Garofolo¹Anna Agata Janowicz¹

• ¹Experimental Zooprophylactic Institute of Abruzzo and Molise G. Caporale, Teramo, Italy
• ²Pathology Unit, Department of Services, ASL 04, Teramo, Italy

The global dissemination of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) poses a significant public health challenge, particularly in regions with high antimicrobial resistance (AMR) occurrence. This study investigated the occurrence, genomic characteristics, and dissemination dynamics of ESBL-producing E. coli in Abruzzo, Italy, by analyzing 956 isolates from humans, livestock, wildlife, and food products. Phenotypic and genomic analyses revealed an overall ESBL-E. coli occurrence of 14.1% (135/956 samples), with significant variation across hosts: companion animals exhibited the highest occurrence (16.2%), followed by livestock and food matrices (14.6%), and wildlife (7.0%). Spatial analysis identified a hotspot in northeastern Abruzzo, where ESBL-positive isolates were 5.34 times more likely to occur (p < 0.001).Multilocus sequence typing (MLST) identified 58 sequence types (STs), with ST131 dominating human isolates (12/19). In cattle, the predominant sequence types were ST16565 (5 isolates) and ST540 (4 isolates), while in poultry, the most common sequence types were ST43 (5 isolates), ST10 (4 isolates), and ST6215 (3 isolates). ST206 (8 isolates) was the predominant sequence type in swine, and in dogs, ST10 (4 isolates) and ST3580 (3 isolates) were the most prevalent. Genomic analysis highlighted host-specific distributions of ESBL genes: blaCTX-M-15 predominated in humans and dogs, while blaCTX-M-1 was most common in pigs. Plasmid profiling revealed IncF and IncI plasmids as key vectors for horizontal gene transfer (HGT). Notably, synteny analysis of blaCTX-M-1 and blaCTX-M-15 demonstrated identical flanking regions across phylogenetically distant strains, suggesting chromosomal integration and stable maintenance of resistance genes.These findings underscore the interconnectedness of human, animal, and environmental reservoirs in AMR dissemination. The high genetic diversity observed within farms and the detection of shared clusters across hosts emphasize the need for integrated One Health interventions, including reduced antibiotic use in livestock and enhanced surveillance of high-risk environments. This study provides critical insights into local AMR dynamics, offering a model for regional mitigation strategies.