Sheep-associated Escherichia coli in Albania show high genomic similarity to European ovine lineages and a conserved core resistome.

Abstract

Sheep and sheep products play a notable role in Albanian culture and economy, particularly in rural regions. This sector is defined by small-scale activities and often faces challenges linked to safety and productivity. These issues necessitate the development of reforms to protect public health, boost productivity, and comply with regulatory requirements. Escherichia coli is a frequent ovine commensal, with an association with pathotypes like Shiga Toxin-encoding E. coli. The relationship between ovine bacteria and antibiotic resistance further remains poorly characterized. In this study, E. coli isolates from sheep across Albania were sequenced using Oxford Nanopore Technologies™ and characterized in silico for serotype, virulence, resistance genes, and phylogenetic relationships as isolates were compared to a global collection of animal and environmentally associated genomes. Isolates exhibited diverse serotypes and a conserved resistome comprising four genes, including EC-type β-lactamases. Four isolates were Shiga toxin-positive (stx1c predominant). Phylogenetic analyses revealed high similarity with European ovine E. coli, indicating regional relatedness and potential for resistance gene dissemination. This work provides the first genomic insight into ovine E. coli in Albania and highlights their potential role in antimicrobial resistance dynamics within livestock systems. These findings are crucial to understand for the development of Albanian agricultural practices.