Tracking Antimicrobial Resistance in Bovine Fecal Material across Farms in Lebanon: Sequencing and Genomic Surveillance Using a Comprehensive One Health Approach

Abstract

Antimicrobial resistance (AMR) poses a worldwide threat to both human and animal health. The rapid spread of extended-spectrum β-lactamase (ESBL)-producing, and carbapenem-resistant Gram-negative bacteria stance a serious challenge, especially in Lebanon, where limited surveillance programs are implemented, and antibiotics are often inappropriately consumed. Animal fecal material is an important reservoir of resistance genes and mobile elements. This study aims to address AMR through an integrated One Health approach. 62 ESBL-producing bacteria were isolated from fecal material collected from healthy and diseased cows. Whole-genome sequencing revealed the prevalence of multi-drug resistant Gram-negative bacteria, with Escherichia coli being the most common. Resistance to amoxicillin (59/62), ceftriaxone (45/62), and cefotaxime (45/62) were common in the recovered isolates, with some being additionally resistant to imipenem (6/62), meropenem (4/62), and ertapenem (4/60). Resistance to β-lactam was mainly linked to blaCTX-M-15 and blaTEM-1B, while plasmid typing revealed 22 replicons, the most common being IncFIB and IncFII. Notably, colistin resistance was detected in one of the recovered E. coli, and upon further characterization, it was linked to mcr-1.1 on an IncHI2A/IncF multi-replicon plasmid. The findings of this study revealed the presence of highly resistant Gram-negative bacteria, including strains with plasmid-mediated resistance to critical antibiotics such as colistin, emphasizing the risks posed to both human and livestock health. Implementing comprehensive surveillance systems, and promoting responsible antibiotic use are essential steps to mitigate the spread of AMR. These efforts must be guided by an integrated One Health approach to effectively tackle the interconnected challenges of AMR across human, animal, and environmental health sectors.