Antimicrobial Resistance Profiles of Escherichia coli Isolated from Laying Hens Reared in Organic and Conventional Housing Systems

Antimicrobial resistance (AMR) in Escherichia coli originating from poultry represents an important public health and veterinary concern. This study investigated phenotypic and genotypic AMR profiles of E. coli isolated from laying hens reared under different housing systems and assessed the occurrence of avian pathogenic E. coli (APEC). A total of 60 E.coli isolates were obtained from fecal samples collected from laying hens reared in organic, cage, and floor housing systems across multiple production sites operating under the same poultry production system in Serbia. Antimicrobial susceptibility was determined using the disk diffusion method and selected AMR and virulence-associated genes were detected by PCR. Regardless of the housing system, the highest levels of phenotypic resistance were observed for tetracycline, ampicillin, and nalidixic acid. Resistance to critically important antimicrobials, including fluoroquinolones, gentamicin, and meropenem, was detected exclusively or predominantly in isolates from floor housing systems. ESBL-producing E. coli and APEC strains were most frequently identified in floor-housed flocks, whereas isolates from the organic production system showed the lowest prevalence of ESBL producers and multidrug-resistant (MDR) strains. Genotypically, the highest proportion of MDR isolates was detected in the cage housing system. The mcr-1 gene was identified in a single isolate originating from the cage system. These findings indicate that housing conditions may influence the distribution of AMR and virulence traits in E. coli. The study provides the first comparative data of this type from Serbia and highlights the importance of continued AMR surveillance across different poultry production systems.