Antimicrobial resistance profiling in poultry industry: a culture-independent resistome analysis and risk factor assessment

Antimicrobial resistance (AMR) is a global health crisis, often termed as the “silent pandemic”. As emphasized by the One Health framework, the food production chain, especially poultry, serves as a critical point for monitoring AMR emergence and spread. In this study, we conducted a culture-independent screening of 27 antimicrobial resistance genes (ARGs) relevant to both human and veterinary health using cloacal samples collected from 9 farms across two of Egypt’s major poultry-producing cities. Alongside ARG screening, farm-level risk and managemental factors were assessed. Results showed that broiler farms had notably higher antimicrobial usage (AMU) and ARG prevalence compared to layer farms. Genes such as sul1 and sul2, tetA and tetM were significantly more abundant in broilers (P < 0.05, Fisher's Exact Test). Beta-lactam and sulphonamide resistance genes were widespread in both production systems. Key risk factors associated with increased ARG richness included bird type, lower farm biosecurity scores, summer season, diseased birds, use of multiple antibiotic classes and absence of veterinary prescriptions. Cluster analysis revealed parC, aac (3)-1a, sul2, blaTEM, intI1, tetM, tetA, and sul1 as the most prevalent genes among the screened samples. Additionally, intI1, a known marker of horizontal transfer, was detected in 79% of the samples and significantly co-occurred with tetracycline, beta-lactam, sulphonamide, and quinolone resistance genes (P >0.05, Fisher's Exact Test). To the best of our knowledge, this is the first study in Kalyoubia and Giza, two of Egypt’s major poultry trading hubs to comprehensively assess ARGs using a rapid, culture-independent PCR-based resistome analysis, highlighting critical AMR risks and its relation to ARGs’ richness in these poultry sectors.