This study assessed the resistance profile, antibiotic resistome, and virulence characteristics of bacteria isolated from healthy broiler chickens in registered farms in Cagayan Province, Philippines. Using a descriptive cross-sectional design, 900 cloacal swab samples were collected from four broiler farms over three production cycles and processed for bacterial isolation, identification, and antimicrobial susceptibility testing. Enterobacteriaceae isolates, mainly Escherichia coli and Salmonella spp., were tested by Kirby-Bauer disc diffusion against clinically relevant antibiotics, and one representative multidrug-resistant E. coli isolate underwent whole-genome sequencing and annotation. Phenotypic results showed widespread multidrug resistance across farms and sampling periods, with particularly high resistance to tetracycline and trimethoprim-sulfamethoxazole, and notable resistance to ciprofloxacin and ceftazidime. Salmonella isolates also consistently showed tetracycline resistance. Farm interviews indicated no reported antibiotic use, yet resistance remained prevalent, suggesting that transmission may be sustained through plasmid-mediated horizontal gene transfer, sanitation gaps, transport-related contamination, litter persistence, and human or vehicle movement. Whole-genome analysis of the representative MDR isolate identified E. coli with a complex resistome and virulence repertoire, including the plasmid-associated virulence marker cvaC and multiple resistance determinants linked to efflux, target alteration, and regulatory mutations such as marR, soxR, and soxS. These findings establish a baseline for antimicrobial resistance in broiler farms and highlight the need for stronger surveillance, biosecurity validation, and antimicrobial stewardship in poultry production.
