Abstract
The emergence and dissemination of antimicrobial resistance genes (ARGs) in poultry-origin Salmonella spp. pose a threat to food safety. This study characterized the genotypic antimicrobial resistance (AMR) in Salmonella spp. isolates across the broiler chicken production chain in Karnataka, India, and the co-occurrence between AMR phenotypes and genotypes. Samples were collected from hatcheries (HAT), commercial broiler farms (CBFs), and retail meat shops (RMSs). A total of 106 Salmonella spp. isolates were obtained and screened for 35 ARGs belonging to seven antimicrobial classes using polymerase chain reaction (PCR). In total, 20/35 ARGs (57%) were detected in Salmonella spp. isolates from the entire production chain. The tetA (70%), bla (TEM) (50%), mcr-2-mcr-5 (29%-35%), aac (6 ('))-Ib-cr (21%), qnrS (19%), qnrD (18%), cmlA1 (13%), and sul1 (8%) were the most prevalent ARGs detected. The principal component analysis revealed distinct ARG profiles by production stage, with the highest diversity of ARGs found in RMS. All five mcr genes were detected in CBFs and RMSs, raising concerns about resistance to colistin, a last-resort antibiotic for human medicine. The highest co-occurrence was observed between doxycycline resistance and the tetA gene. Hierarchical clustering for AMR phenotypes and genotypes was performed using Ward's minimum variance method. A main cluster was identified, which included co-occurrence of resistance to tetracyclines, quinolones, aminoglycosides, and β-lactams within the same isolates. Clustering of AMR phenotypes did not result in clear separation of isolates by source (HAT, CBFs, or RMSs), suggesting dissemination or persistence of shared resistance profiles across production stages. This study highlights the presence and diversity of ARGs, as well as resistance to critically important antimicrobials, and calls for interventions, including antimicrobial stewardship, enhanced biosecurity, good farming and meat processing practices, and routine surveillance to mitigate AMR.