Investigating antimicrobial resistancegenes in Kenya, Uganda and Tanzania cattle using metagenomics

Antimicrobial resistance (AMR) is a growing issue in African cattle production systems, threatening human and animal health and the economic value chain. This study examines the distribution of ARGs in Kenya, Tanzania, and Uganda cattle using metagenomics. The results reveal a significant number of ARGs of critical medical and economic importance, including resistance to drugs of last resort. Shared ARGs such as aph(6)-id, tet, sul2, and cfxA_gen were detected. Assembly-based methods revealed fewer ARGs than read-based methods, indicating the sensitivity and specificity of read-based methods in resistome characterization. Further surveillance is needed to estimate the intensity of antibiotic resistance and classify resistomes.