Omar, Kauthar M.Babajide, Abiola A.Kitundu, George L.2024-11-142024-11-142024Omar, K.M., Kitundu, G.L., Jimoh, A.O., Namikelwa, D.N., Lisso, F.M., Babajide, A.A., Olufemi, S.E. and Awe, O.I., 2024. Investigating antimicrobial resistance genes in Kenya, Uganda and Tanzania cattle using metagenomics. PeerJ, 12, p.e17181.https://doi.org/10.7717/peerj.17181https://hdl.handle.net/10566/19666Antimicrobial resistance (AMR) is a growing problem in African cattle production systems, posing a threat to human and animal health and the associated economic value chain. However, there is a poor understanding of the resistomes in small-holder cattle breeds in East African countries. This study aims to examine the distribution of antimicrobial resistance genes (ARGs) in Kenya, Tanzania, and Uganda cattle using a metagenomics approach. We used the squeezemeta-abricate (assemblybased) pipeline to detect ARGs and benchmarked this approach using the centifuge-AMRplusplus (read-based) pipeline to evaluate its efficiency. Our findings reveal a significant number of ARGs of critical medical and economic importance in all three countries, including resistance to drugs of last resort such as carbapenems, suggesting the presence of highly virulent and antibiotic-resistant bacterial pathogens (ESKAPE) circulating in East Africa.enAntimicrobial resistanceAntimicrobial Resistance Genes (ARGs)CattleMetagenomicsResistomesArticle