Escherichia coli is known to cause bloodstream, urinary tract, and other common infections ranging from mild to severe. An ever-increasing range of infections and antimicrobial resistance (AMR) is the major public health concern. There is a scarcity of all-inclusive (human-animals-environment) research on AMR in E. coli, thereby urgent investigation of molecular mechanisms of AMR on this organism will have paramount health and economic importance. Therefore, the aim of this research is, to determine AMR pattern, investigate the molecular mechanisms of AMR in E. coli isolates. In this study, cross-sectional research design and purposive sampling technique will be employed. E. coli will be collected from diarrheagenic calves, in contact with humans and the environment. Pathogens will further be characterized by morphologically, biochemically, and molecularly. Antimicrobial susceptibility assay will be carried out to determine their AMR profiles. E. coli genomic DNA will be extracted using the Bio Basic DNA extraction Kit and plasmid using HipurA® Plasmid Purification kit from resistant E. coli isolates. E. coli isolate Pathotyping will be carried out using simple PCR. Molecular mechanisms of AMR (plasmid and genomic-based) will be investigated using whole-genome sequencing techniques to efficiently determine multiple AMR mechanisms. A phylogenetic tree will also be constructed for identifying the genetic diversity of resistant E. coli isolates. Statistical analyses will be performed using various biological databases and freely available software tools to analyze plasmid and genomic driven resistant genes and their distribution among E. coli isolates and pathotypes.