Escherichia coli Genome sequencing and assembly

This project focuses on the detection and genomic characterization of colistin- and carbapenem-resistant Escherichia coli isolated from dairy cattle, poultry, and associated farm environments. Samples were collected from multiple sources including animal rectal swabs and environmental sites such as feed troughs within farm settings. Bacterial isolates were cultured and identified as Escherichia coli using standard microbiological and molecular methods. Whole genome sequencing was performed to investigate antimicrobial resistance determinants, particularly genes associated with resistance to colistin and carbapenems, as well as to analyze virulence factors, plasmid content, and genomic diversity among the isolates. The genomic data generated in this project will help improve understanding of the distribution, evolution, and potential transmission pathways of critically important antimicrobial-resistant E. coli within livestock production systems and their surrounding environments. These data will contribute to global surveillance efforts on antimicrobial resistance and support strategies aimed at mitigating the spread of multidrug-resistant bacteria across animal, environmental, and potentially human interfaces within the One Health framework.