Escherichia coli is a commensal of vertebrates but it is also the most frequently isolated Gram negative pathogen affecting human health. Antibiotics are widely used to mitigate economic losses caused by E. coli infections. The acquisition of genetic material (mobile genetic elements) by lateral gene transfer has enabled E. coli to cause a range of intestinal and extraintestinal diseases in humans, companion animals, and food animals and to counter the effective use of antimicrobials. However, antibiotics are only partially metabolised and the remainder is released, via waste into the environment. Human and animal waste contains diverse microbial gut flora, including multiple drug resistant commensal and pathogenic enterobacterial species. Animal waste is used to fertilise prime agricultural land where there is potential for contamination of fresh produce. Cost effective strategies to remove or inactivate antibiotic pollutants from human and animal waste are yet to be developed. Current practices pollute the environment and drive the evolution of multidrug resistance and pathogen evolution. Whole genome sequencing (WGS) studies are beginning to shed light on the enterobacterial populations, particularly Escherichia coli, which play an important role in colonising the gastrointestinal tracts of our major food production animals, and the mobile genetic elements they carry. We have used a combination of short and long-read sequencing to characterise the genomes (and plasmids) of over 500 multiple drug resistant commensal E. coli from several commercial swine production systems in Australia and avian pathogenic E. coli from a number Australian and international avian production systems. These datasets complement WGS of pathogenic E. coli sourced from Australian hospitals and are part of a larger body of data that will be used to gain insight into how mobile elements traffic between humans, food and companion animals, wildlife, and the environment.