Food poisoning is a major global human health threat causing high morbidity and mortality every year. Among other pathogens, bacterial foodborne pathogens, such as non-typhoidal Salmonella enterica and Escherichia coli, play an important role in these infections. Given the complex epidemiology of these zoonotic pathogens that can infect various hosts (e.g. food products and environment), the direct link between their livestock host and human infections (from ‘farm to fork’) is not always simple to identify. Moreover, the risk posed by these pathogens is aggravated due to an increase in antimicrobial resistance, which result in even higher risk for public health. We combine phenotypic and genotypic information to elucidate the epidemiology of zoonotic foodborne bacterial pathogens. We study the evolution and transmission pathways of these pathogens and the resistance determinants (such as plasmids) they harbor.