Food-animal production and the spread of antibiotic resistance: the role of ecology

Antibiotic-resistant pathogens increasingly threaten human health. Widespread application of antibiotics to animal populations raised for food, including chickens, cattle, and pigs, selects for resistance and contributes to the evolution of those pathogens. Despite a half century of research establishing the mechanisms and pathways by which antibiotic-resistant bacteria spread from food animals to people, scientists lack the appropriate data and models to estimate the public health burden of antibiotic-resistant human infections attributable to antibiotic use in food-animal production. Genomic technologies are enabling researchers to track the bidirectional transmissions of specific bacterial strains from livestock to people – and from people to livestock – that can amplify resistance traits. Concepts in ecology, which were developed to understand resource subsidies, metapopulations, and biological invasions, provide insight into the epidemiology of antibiotic resistance from genomic data. By applying ecological principles to highly resolved phylogenetic data, researchers can improve strategies for controlling antibiotic resistance.