Analysis of Genomes of Bacterial Isolates from Lameness Outbreaks in Broilers

We investigated lameness outbreaks at commercial broiler farms in Arkansas. From Bacterial Chondronecrosis with Osteomyelitis (BCO) lesions, we obtained different isolates of distinct bacterial species. Genome assemblies for Escherichia coli and Staphylococcus aureus isolates show that BCO-lameness pathogens on farms can differ significantly. Genomes assembled from Escherichia coli isolates from three different farms were quite different from each other, and more similar to isolates from different hosts and geographical locations. The S aureus genomes were closely related to chicken isolates from Europe, and appear to have been restricted to chicken hosts for more than 40 years. Detailed analyses of genomes from this clade of chicken isolates with a sister clade of human isolates, suggests the acquisition of a particular pathogenicity island in the transition from human to chicken pathogen and that pathogenesis in chickens may depend on this mobile element. Phylogenomics is consistent with more frequent host shifts for E. coli , while S. aureus appears to be highly host restricted. Isolate-specific genome characterizations will help further our understanding of the disease mechanisms and spread of BCO-lameness, a significant animal welfare issue. Importance Detailed inspection of the genome sequences of different bacterial species associated with causing lameness in broiler chickens reveals that one species, E. coli , appears to easily switch hosts from humans to chickens and other host species. Conversely, isolates of S. aureus appear to be restricted to specific hosts. One potential mobile DNA element has been identified that may be critical for causing disease in chickens for S. aureus . ### Competing Interest Statement The authors have declared no competing interest.