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 isolated several distinct bacterial species. The results show that BCO-lameness pathogens on particular farms can differ significantly.

Genomes for Staphylococcus aureus were highly related to chicken isolates from Europe, but present in the Arkansas area for at least a decade. Phylogenomics suggest that this S. aureus has been restricted to poultry for more than 40 years. Detailed analysis of genomes from two neighboring clades of S. aureus human and chicken isolates, identifies 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.

Genomes assembled from Escherichia coli isolates were quite different between farms, and more similar to genomes from different geographical locations. The E. coli phylogenomics suggests frequent host shifts for this species, in contrast to S. aureus. Isolate-specific genome characterizations will help further our understanding of the disease mechanisms 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.