Analysis of Genomes of Bacterial Isolates from Lameness Outbreaks in Broilers

Abstract

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.

Embryo Lethality Assay for Evaluating Virulence of Isolates from Bacterial Chondronecrosis with Osteomyelitis in Broilers

“…We sampled 11 lame birds from that farm and determined that 7 of the birds were infected with S. aureus . Genome analyses showed that the BCO S. aureus isolates were highly related and very closely related to S. aureus isolates obtained from diseased birds or broiler meat dating from 2010 in Oklahoma all the way back to the 1970s in Europe (36, 37). The clade has been identified multiple times in Arkansas and Oklahoma for at least a decade.…”

“…Kinky back isolates showed lethality of >70% while cecal isolates showed lethality of <40%. We used E. cecorum 1415 collected from an infected vertebrae in a kinky back bird (36) but it showed no significant lethality (<40%) in the ELA. We compared three E. coli isolates from BCO lame birds (36) and found they had very different apparent virulence in the ELA.…”

“…We used E. cecorum 1415 collected from an infected vertebrae in a kinky back bird (36) but it showed no significant lethality (<40%) in the ELA. We compared three E. coli isolates from BCO lame birds (36) and found they had very different apparent virulence in the ELA. Even though these three isolates were from three different commercial broiler farms in Arkansas that were experiencing BCO outbreaks, we have shown that all 3 are very different based on whole-genome comparisons (36).…”

“…We compared three E. coli isolates from BCO lame birds (36) and found they had very different apparent virulence in the ELA. Even though these three isolates were from three different commercial broiler farms in Arkansas that were experiencing BCO outbreaks, we have shown that all 3 are very different based on whole-genome comparisons (36). This is surprising given that 1409 and 1413 were isolated on the same day from two different farms within 5 km of each other that were operated by the same integrator and supplied from the same hatchery.…”

“…Isolation and handling of the isolates has been described (1, 36). Media included: CHROMagar Orientation (CO; DRG International, Springfield Township, NJ), tryptic soy broth (Difco brand, Becton, Dickinson and Company, Franklin Lakes, NJ); and Luria broth (LB; per liter 10 g tryptone, 5 g yeast extract, 5 g NaCl).…”