Genetic Comparison of Enterococcus Species Isolated from Osteomyelitis Lesions and the Barn Environment of Successive Broiler Chicken Flocks

Osteomyelitis caused by <i>Enterococcus cecorum</i> is an emerging disease in broiler chickens in Canada. Other <i>Enterococcus</i> species have been reported as causative agents in certain outbreaks. The epidemiology of this disease is unknown, but contaminated barns are affected by recurring episodes. A broiler chicken flock located in Quebec, Canada, exhibited osteomyelitis lesions positive for <i>E. cecorum</i> and <i>Enterococcus faecalis</i>. Surprisingly, the following lot, in the same barn, revealed the presence of <i>E. faecalis</i>- and <i>Enterococcus raffinosus</i>-positive lesions but no <i>E. cecorum.</i> To better understand the epidemiology of these two outbreaks, verify the persistence of pathogenic isolates in the barn, and identify the possible transfer of genetic material between the <i>Enterococcus</i> species isolated from both events, 16 isolates (1 <i>E. cecorum</i>, 13 <i>E. faecalis</i>, and 2 <i>E. raffinosus</i> isolates) were sequenced, and their genomes were compared. Interestingly, more than one <i>Enterococcus</i> species could be isolated from the same lesion, while other lesions also revealed several nonclonal isolates from the same species. This might suggest the opportunistic nature of <i>Enterococcus</i> spp. as there was no predominant isolate in the lesions. The number of virulence genes varied from 1 to 34 across three <i>Enterococcus</i> species with no common virulence gene. The number and nature of antimicrobial resistance genes among those isolates were worrisome because they indicate the presence of multidrug resistance on the farm. Both plasmids and phages were shared by different <i>Enterococcus</i> species, which suggests potential horizontal gene transfer of mobile genetic elements within this enterococci population.