Molecular Genomic Analyses of Enterococcus cecorum from Sepsis Outbreaks in Broilers

Area of Science:

• Veterinary microbiology
• Avian pathology
• Genomics

Background:

• Enterococcus cecorum is a normal avian intestinal flora.
• Specific isolates are linked to osteomyelitis in poultry.
• Recently, E. cecorum has caused sepsis outbreaks in young broilers.

Purpose of the Study:

• To investigate the genomic basis of emerging E. cecorum sepsis outbreaks in broilers.
• To differentiate sepsis-causing strains from commensal and osteomyelitis-associated strains.
• To identify genetic factors contributing to the new sepsis phenotype.

Main Methods:

• Phylogenomic analysis of 227 E. cecorum genomes.
• Pangenome analysis to detect gene acquisitions.
• Core genome single nucleotide polymorphism (SNP) analysis.

Main Results:

• Sepsis isolates exhibit a polyphyletic origin, closely related to commensal and osteomyelitis isolates.
• No specific gene acquisitions distinguish all sepsis isolates.
• Enriched core genome mutations, affecting protein-coding sequences, were identified in sepsis isolates.

Conclusions:

• The emergence of E. cecorum sepsis in broilers is likely driven by core genome mutations rather than horizontal gene transfer.
• Understanding these mutations is key to developing control strategies for avian sepsis.