The client wanted to confirm and identify virulence factors in a gut bacterium that normally resides harmlessly in animals but can cause infection under stress or immunosuppression. Population structure complicated the distinction between pathogenic and commensal strains.

Our Approach

We gathered genomic data, analysed phylogenetic structure and identified virulence factors while detecting biases in the data.

• Genomic data gathering & phylogenetic analysis: Collected complete genome sequences and built a phylogenetic tree to distinguish pathogenic and commensal clades.
• Virulence-factor identification: Used BLAST and a phylogenetically corrected method to identify virulence factors predominant in pathogenic strains.
• Literature review & bias detection: Reviewed literature to resolve discrepancies and detected biases such as population structure and sampling.

The Outcome

• Determined virulence factors using both database searches and corrected statistical methods.
• Highlighted the need to account for population structure in comparative genomics.
• Provided recommendations for future analyses, including immunoinformatics to identify epitopes.

Why It Matters

Correcting for phylogenetic confounders is essential to accurately identify virulence factors. This case underscores the importance of rigorous comparative genomics in animal health research.