Simple and accurate genomic classification model for distinguishing between human and pig Staphylococcus aureus

Area of Science:

• Microbiology
• Genomics
• Epidemiology

Background:

• Staphylococcus aureus (S. aureus) causes significant human and animal infections, necessitating control of its transmission between species.
• Understanding host-specific genetic variations in S. aureus is crucial for preventing zoonotic spread.

Purpose of the Study:

• To identify host-associated genetic determinants differentiating human and pig S. aureus strains.
• To develop a simple and accurate method for predicting S. aureus cross-species transmission risk.

Main Methods:

• A two-stage genome-wide association study (GWAS) was conducted comparing human and pig S. aureus genomes.
• Multiple GWAS analyses identified significant k-mers associated with host species.
• Bayesian inference was used to determine transmission directions for specific S. aureus lineages.

Main Results:

• Six consensus significant k-mers were identified, effectively distinguishing between human and pig S. aureus.
• The best k-mer predictor achieved 98.12% classification accuracy, comparable to SNP-based phylogenies.
• A k-mer model predicted 90% of S. aureus isolates from farm workers as livestock-associated, indicating high transmission risk.
• Specific transmission routes were inferred: human-to-pig for ST5 and pig-to-human for ST398.

Conclusions:

• A novel, highly accurate k-mer based model can distinguish S. aureus host origins and predict cross-species transmission risk.
• Findings highlight significant S. aureus transmission between livestock and humans, particularly in farm environments.
• The study provides valuable genetic insights for surveillance and control strategies against S. aureus zoonotic transmission.