PathoFact

PathoFact predicts virulence factors, bacterial toxins, and antimicrobial resistance genes from metagenomic datasets to assess pathogenicity determinants and their genomic context.

Key Features:

• High accuracy and specificity: Predicts virulence factors, bacterial toxins, and antimicrobial resistance genes with accuracy 0.92, 0.83, and 0.99 and specificity 0.96, 0.99, and 0.98, respectively.
• Contextualized predictions: Integrates prediction of mobile genetic elements to consider genomic context and potential mobility of virulence factors, toxins, and resistance genes.
• Modular design: Implemented as independent modules for virulence factors, toxins, and antimicrobial resistance genes, enabling selective use of components.

Scientific Applications:

• Validation on case-control datasets: Validated on three publicly available case-control metagenomic datasets.
• Infection studies: Identifies virulence factors and resistance genes associated with infections to inform pathogenic potential analyses.
• Chronic disease research: Detects bacterial toxins and signature genes distinguishing disease and control groups in chronic disease studies.

Methodology:

Integrates predictions of virulence factors, bacterial toxins, and antimicrobial resistance genes with analysis of mobile genetic elements to contextualize the genomic landscape surrounding these genes.