Rapid assessment of clinical severity for salmonellosis cases via protein family domain analysis and machine learning

<i>Salmonella</i> is a common pathogen, infecting more than a million people yearly. Rapid assessment of clinical case severity is essential for improving patient outcomes and optimizing healthcare resources. Advancements in genome sequencing technologies have enabled the analysis of bacterial genomes from many clinical cases, opening up new opportunities for precise and timely diagnosis. This study proposes a genome-based framework for identifying critical <i>Salmonella</i> cases before the onset of critical symptoms and facilitating early medical intervention. By leveraging protein family (Pfam) domains as the representation for genomic data, the complex genetic profiles of <i>Salmonella</i> cases are simplified into interpretable features. The severity levels of cases were investigated through rigorous data analysis, resulting in a set of 70 Pfam domains that could be potentially used as biomarkers. Machine Learning was employed to assess the predictive power of the curated Pfam biomarkers, achieving high accuracy (~93%) in sorting cases into critical, moderate, and mild categories. The results demonstrate the efficacy of the proposed approach. This framework highlights the potential of using bacterial genomic data in clinical decision-making, opening the window for timely personalized interventions for <i>Salmonella</i> infection management.