Identifying Novel Determinants of Bacterial Pathogenicity using Phylogenetic-based Orthology Analysis

The global rise in antibiotic resistance and emergence of new bacterial pathogens pose a significant threat to public health, highlighting the need for novel diagnostic and therapeutic strategies targeting the molecular mechanisms that underpin bacterial pathogenicity. In this study, we conducted the first large-scale, phylogenetic-based orthology analysis (OA) to compare the proteomes of pathogenic to humans (HP) and non-pathogenic to humans (NHP). A total of 734 strains spanning 514 species were analyzed. After developing a dedicated workflow using OrthoFinder tool, we identified 4,383 hierarchical orthologous groups (HOGs) significantly associated with pathogenicity, many of which are linked to critical factors such as stress tolerance, metabolic versatility, and antibiotic resistance. Notably, our analysis uncovered both previously known virulence factors and novel proteins that have the potential to serve as targets for innovative therapeutic interventions. By integrating curated pathogenicity annotation at the strain level from the Bacterial Strains' Pathogenicity Database (BacSPaD), we ensured the robustness of our findings, providing a reliable framework for the identification of widespread and novel putative targets for antimicrobial development and diagnostic methods. These contribute to a deeper understanding of bacterial virulence mechanisms and lay the groundwork for future research aimed at combating bacterial infections.