🚀 In the framework of the PEST-BIN project, we are thrilled to announce that Sara Ribeiro‘s work titled “Identifying potential novel widespread determinants of bacterial pathogenicity using phylogenetic-based orthology analysis“ has been published in Frontiers in Microbiology. 🧬
This achievement highlights Sara’s exceptional effort in conducting a large-scale, phylogenetic-based orthology analysis (OA) to compare the proteomes of pathogenic to humans (HP) and non-pathogenic to humans (NHP) bacterial strains. The results of this study have the potential to significantly impact public health by contributing to efforts to mitigate the challenges posed by infectious diseases.
Congratulations, Sara, on this remarkable publication! 🎉
#PESTBIN #MSCA #ITN #BacterialPathogenicity #Genomics #Research #Pathogens #InfectiousDiseases
Article Summary:
Introduction:
The global rise in antibiotic resistance and the emergence of new bacterial pathogens pose significant threats to public health. Novel approaches to uncover potential diagnostic and therapeutic targets for these pathogens are urgently needed.
Methods:
In this study, we conducted a large-scale, phylogenetic-based orthology analysis (OA) to compare the proteomes of 734 bacterial strains, including 514 species and 91 families, classified as either HP or NHP.
Results:
Using a dedicated workflow, we identified 4,383 hierarchical orthologous groups (HOGs) significantly associated with the HP label. These HOGs are linked to critical factors such as stress tolerance, metabolic versatility, and antibiotic resistance. Both known virulence factors (VFs) and potential novel widespread pathogenicity determinants were uncovered, supported by statistical testing and complementary protein domain analysis.
Discussion:
By integrating curated strain-level pathogenicity annotations from BacSPaD with phylogeny-based OA, we introduce a novel approach and provide a valuable resource for bacterial pathogenicity research. The growing threat of antibiotic-resistant bacterial pathogens emphasizes the critical need to discover potential new determinants of pathogenicity for advancing therapeutic strategies.
Context and Importance:
The increasing threat of antibiotic-resistant bacterial pathogens underscores the urgent need to discover new determinants of pathogenicity to advance therapeutic strategies. Existing databases, such as the Virulence Factor Database (VFDB), catalog experimentally validated virulence factors (VFs) of HP bacteria. However, the continual emergence of new pathogens necessitates methods that can uncover potential novel widespread pathogenicity determinants not yet captured in existing resources.
Previous Studies and Limitations:
Efforts to computationally identify genes, proteins, or domains associated with bacterial pathogenicity have been conducted in both plant- and human-associated bacteria. However, these studies primarily relied on protein families defined through sequence-based comparisons, which may overlook deeper evolutionary relationships. This complexity necessitates advanced computational approaches that consider both sequence and evolutionary context, such as orthology analysis (OA).
Our Innovative Approach:
We introduce a novel approach for identifying potential new and widespread bacterial pathogenicity determinants by applying a phylogenetic-based OA across a wide spectrum of bacterial taxa. By analyzing 734 strains from 514 species with precise annotations, we could redefine bacterial proteomes with HOGs across 23% of currently known bacterial species able to infect humans. This approach uncovered potential novel widespread pathogenicity determinants, including most common pathogens, as demonstrated by a comparison with a comprehensive list of human-associated pathogens and the FDA-ARGOS Wanted Organism list.