Ribeiro, S.; Chaumet, G.; Alves, K.; Nourikyan, J.; Shi, L.; Lavergne, J.-P.; Mijakovic, I.; de Bernard, S.; Buffat, L. BacSPaD: A Robust Bacterial Strains’ Pathogenicity Resource Based on Integrated and Curated Genomic Metadata. Preprints2024, 2024070837. https://doi.org/10.20944/preprints202407.0837.v1
APA Style
Ribeiro, S., Chaumet, G., Alves, K., Nourikyan, J., Shi, L., Lavergne, J. P., Mijakovic, I., de Bernard, S., & Buffat, L. (2024). BacSPaD: A Robust Bacterial Strains’ Pathogenicity Resource Based on Integrated and Curated Genomic Metadata. Preprints. https://doi.org/10.20944/preprints202407.0837.v1
Chicago/Turabian Style
Ribeiro, S., Simon de Bernard and Laurent Buffat. 2024 "BacSPaD: A Robust Bacterial Strains’ Pathogenicity Resource Based on Integrated and Curated Genomic Metadata" Preprints. https://doi.org/10.20944/preprints202407.0837.v1
Abstract
The vast array of omics data in microbiology presents significant opportunities for studying bacterial pathogenesis and creating computational tools for predicting pathogenic potential. However, the field lacks a comprehensive, curated resource that catalogs bacterial strains and their ability to cause human infections. Current methods for identifying pathogenicity determinants often introduce biases and miss critical aspects of bacterial pathogenesis.In response to this gap, we introduce BacSPaD (Bacterial Strains’ Pathogenicity Database), a thoroughly curated database focusing on pathogenicity annotations for a wide range of high-quality, complete bacterial genomes. Our rule-based annotation workflow combines metadata from trusted sources with automated keyword matching, extensive manual curation, and detailed literature review. Our analysis classified 5,502 genomes as pathogenic to humans (HP) and 490 as non-pathogenic to humans (NHP), encompassing 532 species, 193 genera, and 96 families. Statistical analysis demonstrated a significant but moderate correlation between virulence factors and HP classification, highlighting the complexity of bacterial pathogenicity and the need for ongoing research. This resource is poised to enhance our understanding of bacterial pathogenicity mechanisms and aid in the development of predictive models. To improve accessibility and provide key visualization statistics, we developed a user-friendly web interface, accessible at https://bacspad.altrabio.com.
Keywords
Bacterial pathogenicity; Genomic metadata analysis; Bioinformatics; Microbiology research; Public health surveillance
Subject
Biology and Life Sciences, Immunology and Microbiology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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