BacSPaD: A Robust Bacterial Strains’ Pathogenicity Resource Based on Integrated and Curated Genomic Metadata
Journal article, 2024

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 5502 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.

microbiology research

public health surveillance

bacterial pathogenicity

bioinformatics

genomic metadata analysis

Author

Sara Ribeiro

Institut de Biologie et Chimie des Protéines

AltraBio SAS

Guillaume Chaumet

AltraBio SAS

Karine Alves

AltraBio SAS

Julien Nourikyan

AltraBio SAS

Shi Lei

Chalmers, Electrical Engineering, Communication, Antennas and Optical Networks

Jean Pierre Lavergne

Institut de Biologie et Chimie des Protéines

Ivan Mijakovic

Chalmers, Life Sciences, Systems and Synthetic Biology

Novo Nordisk Foundation

Simon de Bernard

AltraBio SAS

Laurent Buffat

AltraBio SAS

Pathogens

20760817 (eISSN)

Vol. 13 8 672

Commercializing a new class of antibacterial surfaces: polymer graphene nanocomposites

European Commission (EC) (EC/H2020/955605), 2021-08-17 -- 2024-08-16.

Subject Categories

Microbiology

Bioinformatics (Computational Biology)

Bioinformatics and Systems Biology

DOI

10.3390/pathogens13080672

More information

Latest update

9/23/2024