BacSPaD: A Robust Bacterial Strains’ Pathogenicity Resource Based on Integrated and Curated Genomic Metadata
Artikel i vetenskaplig tidskrift, 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

Författare

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, Elektroteknik, Kommunikation, Antenner och Optiska Nätverk

Jean Pierre Lavergne

Institut de Biologie et Chimie des Protéines

Ivan Mijakovic

Chalmers, Life sciences, Systembiologi

Novo Nordisk Fonden

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

Europeiska kommissionen (EU) (EC/H2020/955605), 2021-08-17 -- 2024-08-16.

Ämneskategorier

Mikrobiologi

Bioinformatik (beräkningsbiologi)

Bioinformatik och systembiologi

DOI

10.3390/pathogens13080672

Mer information

Senast uppdaterat

2024-09-23