gcPathogen

gcPathogen provides a curated genomic database of human pathogens by integrating assemblies and associated metadata from infected patients, animal hosts, food products, and environmental samples to support analyses of epidemiology, antibiotic resistance, virulence factors, and mobile genetic elements.

Key Features:

• Extensive Pathogen Collection: gcPathogen includes 1,164,974 bacterial assemblies (986,044 strains, 497 taxa), 4,794 fungal assemblies (4,319 strains, 265 taxa), 89,965 viral assemblies (13,687 strains, 222 taxa), and 646 parasitic assemblies (387 strains, 159 taxa).
• Evidence-Based Compilation: The pathogen list is supported by evidence from recognized medical and governmental pathogenic lists and relevant scientific publications.
• Comprehensive Analysis Capabilities: The database supports analyses of sequence types, antibiotic resistance genes, virulence factors, and mobile genetic elements across countries, diseases, and hosts.
• Public Health Surveillance: gcPathogen enables global, long-term tracking and monitoring of pathogen evolution and dissemination for surveillance purposes.

Scientific Applications:

• Epidemiological Research: Tracking pathogen spread and evolution to aid outbreak investigations and public health responses.
• Antibiotic Resistance Monitoring: Studying resistance gene patterns to inform antimicrobial resistance surveillance and mitigation strategies.
• Virulence Factor Analysis: Investigating virulence determinants across taxa to enhance understanding of pathogenic mechanisms.

Methodology:

Integration and analysis of genomic assemblies and associated metadata with curation supported by evidence from medical and governmental pathogenic lists and scientific publications.