Pathogen Detection Beta
NCBI Pathogen Detection integrates bacterial and fungal pathogen genomic sequences from numerous ongoing surveillance and research efforts whose sources include food, environmental sources such as water or production facilities, and patient samples. Foodborne, hospital-acquired, and other clinically infectious pathogens are included.
The system provides two major automated real-time analyses: 1) it quickly clusters related pathogen genome sequences to identify potential transmission chains, helping public health scientists investigate disease outbreaks, and 2) as part of the National Database of Antibiotic Resistant Organisms (NDARO), NCBI screens genomic sequences using AMRFinderPlus to identify the antimicrobial resistance, stress response, and virulence genes found in bacterial genomic sequences, which enables scientists to track the spread of resistance genes and to understand the relationships among antimicrobial resistance, stress response, and virulence.
New Milestone! NCBI Pathogen Detection Reaches 2 Million Isolates
The Vibrio parahaemolyticus organism group clustering method has been changed to use a wgMLST schema, starting with edition PDG000000023.956. Clustering results for the existing isolates have changed. In addition, other species formerly in this organism group were split to new organism groups:
- Vibrio alginolyticus (PDG000000136.1)
- Vibrio antiquarius (PDG000000137.1)
- Vibrio diabolicus (PDG000000138.1)
Search isolates:
Examples:
1. Search for isolates encoding a mobile colistin resistance gene and a KPC beta-lactamase
search: AMR_genotypes:mcr* AND AMR_genotypes:blaKPC*
2. Search for Salmonella isolates from the USA
search: geo_loc_name: USA AND taxgroup_name:"Salmonella enterica"
Explore the Data
Learn More
Data Resources
- Isolates Browser
- Microbial Browser for Identification of Genetic and Genomic Elements (MicroBIGG-E)
- MicroBIGG-E Map
Antibiotic Susceptibility Test (AST) Browser
- Pathogen Detection data on Google Cloud
- Reference Gene Catalog
- Reference Gene Hierarchy
- Reference HMM Catalog
- Isolates with antibiotic resistant phenotypes
- Download analysis results (FTP)