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.
The new MicroBIGG-E Map interface shows the geographical distribution of acquired resistance alleles/genes and point mutations.
January 2024 - Organism Group change: The Enterococcus faecium organism group (PDG000000071) has been split into its constituent species-specific organism groups as follows: Enterococcus faecium remains PDG000000071, and Enterococcus hirae has been split to a new organism group (PDG000000122). In addition, the wgMLST locus found QC threshold has been lowered for Enterococcus faecium thus admitting more isolates into the SNP clustering process.
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
- Isolates Browser
- Microbial Browser for Identification of Genetic and Genomic Elements (MicroBIGG-E)
- MicroBIGG-E Map
- Pathogen Detection data on Google Cloud
- Reference Gene Catalog
- Reference Gene Hierarchy
- Reference HMM Catalog
- Isolates with antibiotic resistant phenotypes
- Download analysis results (FTP)