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Pathogen Detection Beta

To assist the National Database of Antibiotic Resistant Organisms (NDARO), NCBI Pathogen Detection identifies the antimicrobial resistance, stress response, and virulence genes found in bacterial genomic sequences. This enables scientists to track the spread of resistance genes and to understand the relationships between antimicrobial resistance and virulence.

NCBI Pathogen Detection integrates bacterial pathogen genomic sequences originating in food, environmental sources, and patients. It quickly clusters and identifies related sequences to uncover potential food contamination sources, helping public health scientists investigate foodborne disease outbreaks.

Pathogen Detection received the 2020 Federal Laboratory Consortium for Technology Transfer (FLC) Interagency Partnership Award. For more info on how this project is transforming food safety click here.

Find isolates now!

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