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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.

There has been a change to the Isolation type / epi_type attribute that affects min-same/min-diff computation. Now where an isolate has no information to support the setting environmental/other the Browser will no longer default to that value but instead present as NULL. This means that the min-same/min-diff values for this isolate will present as n/a, and other min-same/min-diff values for isolates clustered with this isolate may change. Please see the Help text for more details.

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"

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