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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 MDU PHL (Melbourne, Victoria, Australia) has incorporated AMRFinderPlus into an ISO-certified pipeline for the detection of AMR determinants from whole genome sequencing data.

Pathogen Detection data are now available on Google Cloud. See Pathogen Detection Resources at Google Cloud Platform for more information.

The Neisseria organism group (PDG000000032) has been split into its constituent species organism groups as follows:

  • Neisseria gonorrhoeae (still called Neisseria; still PDG000000032)
  • Neisseria meningitidis (PDG000000097)
  • Neisseria lactamica (PDG000000095)
  • Neisseria polysaccharea (PDG000000096)

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