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Explore specialty resources for pathogenic viruses & bacteria


NCBI Virus

A team of viral taxonomists and genomics specialists has been working to effectively curate and catalog NCBI viral data for a long time. Recently, they have teamed up a specific development team to produce a community portal to help the scientific community easily find and explore viral sequence data from RefSeq, GenBank and other NCBI repositories.

NCBI Virus is an integrative, interactive resource designed to support retrieval, display and analysis of a curated collection of virus sequences and large sequence datasets. 

Ways to search NCBI Virus - with name or sequenceNCBI Virus table, features and functionality
The team is continuing to add functionality to this resource including a new Dashboard with a map to visualize where the samples originated!
 
NCBI Dashboard example - SARS-CoV-2
This section isn't very long because, frankly, it is a pretty easy to understand and use resource!

For advanced work....



The Pathogen Detection Project and Resources

The NCBI Pathogen Detection Program was developed to facilitate the rapid identification and comparison of bacterial pathogen genomic sequences from food, environmental sources, and patients. Thereby assisting public health scientists investigate foodborne disease outbreaks by providing insight into potential food contamination sources.

Pathogen Outbreak Surveillance Partners
Several pathogen outbreak surveillance collaborators: FDA, USDA, APHL, CDC, and others....Foodborne Illness Outbreak Surveillance
Outbreak surveillance schematic

Pathogen Community Support Efforts
In addition to the RefSeq Project genome curation efforts, the NCBI has other partnerships which are specific in the microbial pathogen community.
  • NCBI runs a sequence analysis pipeline for public health laboratory genomic isolates that assembles short-read Illumina sequence data and analyzes it in the context of all other sequences in the system for both genetic relatedness and for AMR surveillance - and then provides a report back to the submitting laboratory. 
    • To facilitate public health monitoring and anti-microbial resistance research, NCBI also manages and provides access to databases for accessing the isolate information and to identify genes relevant to public health (see below).
  • NCBI participates in the consortium of agencies and laboratories for the National Antibiotic Resistance Monitoring System (NARMS) - a unique, publicly available resource that brings together isolate information, AMR phenotypes and genome sequences. One of the products is the National Database of Antibiotic Resistant Organisms (NDARO) which includes:
    • a collection of isolates with antibiogram information (measured sensitivity or resistance of a bacterial strain for antibiotic compounds).
    • and interactive Reference Gene Hierarchy and Catalog tables - containing information on key gene families including antimicrobial resistance, biocide and stress resistance, efflux potential, virulence, and antigenicity and links to relevant RefSeq and GenBank nucleotide and protein sequence records. 

To make sure that the research community has access to this critical information, the NCBI Pathogen resource has created: 
    • Isolates Browser - an interactive table that displays data for all available isolates including things such as: identified strain name, isolation type (environmental or clinical) and location, host, and curated antimicrobial resistance, virulence, or stress response genotypes and phenotypes, when available.  In addition, they may also have a link to a calculated “SNP Cluster” or other isolates of similar nucleotide sequence.
    • Microbial Browser for Identification of Genetic and Genomic Elements (MicroBIGG-E) - an interactive table providing access to genetic and genomic elements with gene family annotations, including those for antimicrobial resistance, stress response or virulence with information about the method and supporting evidence used to identify the element.  NEW: a very early prototype, interactive graphical view displaying microbial pathogen isolate information in a map and with specific genetic elements. 
Example of various NCBI Pathogen views - showing Klebiella pneumonia data
You can also read about some Success stories! 


For advanced work....

Last Reviewed: July 26, 2023