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<h1 id="pathgen-about-main">About the NCBI Pathogen Detection system</h1>
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<p><a href="/pathogens/">NCBI Pathogen Detection</a> project is a centralized system that
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integrates sequence data for bacterial pathogens</p>
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<p>NCBI Pathogen Detection integrates bacterial and fungal pathogen genomic
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sequences from numerous ongoing surveillance and research efforts whose sources
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include food, environmental sources such as water or production facilities, and
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patient samples. Foodborne, hospital-acquired, and other clinically infectious
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pathogens are included.</p>
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<p>The system provides two major automated real-time analyses:</p>
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<ol>
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<li>It quickly clusters related pathogen genome sequences to identify potential
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transmission chains, helping public health scientists investigate disease
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outbreaks</li>
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<li>As part of the National Database of Antibiotic Resistant Organisms (NDARO),
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NCBI screens genomic sequences using AMRFinderPlus to identify the
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antimicrobial resistance, stress response, and virulence genes found in
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bacterial genomic sequences, which enables scientists to track the spread of
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resistance genes and to understand the relationships among antimicrobial
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resistance, stress response, and virulence. </li>
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</ol>
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<p>A number of public health agencies and researchers in the US and
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internationally are collecting samples from clinical cases, from the
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environment, from food products, and from industrial production facilities to
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facilitate active, real-time surveillance of pathogens, including foodborne
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disease. Public health agencies and researchers sequence the samples and submit
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the data to NCBI, which analyzes the sequences and compares them to others in
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its database, including all genomes in GenBank, to identify closely related
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sequences. The aim is to identify closely or clonally related isolates to aid
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||
in outbreak investigation. For example the FDA, CDC, and USDA use isolates
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||
from food and the environment linked to isolates associated with human illness
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||
to aid traceback investigations and outbreak response. </p>
|
||
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<p>The <a href="https://www.ncbi.nlm.nih.gov/pathogens/isolates">NCBI Pathogen Detection Isolates Browser</a> is a web-based portal that integrates the genomic sequence, metadata, antibiotic susceptibility and resistance gene information, and the SNP cluster information.</p>
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||
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<p>The NCBI Pathogen Detection Project also analyzes the assemblies in its database in real-time for known anti-microbial resistance (AMR) genes and other genes of interest and maintains <a href="/pathogens/antimicrobial-resistance/">software and databases</a> to facilitate monitoring and research including the <a href="/pathogens/antimicrobial-resistance/">National Database of Antibiotic Resistant Organisms</a>.</p>
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<h2 aria-expanded="false" id="list-of-pathogens"><strong>List of Pathogens</strong></h2>
|
||
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||
<p>Our public health partners initially focused on sequencing and analyzing the
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||
four bacterial groups that are the major causes of foodborne illness in the US
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<em>Salmonella</em>, <em>Escherichia coli</em> and <em>Shigella</em>, and <em>Listeria</em>; but NCBI
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Pathogen Detection has since expanded our analyses to over <a href="/pathogens/organisms/">50
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||
taxa</a> such as <em>Klebsiella penumoniae</em>, <em>Staphyloccus
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aureus</em>, and <em>Streptococcus pneumoniae</em>. </p>
|
||
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<p>Additional pathogens are added as capacity permits. The <a href="/pathogens/organisms/">Organism
|
||
Groups</a> page lists the current set of organisms that are
|
||
being tracked.</p>
|
||
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<h2 aria-expanded="false" id="analysis">Analysis</h2>
|
||
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||
<p>NCBI has developed a pipeline that assembles short-read Illumina sequence data
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||
and analyzes it in the context of all other sequences in the system for both
|
||
genetic relatedness and for AMR surveillance. The pipeline compares assemblies
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||
to all other assemblies from the same taxonomic group to identify clusters of
|
||
closely related isolates using wgMLST or K-mer comparisons. Within each of
|
||
these clusters SNPs are called and phylogenetic trees inferred. Individual
|
||
phylogenetic trees for each SNP clusters are available on
|
||
<a href="http://ftp.ncbi.nlm.nih.gov/pathogen/Results/">FTP</a> as well as the <a href="/pathogens/isolates">NCBI
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Pathogen Detection Isolates Browser</a>. Results of assembly
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||
analysis for gene content are available in the <a href="/pathogens/isolates">NCBI Pathogen Detection
|
||
Isolates Browser</a> as well as the <a href="/pathogens/microbigge/">Microbial Browser for
|
||
the Identification of Genetic and Genomic Elements</a>.
|
||
Assemblies and annotations generated by our system are deposited in GenBank and
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||
made publicly available. Details of the analysis system will be published at a
|
||
future date.</p>
|
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<p>To facilitate public health monitoring and anti-microbial resistance research
|
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NCBI also maintains databases and software to identify AMR and other genes
|
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relevant to public health. Sequences associated with these databases are
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||
available in the <a href="/pathogens/refgene">Pathogen Detection Reference Gene
|
||
Catalog</a>. HMMs, and the hierarchical relationships used for naming and identifying function are in the <a href="/pathogens/hmm">Reference HMM Catalog</a> and <a href="/pathogens/genehierarchy">Reference Gene Hierarchy</a> respectively. </p>
|
||
|
||
<p>NCBI has also taken over for the Lahey
|
||
Clinic as the allele assigning authority for many beta-lactamase genes as well
|
||
as some additional families. See our <a href="/pathogens/submit-beta-lactamase/">allele request submission
|
||
page</a> for more information on allele
|
||
submissions and the <a href="/pathogens/refgene">Reference Gene Catalog</a> for existing allele assignments. The <a href="/pathogens/antimicrobial-resistance/AMRFinder/">AMRFinderPlus
|
||
software</a> is open source and
|
||
<a href="https://github.com/ncbi/amr/wiki">publicly available</a>, see our <a href="/pathogens/antimicrobial-resistance/">National
|
||
Database of Antibiotic Resistant Organisms
|
||
(NDARO)</a> page for links to all of our
|
||
publicly available AMR resources.</p>
|
||
|
||
<p>Please see the Pathogens <a href="/pathogens/pathogens_help/">Help page</a> for more detailed information on how to use these resources.</p>
|
||
|
||
<h2 aria-expanded="false" id="contributing-agencies">Contributing Agencies</h2>
|
||
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||
<p>Several U.S. health agencies and international partners are currently contributing pathogen sequence data for real-time analysis.</p>
|
||
|
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<h3 id="centers-for-disease-control-and-">Centers for Disease Control and Prevention (CDC)</h3>
|
||
|
||
<ul>
|
||
<li><a href="https://www.cdc.gov/amd/">CDC Advanced Molecular Detection</a></li>
|
||
<li><a href="https://www.cdc.gov/foodsafety/outbreaks/index.html">CDC Foodborne Outbreaks</a></li>
|
||
</ul>
|
||
|
||
<h3 id="food-and-drug-administration-fda">Food and Drug Administration (FDA)</h3>
|
||
|
||
<ul>
|
||
<li><a href="https://www.fda.gov/Food/FoodScienceResearch/WholeGenomeSequencingProgramWGS/">FDA Whole Genome Sequencing Program</a></li>
|
||
<li><a href="https://www.fda.gov/Food/FoodScienceResearch/WholeGenomeSequencingProgramWGS/#Investigators">FDA GenomeTrakr</a></li>
|
||
<li><a href="http://www.fda.gov/AnimalVeterinary/SafetyHealth/AntimicrobialResistance/NationalAntimicrobialResistanceMonitoringSystem/default.htm">The National Antimicrobial Resistance Monitoring System</a></li>
|
||
</ul>
|
||
|
||
<h3 id="us-department-of-agriculture-usd">U.S. Department of Agriculture (USDA)</h3>
|
||
|
||
<ul>
|
||
<li><a href="https://www.fsis.usda.gov/wps/portal/fsis/home">Food Safety Inspection Service (FSIS)</a></li>
|
||
<li><a href="https://www.fsis.usda.gov/sites/default/files/media_file/2020-06/Molecular-Subtyping-White-Paper.pdf">FSIS Molecular Subtyping</a></li>
|
||
</ul>
|
||
|
||
<h3 id="public-health-england-phe">Public Health England (PHE)</h3>
|
||
|
||
<ul>
|
||
<li><a href="https://www.gov.uk/government/news/whole-genome-sequencing-to-revolutionise-investigation-of-outbreaks-of-infectious-disease">PHE Whole Genome Sequencing</a></li>
|
||
</ul>
|
||
|
||
<h3 id="other-associations">Other Associations</h3>
|
||
|
||
<p>Many state public health laboratories and others are contributing data. </p>
|
||
|
||
<p><a href="http://www.aphl.org/Pages/default.aspx">Association of Public Health Laboratories (APHL)</a></p>
|
||
|
||
<h2 aria-expanded="false" id="other-initiatives"><strong>Other initiatives</strong></h2>
|
||
|
||
<p><a href="http://www.globalmicrobialidentifier.org/">Global Microbial Identifier (GMI)</a> is a grassroots attempt to build a global system of DNA genome databases for microbial and infectious disease identification and diagnostics. Projects that are flagged with the 'GMI' keyword can be found via this search <a href="/bioproject/?term=GMI%5Bkeyword%5D">/bioproject/?term=GMI[keyword]</a></p>
|
||
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<h2 aria-expanded="false" id="contact"><strong>Contact</strong></h2>
|
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<p>If you have additional questions or wish to contact the NCBI Pathogen Detection team then please send an email to:</p>
|
||
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<p><a href="mailto:pd-help@ncbi.nlm.nih.gov">pd-help@ncbi.nlm.nih.gov</a></p>
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