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<h1>Pathogen Detection <span class="usa-label-big pathogens-title-label" style="background-color: #0071bc;">Beta</span> </h1>
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NCBI Pathogen Detection integrates <a href="/pathogens/organisms/" target="_blank">bacterial and fungal pathogen genomic sequences</a> 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.</p>
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<p>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.
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<p style="margin:0">Examples:</p>
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<p style="font-size:0.9em; margin-left:0.5em; margin-top:0; margin-bottom:0">
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1. Search for isolates encoding a mobile colistin resistance gene and a KPC beta-lactamase
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<br/>
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search: <a href="/pathogens/isolates/#AMR_genotypes:mcr*%20AND%20AMR_genotypes:blaKPC*">AMR_genotypes:mcr* AND AMR_genotypes:blaKPC*</a>
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<br/>
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2. Search for Salmonella isolates from the USA
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<br/>
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search: <a href="/pathogens/isolates/#geo_loc_name:%20USA%20AND%20taxgroup_name:%22Salmonella%20enterica%22">geo_loc_name: USA AND taxgroup_name:"Salmonella enterica"</a>
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<h2 style="margin-top:1em">Explore the Data</h2>
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<div id="pathogentable" data-isolate-browser-url="/pathogens/isolates/#" data-organisms-url="/pathogens/organisms/" data-ngram-url="https://www.ncbi.nlm.nih.gov/pathogens/ngram" data-srv-url="https://www.ncbi.nlm.nih.gov/pathogens/pathogens-srv"></div>
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<li><a href="https://ftp.ncbi.nlm.nih.gov/pub/factsheets/Factsheet_Pathogen_Detection.pdf" id="pathogens_factsheet" target=_blank >Browser Factsheet</a></li>
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<li><a href="https://ftp.ncbi.nlm.nih.gov/pub/factsheets/Factsheet_AMR_Project.pdf" id="amr_factsheet">Antimicrobial Resistance Factsheet</a></li>
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<li><a style="text-decoration-skip-ink: none;" href=/pathogens/antimicrobial-resistance/ id="ndaro_about">Antimicrobial Resistance (NDARO)</a></li>
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<li><a href="/pathogens/antimicrobial-resistance/resources/" id="amr_tools">Antimicrobial Resistance Tools and Resources</a></li>
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<!-- <li><a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA313047" id="project_amr_refseq">Antimicrobial resistance reference gene database</a></li> -->
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||
<li><a style="text-decoration-skip-ink: none;" href="/pathogens/microbigge/" id="microbigge_link">Microbial Browser for Identification of Genetic and Genomic Elements <span style="white-space: nowrap;">(MicroBIGG-E)</span></a></li>
|
||
<li><a style="text-decoration-skip-ink: none;" href="/pathogens/microbigge_map/" id="microbigge_map_link">MicroBIGG-E Map</a></li>
|
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<li><a style="text-decoration-skip-ink: none;" href="/pathogens/ast" id="ast_link">Antibiotic Susceptibility Test (AST) Browser</a></li>
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<li><a style="text-decoration-skip-ink: none;" href=/pathogens/docs/gcp/ id="pathogens_data_on_cloud">Pathogen Detection data on Google Cloud</a></li>
|
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<li><a href="/pathogens/refgene/" id="refgene_link">Reference Gene Catalog</a></li>
|
||
<li><a href="/pathogens/genehierarchy/" id="genehierarchy_link">Reference Gene Hierarchy</a></li>
|
||
<li><a href="/pathogens/hmm/" id="hmm_link">Reference HMM Catalog</a></li>
|
||
<li><a href="https://www.ncbi.nlm.nih.gov/biosample/?term=antibiogram%5bfilter%5d" id="biosample_ast">Isolates with antibiotic resistant phenotypes</a></li>
|
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<!-- <li><a href=/pathogens/beta-lactamase-data-resources/ id="pathogens_lac_resource">Beta-lactamase resources</a></li> -->
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<li><a style="text-decoration-skip-ink: none;" href="https://ftp.ncbi.nlm.nih.gov/pathogen/Results/" id="pathogens_ftp">Download analysis results (FTP)</a></li>
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<h3>Submit</h3>
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<li><a href=/pathogens/submit-data/ id="pathogens_submit">How to submit data</a></li>
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<li><a href=/pathogens/submit-data/#ast id="pathogens_submit_ast">How to submit antibiotic resistance phenotypes</a></li>
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<li><a href=/pathogens/submit-beta-lactamase/ id="pathogens_submit_lac">How to submit beta-lactamases, MCR, and QNR genes</a></li>
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<li><a href="https://submit.ncbi.nlm.nih.gov/" id="submission_portal">NCBI Submission Portal</a></li>
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