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AMR Resources -
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Pathogen Detection - NCBI
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<h1 id="amr-resources">AMR Resources</h1>
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<p><img alt="Resources Hero" src="/core/assets/pathogens/images/resources-hero.jpg"/></p>
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<p><em>Antibiotic susceptibility testing using a disk diffusion assay</em></p>
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<div class="usa-width-one-whole">
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<h3 style="text-align: center;">NCBI Resources</h3>
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<ul class="usa-accordion">
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<p>
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In response to the rising threat of AMR, the White House developed the <a href="https://obamawhitehouse.archives.gov/blog/2015/03/27/our-plan-combat-and-prevent-antibiotic-resistant-bacteria">National Action Plan</a> for Combating Antibiotic-Resistant Bacteria in 2015. NCBI has built resources and tools to achieve several specific project goals.
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</p>
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<li><button aria-controls="resource-1" aria-expanded="true" class="usa-accordion-button">Pathogen Detection Isolates Browser</button>
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<div class="usa-accordion-content" id="resource-1">
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<p>The Isolates Browser was built to answer two specific questions for incoming pathogen genomes: 1) is this isolate clonally related to anything else in the database? and 2) what is the AMR repertoire of this isolate? It integrates pathogen metadata, links to SNP clusters for genetically related isolates, and antimicrobial resistance genotypes and phenotypes, allowing users to browse and search over 300,000 pathogen isolates, effectively and efficiently providing access to the National Database of Antibiotic Resistant Organisms</p>
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<p><a href="/pathogens/isolates#search/">Browse
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genomes with AMR genotypes or phenotypes</a></p>
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<p>Example searches:</p>
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||
<ul>
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||
<li><a href="/pathogens/isolates/#PRJNA844926%20PRJNA835887%20PRJNA635420%20PRJNA635383%20PRJNA592083%20PRJNA577141%20PRJNA562719%20PRJNA523732%20PRJNA523730%20PRJNA523433%20PRJNA523429%20PRJNA523428%20PRJNA523427%20PRJNA523425%20PRJNA391514%20PRJNA391513%20PRJNA391510%20PRJNA317148%20PRJNA317143%20PRJNA317141%20PRJNA316321%20PRJNA292904%20PRJNA292902%20PRJNA292901">Retrieve all isolates from the FDA-CDC Antimicrobial Resistance Bank</a></li>
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<li><a href="/pathogens/isolates#/search/AMR_genotypes:blaKPC*">Search for pathogen isolates containing blaKPC genes</a></li>
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<li><a href="/pathogens/isolates#/search/AMR_genotypes:mcr*">Search for pathogen isolates containing mobile colistin resistant genes</a></li>
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<li><a href="/pathogens/isolates#/search/AMR_genotypes:blaKPC*%20AND%20AST_phenotypes:(+meropenem=R%20+imipenem=R)%20AND%20AST_phenotypes:(+doripenem=S)">Search for pathogen isolates with blaKPC with resistance to meropenem and imipenem but sensitive to doripenem</a></li>
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</ul>
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<p><a href="https://ftp.ncbi.nlm.nih.gov/pub/factsheets/Factsheet_AMR_Project.pdf">To find out more about how to use the Isolate Browser to identify antimicrobial resistant organisms see the AMR Factsheet </a></p>
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</div>
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</li>
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<!-- MicroBIGG-E -->
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<li><button aria-controls="microbigge" class="usa-accordion-button" aria-expanded="false">Microbial Browser for Identification of Genetic and Genomic Elements (MicroBIGG-E)</button>
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<div class="usa-accordion-content" id="microbigge">
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||
<p>MicroBIGG-E contains genetic and genomic elements identifyed in assemblies
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analyzed by <a href="/pathogens/antimicrobial-resistance/AMRFinder/">AMRFinderPlus</a> as part of the Pathogen Detection Pipeline. See the <a href="/pathogens/pathogens_help/#microbigge">MicroBIGG-E
|
||
documentation</a>, the <a href="https://github.com/ncbi/amr/wiki">AMRFinderPlus
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||
wiki</a> for more information on how
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AMRFinderPlus works, and the Pathogen Detection <a href="/pathogens/pathogens_help/#refgene-what-is">Reference Gene
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||
Catalog</a> and <a href="/pathogens/docs/gene_hierarchy/#what-is-the-reference-gene-hiera">Reference Gene
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Hierarchy</a>
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for the elements that AMRFinderPlus is searching for.</p>
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Example searches:
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||
<ul>
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<li>Search for all Shigatoxin genes in MicroBIGG-E: <a href="/pathogens/microbigge/#element_symbol:stx*">element_symbol:stx*</a></li>
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<li>Search for all Carbapenemases resistance genes and point mutations in E. coli: <a href="/pathogens/microbigge/#subclass:CARBAPENEM%20AND%20taxgroup_name:%22E.coli%20and%20Shigella%22%20">subclass:CARBAPENEM AND taxgroup_name:"E.coli and Shigella"</a></li>
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</ul></div>
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</li>
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<!-- End MicroBIGG-E -->
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<li><button aria-controls="resource-2" class="usa-accordion-button" aria-expanded="false">Pathogen Detection Reference Gene Catalog</button>
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<div class="usa-accordion-content" id="resource-2">
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||
<p>The AMR Reference Database.
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NCBI curates an ever-growing reference set of antimicrobial resistance genes and proteins, point mutations, and is now starting to incorporate stress response (biocide, metal, heat resistance) and virulence genes. The source of input for this curated database include: 1) allele assignments, 2) exchanges with other external curated resources, 3) reports of novel antimicrobial resistance proteins in the literature.</p>
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<p><a href="/pathogens/isolates#refgene/">Browse
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NCBI's Pathogen Detection Reference Gene Catalog</a></p>
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<p><a href="/pathogens/hmm/">Browse NCBI's Pathogen Detection Reference HMM Catalog</a></p>
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<p> Example searches:</p>
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<ul>
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<li><a href="/pathogens/isolates#/refgene/subclass:CARBAPENEM">Search for all carbapenem resistant genes</a></li>
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||
<li><a href="/pathogens/isolates#/refgene/subtype:%22POINT%22%20AND%20organism:%22Escherichia%22%20AND%20class:*QUINOLONE">Search for all point mutations in Escherichia that confer resistance to quinolones</a></li>
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||
</ul>
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||
<p><a href="https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/Data/">Download
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NCBI's AMR reference gene database</a></p>
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<p><a href="/bioproject/PRJNA313047">NCBI BioProject for AMR reference gene database</a></p>
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||
</div>
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||
</li>
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||
<li><button aria-controls="refgenehierarchy" class="usa-accordion-button" aira-expanded="false">Pathogen Detection Reference Gene Hierarchy</button>
|
||
<div class="usa-accordion-content" id="refgenehierarchy">
|
||
<p>The <a href="/pathogens/genehierarchy">Pathogen Detection Reference Gene Hierarchy</a> is a web-based view into the hierarchy of genes, families, and upstream nodes that our curators use to organize and relate the genes and HMMs in the Pathogen Detection Reference Gene Catalog and Pathogen Detection Reference HMM Catalog. This hierarchy drives the gene identification and naming algorithm of AMRFinderPlus. is
|
||
a web-based view into the hierarchy of genes, families, and upstream nodes that
|
||
our curators use to organize and relate the genes and HMMs in the <a href="/pathogens/refgene">Pathogen
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||
Detection Reference Gene Catalog</a> and <a href="/pathogens/hmm">Pathogen Detection
|
||
Reference HMM Catalog</a>. This hierarchy drives the gene
|
||
identification and naming algorithm of
|
||
<a href="https://github.com/ncbi/amr/wiki">AMRFinderPlus</a>. </p>
|
||
|
||
Example searches:
|
||
<ul>
|
||
<li><a href="/pathogens/genehierarchy/#blaOXA">View NCBI's organization of blaOXA gene families</a></li>
|
||
<li><a href="/pathogens/genehierarchy/#symbol%3Aaac%286%27%29-Ib%2A%0A">Investigate the different drug resistance profiles of aac(6')-Ib aminoglycoside modifying ezymes</a></li>
|
||
</ul>
|
||
<li><button aria-controls="refHMMcatalog" class="usa-accordion-button" aria-expanded="false">Pathogen Detection Reference HMM Catalog</button>
|
||
<div class="usa-accordion-content" id="refHMMcatalog">
|
||
|
||
The <a href="/pathogens/hmm">Pathogen Detection Reference HMM Catalog</a> is a
|
||
web-based portal to our highly curated database of reference <a href="/genome/annotation_prok/evidence/#hmm-def">hidden Markov models</a>
|
||
(HMMs) used by <a href="/pathogens/antimicrobial-resistance/AMRFinder/">AMRFinderPlus</a> in
|
||
concert with gene sequences in the <a href="/pathogens/refgene">Pathogen
|
||
Detection Reference Gene Catalog]</a> to identify antimicrobial resistance
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||
(AMR) genes as well as some stress resistance and virulence genes.
|
||
|
||
</div>
|
||
</li>
|
||
<li><button aria-controls="AST_browser" class="usa-accordion-button" aria-expanded="false">Pathogen Detection AST Browser</button>
|
||
<div class="usa-accordion-content" id="AST_browser">
|
||
|
||
The <a href="/pathogens/ast">Pathogen Detection AST Browser</a> is a
|
||
web-based portal to view antibiotic susceptibility test (AST) results for isolates in the Pathogen Detetction system. This data is not submitters for all isolates in our system. Summary information (e.g., SIR calls) are also included in the "AST Phenotypes" column in the <a href="/pathogens/isolates">Isolates Browser</a>.
|
||
</div>
|
||
</li>
|
||
<li><button aria-controls="resource-3" class="usa-accordion-button" aria-expanded="false">AMRFinderPlus </button>
|
||
<div class="usa-accordion-content" id="resource-3">
|
||
<p> The AMRFinderPlus software and databases identify acquired antimicrobial resistance genes in bacterial protein and/or assembled nucleotide sequences as well as known resistance-associated point mutations for several taxa. With AMRFinderPlus we added select members of additional classes of genes such as virulence factors, biocide, heat, acid, and metal resistance genes. AMRFinderPlus uses a combination of BLAST alignments, HMMER hidden Markov model searches, the <a href="/pathogens/refgene">Reference Gene Catalog</a>, the <a href="/pathogens/genehierarchy">Reference Gene Hierarchy</a>, the <a href="/pathogens/hmm">Reference HMM Catalog</a>, curated cutoffs, and a tuned ruleset to accurately detect and name genes and point mutations in assembled nucleotide and/or protein sequences.</p>
|
||
|
||
- <a href="/pathogens/antimicrobial-resistance/AMRFinder/">Download
|
||
AMRFinderPlus to identify AMR genes</a><br/>
|
||
- <a href="https://github.com/ncbi/amr/wiki">AMRFinderPlus wiki</a><br/>
|
||
- <a href="https://github.com/ncbi/amr/wiki/Methods">For more information on how AMRFinderPlus operates</a><br/>
|
||
- <a href="https://github.com/ncbi/amr/wiki/Installing-AMRFinder">Installation instructions</a><br/>
|
||
</div>
|
||
</li>
|
||
<li><button aria-controls="resource-5" class="usa-accordion-button" aria-expanded="false">Submit
|
||
sequence and phenotype data related to AMR</button>
|
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<p><a href="/pathogens/submit">Submit
|
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sequence and phenotype data related to AMR</a></p>
|
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<p><a href="/biosample/docs/antibiogram/">BioSample documentation on antibiogram submissions</a></p>
|
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<p><a href="/pathogens/submit-beta-lactamase/">How to Request New Alleles for Beta-Lactamase, MCR, and Qnr Genes</a></p>
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<p><a href="https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/MiCId.html">Microorganism Classification and Identification – using mass spectrometry data (MS/MS spectra)</a></p>
|
||
<p><a href="https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/MiCId.html">MiCId</a> is a software tool that processes mass spectrometry tandem spectra (MS/MS) data for identification and classification of microorganisms. Identify microorganism, biomass estimation, and antimicrobial resistance proteins.</p>
|
||
<p><a href="https://ftp.ncbi.nlm.nih.gov/pub/qmbp/qmbp_ms/MiCId">C++ source code: FTP (includes GUI)</a></p>
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<h3 style="text-align: center;">Other Resources</h3>
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<p>
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There are signficant contributions towards combatting antibiotic resistant bacteria across multiple federal agenices.</p>
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|
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<p><a href="https://www.niaid.nih.gov/research/antimicrobial-resistance">NIAID AMR Summary</a></p>
|
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<p><a href="https://www.niaid.nih.gov/research/antibacterial-resistance-leadership-group">NIAID Antibiotic Resistance Leadership Group</a></p>
|
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<p><a href="https://www.patricbrc.org/">NIAID PATRIC</a></p>
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|
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<p><a href="https://www.cdc.gov/drugresistance/index.html">CDC AMR Page</a></p>
|
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<p><a href="https://www.cdc.gov/drugresistance/solutions-initiative/index.html">CDC Investments and Initiatives</a></p>
|
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<p><a href="https://www.cdc.gov/drugresistance/laboratories.html">CDC AR Lab Network</a></p>
|
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<p><a href="https://www.cdc.gov/drugresistance/resistance-bank/index.html">CDC AR Isolate Bank</a></p>
|
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<p>Isolate Bank isolates that are sequenced are deposited at NCBI and <a href="/pathogens/isolates/#PRJNA844926%20PRJNA835887%20PRJNA635420%20PRJNA635383%20PRJNA592083%20PRJNA577141%20PRJNA562719%20PRJNA523732%20PRJNA523730%20PRJNA523433%20PRJNA523429%20PRJNA523428%20PRJNA523427%20PRJNA523425%20PRJNA391514%20PRJNA391513%20PRJNA391510%20PRJNA317148%20PRJNA317143%20PRJNA317141%20PRJNA316321%20PRJNA292904%20PRJNA292902%20PRJNA292901">can be found in Pathogen Detection</a>
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|
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|
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<p><a href="https://www.fda.gov/consumers/consumer-updates/combating-antibiotic-resistance">FDA AMR Summary</a></p>
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|
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|
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<p>WHO recognizes increasing AR threat.
|
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</p>
|
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<p><a href="https://www.who.int/news-room/fact-sheets/detail/antibiotic-resistance">WHO AMR Summary</a></p>
|
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<p><a href="https://www.who.int/publications/i/item/9789241509763">WHO Global Action Plan</a></p>
|
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<p><a href="https://www.who.int/publications/i/item/9789241564748">WHO Surveillance Report</a></p>
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|
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|
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<p><a href="https://www.fao.org/antimicrobial-resistance/en/">FAO AMR Summary</a></p>
|
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<p><a href="https://www.fao.org/documents/card/en/c/cc0822en">FAO InFARM System</a></p>
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<p>Accelerating drug development through incentives.
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<p><a href="https://carb-x.org/">CARB-X page</a></p>
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</footer>
|
||
<!-- ========== END FOOTER ========== -->
|
||
<!-- javascript to inject NWDS meta tags. Note: value of nwds_version is updated by "npm version" command -->
|
||
|
||
<script type="text/javascript">
|
||
var nwds_version = "1.2.3";
|
||
|
||
var meta_nwds_ver = document.createElement('meta');
|
||
meta_nwds_ver.name = 'ncbi_nwds_ver';
|
||
meta_nwds_ver.content = nwds_version;
|
||
document.getElementsByTagName('head')[0].appendChild(meta_nwds_ver);
|
||
|
||
var meta_nwds = document.createElement('meta');
|
||
meta_nwds.name = 'ncbi_nwds';
|
||
meta_nwds.content = 'yes';
|
||
document.getElementsByTagName('head')[0].appendChild(meta_nwds);
|
||
|
||
var alertsUrl = "/core/alerts/alerts.js";
|
||
if (typeof ncbiBaseUrl !== 'undefined') {
|
||
alertsUrl = ncbiBaseUrl + alertsUrl;
|
||
}
|
||
</script>
|
||
|
||
|
||
|
||
|
||
|
||
<!-- JavaScript -->
|
||
|
||
<script src="/pathogens/static/django_uswds/uswds/js/uswds.js"></script>
|
||
|
||
|
||
|
||
<script src="https://code.jquery.com/jquery-3.5.0.min.js"
|
||
integrity="sha256-xNzN2a4ltkB44Mc/Jz3pT4iU1cmeR0FkXs4pru/JxaQ="
|
||
crossorigin="anonymous">
|
||
</script>
|
||
<script>
|
||
var fallbackJquery = "/pathogens/static/base/js/jquery-3.5.0.min.js";
|
||
window.jQuery || document.write("<script src=" + fallbackJquery + ">\x3C/script>")
|
||
</script>
|
||
|
||
|
||
|
||
<script src="/pathogens/static/nwds/js/nwds.js" type="text/javascript"> </script>
|
||
<script src="/pathogens/static/nwds/js/header.js" type="text/javascript"> </script>
|
||
<script src="/pathogens/static/nwds/js/ncbipopup.js" type="text/javascript"> </script>
|
||
<script src="/pathogens/static/nwds/js/ncbiclearbutton.js" type="text/javascript"> </script>
|
||
<script src="/pathogens/static/nwds/js/override-uswds.js" type="text/javascript"> </script>
|
||
<script src="/pathogens/static/nwds/js/ncbifeedback.js" type="text/javascript"> </script>
|
||
|
||
|
||
|
||
<script type="text/javascript" src="https://www.ncbi.nlm.nih.gov/core/pinger/pinger.js"> </script>
|
||
|
||
|
||
|
||
<script type="text/javascript" src="/pathogens/static/main/scripts/page-search.js" charset="utf-8"></script>
|
||
|
||
|
||
|
||
</body>
|
||
</html> |