FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences

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Detection of low abundance pathogen sequences remains a challenge for metagenomic Next Generation Sequencing (NGS). We introduce FLASH (Finding Low Abundance Sequences …"><meta name="keywords" content="pmid:31114866, PMC6698650, doi:10.1093/nar/gkz418, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, Jenai Quan, Charles Langelier, Emily D Crawford, Anti-Bacterial Agents / pharmacology*, Bacteria / classification, Bacteria / drug effects, Bacteria / genetics, Bacterial Infections / diagnosis, Bacterial Infections / genetics, Bacterial Infections / prevention & control, CRISPR-Cas Systems*, Computational Biology / methods*, Drug Resistance, Bacterial / drug effects*, Drug Resistance, Bacterial / genetics, High-Throughput Nucleotide Sequencing / methods*, Humans, Metagenomics / methods, Reproducibility of Results, Sensitivity and Specificity, PubMed Abstract, NIH, NLM, NCBI, National Institutes of Health, National Center for Biotechnology Information, National Library of Medicine, MEDLINE"><meta name="robots" content="index,nofollow,noarchive"><meta property="og:title" content="FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences - PubMed"><meta property="og:url" content="https://pubmed.ncbi.nlm.nih.gov/31114866/"><meta property="og:description" content="The growing prevalence of deadly microbes with resistance to previously life-saving drug therapies is a dire threat to human health. Detection of low abundance pathogen sequences remains a challenge for metagenomic Next Generation Sequencing (NGS). 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Detection of low abundance pathogen sequences remains a challenge for metagenomic Next Generation Sequencing (NGS). 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new collection</label> </li> <li> <input type="radio" id="collections-action-panel-existing" class="collections-existing" name="collections" value="existing" checked="true" data-ga-category="save_share" data-ga-action="collections" data-ga-label="collections_radio_existing"> <label for="collections-action-panel-existing">Add to an existing collection</label> </li> </ul> </div> <div class="controls-wrapper"> <div class="action-panel-control-wrap new-collections-controls"> <label for="collections-action-panel-add-to-new" class="action-panel-label required-field-asterisk"> Name your collection: </label> <input type="text" name="add-to-new-collection" id="collections-action-panel-add-to-new" class="collections-action-add-to-new" pattern="[^"&=<>\/]*" title="The following characters are not allowed in the Name field: "&=<>/" maxlength="100" data-ga-category="save_share" data-ga-action="create_collection" data-ga-label="non_favorties_collection"> <div class="collections-new-name-too-long usa-input-error-message selection-validation-message"> Name must be less than 100 characters </div> </div> <div class="action-panel-control-wrap existing-collections-controls"> <label for="collections-action-panel-add-to-existing" class="action-panel-label"> Choose a collection: </label> <select id="collections-action-panel-add-to-existing" class="action-panel-selector collections-action-add-to-existing" data-ga-category="save_share" data-ga-action="select_collection" data-ga-label="($('#collections-action-add-to-existing').val() === 'Favorites') ? 'Favorites' : 'non_favorites_collection'"> </select> <div class="collections-retry-load-on-error usa-input-error-message selection-validation-message"> Unable to load your collection due to an error<br> <a href="#">Please try again</a> </div> </div> </div> <div class="action-panel-actions"> <button class="action-panel-submit" type="submit" data-loading-label="Adding..." data-pinger-ignore data-ga-category="save_share" data-ga-action="collections" data-ga-label="add"> Add </button> <button class="action-panel-cancel" aria-label="Close 'Add to Collections' panel" ref="linksrc=close_collections_panel" aria-controls="collections-action-panel" aria-expanded="false" data-ga-category="save_share" data-ga-action="collections" data-ga-label="cancel"> Cancel </button> </div> </form> </div> </div> <div id="bibliography-action-panel" class="bibliography-action-panel action-panel in-progress-dots-panel" aria-hidden="true" data-bibliography-open-panel-enabled="false" data-bibliography-open-panel-url-hash="#open-bibliography-panel"> <div class="inner-wrap"> <h3 class="action-panel-heading"> Add to My Bibliography </h3> <form id="bibliography-action-panel-form" class="bibliography-action-panel-form action-panel-content action-form action-panel-smaller-selectors" data-add-to-bibliography-max-amount="100" data-add-to-bibliography-batch-size="10" data-bibliography-delegates-url="/list-bibliography-delegates/" data-add-to-bibliography-url="/add-to-bibliography/" data-get-article-ids-by-search-url="/get-article-ids-by-search/" data-mybib-root-url="https://www.ncbi.nlm.nih.gov/myncbi/collections/mybibliography/"> <input type="hidden" name="csrfmiddlewaretoken" value="vgshRgroQY3VSusCMRRiYnCmdfknzVB6D6QA68CD2diPhTcD70dat46p9o6qJ22G"> <div class="action-panel-control-wrap bibliographies-controls"> <div class="choice-group"> <ul class="bibliographies-action-add radio-group-items"> <li> <input name="bibliography" id="my-bibliography" class="my-bibliography" type="radio" checked/> <label for="my-bibliography">My Bibliography</label> </li> </ul> </div> </div> <div class="bibliographies-retry-load-on-error usa-input-error-message selection-validation-message"> Unable to load your delegates due to an error<br> <a href="#">Please try again</a> </div> <div class="action-panel-actions"> <button class="action-panel-submit" type="submit" data-loading-label="Adding..." data-pinger-ignore> Add </button> <button class="action-panel-cancel" aria-label="Close 'Add to bibliography' panel" ref="linksrc=close_bibliography_panel" aria-controls="bibliography-action-panel" aria-expanded="false" data-ga-category="save_share" data-ga-action="mybib" data-ga-label="cancel"> Cancel </button> </div> </form> </div> </div> <div id="saved-search-action-panel" class="saved-search-action-panel action-panel " aria-hidden="true" data-saved-search-open-panel-enabled="false" data-saved-search-open-panel-url-hash="#open-saved-search-panel"> <div class="inner-wrap"> <h2 class="action-panel-heading"> Your saved search </h2> <form id="saved-search-action-panel-form" class="saved-search-action-panel-form action-panel-content action-form" data-create-saved-search-url="/create-saved-search/" data-try-search-terms-url="/try-search-term/" data-saved-search-root-url="https://www.ncbi.nlm.nih.gov/myncbi/searches/"> <input type="hidden" name="csrfmiddlewaretoken" value="vgshRgroQY3VSusCMRRiYnCmdfknzVB6D6QA68CD2diPhTcD70dat46p9o6qJ22G"> <div class="action-panel-control-wrap"> <label for="saved-search-name" class="action-panel-label saved-search-name-label required-field-asterisk"> Name of saved search: </label> <input maxlength="200" type="text" name="saved-search-name" id="saved-search-name" class="saved-search-name" value="" required pattern="[^"&=<>\/]*" title="The following characters are not allowed in the Name field: "&=<>/"> </div> <div class="action-panel-control-wrap"> <label for="saved-search-term" class="action-panel-label required-field-asterisk"> Search terms: </label> <textarea name="saved-search-term" id="saved-search-term" class="saved-search-term" required></textarea> </div> <div class="test-search-term-wrap"> <a href="#" class="try-search-term">Test search terms</a> </div> <div class="choice-group action-panel-extra-margin-top"> <span class="action-panel-label" id="fieldset-label"> Would you like email updates of new search results? </span> <fieldset id="saved-search-alert" aria-describedby="fieldset-label"> <legend class="usa-sr-only">Saved Search Alert Radio Buttons</legend> <ul class="radio-group-items"> <li> <input type="radio" id="saved-search-alert-yes" class="saved-search-alert-yes" name="saved-search-alert" value="yes" checked> <label for="saved-search-alert-yes" class="action-panel-label">Yes</label> </li> <li> <input aria-label="No radio input" type="radio" id="saved-search-alert-no" class="saved-search-alert-no" name="saved-search-alert" value="no"> <label for="saved-search-alert-no" class="action-panel-label">No</label> </li> </ul> </fieldset> </div> <div class="alert-schedule-wrap"> <div class="action-panel-control-wrap"> <label class="action-panel-label"> Email: </label> <span aria-label="Email address" id="saved-search-email" class="action-panel-label"><span class="action-panel-label-bold"></span> (<a class="myncbi-account-settings" href="https://www.ncbi.nlm.nih.gov/account/settings/">change</a>)</span> </div> <div class="action-panel-control-wrap action-panel-extra-margin-top"> <label for="saved-search-frequency" class="action-panel-label"> Frequency: </label> <select id="saved-search-frequency" class="no-border-panel-selector saved-search-frequency"> <option value="monthly">Monthly</option> <option value="weekly">Weekly</option> <option value="daily">Daily</option> </select> </div> <div class="action-panel-control-wrap saved-search-monthly-additional"> <label for="saved-search-monthly-on-day" class="action-panel-label"> Which day? </label> <select id="saved-search-monthly-on-day" class="no-border-panel-selector"> <option value="Sunday">The first Sunday</option> <option value="Monday">The first Monday</option> <option value="Tuesday">The first Tuesday</option> <option value="Wednesday">The first Wednesday</option> <option value="Thursday">The first Thursday</option> <option value="Friday">The first Friday</option> <option value="Saturday">The first Saturday</option> <option value="day">The first day</option> <option value="weekday">The first weekday</option> </select> </div> <div class="action-panel-control-wrap saved-search-weekly-additional"> <label for="saved-search-weekly-on-day" class="action-panel-label"> Which day? </label> <select id="saved-search-weekly-on-day" class="no-border-panel-selector saved-search-weekly-on-day"> <option value="Sunday">Sunday</option> <option value="Monday">Monday</option> <option value="Tuesday">Tuesday</option> <option value="Wednesday">Wednesday</option> <option value="Thursday">Thursday</option> <option value="Friday">Friday</option> <option value="Saturday">Saturday</option> </select> </div> <div class="action-panel-control-wrap"> <label for="saved-search-report" class="action-panel-label"> Report format: </label> <select id="saved-search-report" class="no-border-panel-selector saved-search-report"> <option value="DocSum">Summary</option> <option value="DocSumText">Summary (text)</option> <option value="Abstract">Abstract</option> <option value="AbstractText">Abstract (text)</option> <option value="MEDLINE">PubMed</option> </select> </div> <div class="action-panel-control-wrap"> <label for="saved-search-amount" class="action-panel-label"> Send at most: </label> <select id="saved-search-amount" class="no-border-panel-selector saved-search-amount"> <option value="1">1 item</option> <option value="5" selected>5 items</option> <option value="10">10 items</option> <option value="20">20 items</option> <option value="50">50 items</option> <option value="100">100 items</option> <option value="200">200 items</option> </select> </div> <div> <input type="checkbox" id="saved-search-send-if-no-result" class="saved-search-send-if-no-result" name="saved-search-send-if-no-result"> <label for="saved-search-send-if-no-result" class="action-panel-label smaller-checkbox"> Send even when there aren't any new results </label> </div> <div class="action-panel-control-wrap option-text-in-email-wrap"> <label for="saved-search-email-text" class="action-panel-label"> Optional text in email: </label> <textarea name="saved-search-email-text" id="saved-search-email-text" class="saved-search-email-text"></textarea> </div> </div> <div class="action-panel-actions"> <button class="action-panel-submit" type="submit" data-loading-label="Saving..." data-ga-category="save_share" data-ga-action="alert" data-ga-label="save"> Save </button> <button class="action-panel-cancel" aria-label="Close 'Your saved search' panel" ref="linksrc=close_saved_search_panel" aria-controls="saved-search-action-panel" aria-expanded="false" data-ga-category="save_share" data-ga-action="alert" data-ga-label="cancel"> Cancel </button> </div> </form> </div> </div> <div id="citation-manager-action-panel" class="citation-manager-action-panel action-panel" aria-hidden="true"> <div class="inner-wrap"> <h2 class="action-panel-heading"> Create a file for external citation management software </h2> <form id="citation-manager-action-panel-form" class="action-panel-content action-form" action="/results-export-ids/" data-by-search-action="/results-export-search-data/" data-by-ids-action="/results-export-ids/" method="post" data-by-search-method="post" data-by-ids-method="post"> <input type="hidden" name="csrfmiddlewaretoken" value="vgshRgroQY3VSusCMRRiYnCmdfknzVB6D6QA68CD2diPhTcD70dat46p9o6qJ22G"> <input name="results-format" type="hidden" value="pubmed"/> <div class="action-panel-actions"> <button class="action-panel-submit" type="submit" data-loading-label="Sending..." data-ga-category="save_share" data-ga-action="citation_manager" data-ga-label="save"> Create file </button> <button class="action-panel-cancel" aria-label="Close 'Send citations to citation manager' panel" ref="linksrc=close_citation_manager_panel" aria-controls="citation-manager-action-panel" aria-expanded="false" data-ga-category="save_share" data-ga-action="citation_manager" data-ga-label="cancel"> Cancel </button> </div> </form> </div> </div> <div id="rss-action-panel" class="rss-action-panel action-panel " aria-hidden="true"> <div class="inner-wrap"> <h2 class="action-panel-heading"> Your RSS Feed </h2> <form id="rss-action-panel-form" class="rss-action-panel-form action-panel-content action-form" data-create-rss-feed-url="/create-rss-feed-url/" data-search-form-term-value=""> <input type="hidden" name="csrfmiddlewaretoken" value="vgshRgroQY3VSusCMRRiYnCmdfknzVB6D6QA68CD2diPhTcD70dat46p9o6qJ22G"> <div class="action-panel-control-wrap"> <label for="rss-name" class="action-panel-label required-field-asterisk"> Name of RSS Feed: </label> <input maxlength="200" placeholder="Name" type="text" name="rss-name" id="rss-name" class="rss-name" value='' required pattern="[^"&=<>\/]*" title="The following characters are not allowed in the Name field: "&=<>/"> </div> <div class="rss-limit-wrap"> <div class="action-panel-control-wrap action-panel-extra-margin-top"> <label for="rss-limit" class="action-panel-label"> Number of items displayed: </label> <select id="rss-limit" class="no-border-panel-selector rss-limit"> <option value="5">5</option> <option value="10">10</option> <option value="15" selected="selected">15</option> <option value="20">20</option> <option value="50">50</option> <option value="100">100</option> </select> </div> </div> <div class="action-panel-actions"> <button class="action-panel-submit" type="submit" data-loading-label="Creating..." data-ga-category="save_share" data-ga-action="alert" data-ga-label="save"> Create RSS </button> 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</button><div id="full-view-journal" class="journal-actions-dropdown dropdown dropdown-container" hidden aria-label="Dropdown menu for journal Nucleic acids research"><div class="title">Actions</div><div class="content"><ul class="journal-actions-links"><li><a class="search-in-pubmed-link dropdown-block-link" href="/?term=%22Nucleic+Acids+Res%22%5Bjour%5D&sort=date&sort_order=desc" data-href="/?term=%22Nucleic+Acids+Res%22%5Bjour%5D&sort=date&sort_order=desc" ref="linksrc=search_in_pubmed_journal_name_link&journal_abbrev=Nucleic Acids Res" data-ga-category="search" data-ga-action="journal_link" data-ga-label="Nucleic Acids Res"> Search in PubMed </a></li><li><a class="search-in-nlm-catalog-link dropdown-block-link" ref ="linksrc=search_in_nlm_catalog_link" href="https://www.ncbi.nlm.nih.gov/nlmcatalog?term=%22Nucleic+Acids+Res%22%5BTitle+Abbreviation%5D" data-ga-category="search_catalog" data-ga-action="journal_link" data-ga-label="Nucleic Acids Res"> Search in NLM Catalog </a></li><li><a class="add-to-search-link dropdown-block-link" ref ="linksrc=add_to_search_link" role="button" data-search-term='"Nucleic Acids Res"[jour]' data-ga-category="search" data-ga-action="add_to_search" data-ga-label='"Nucleic Acids Res"[jour]' href="#"> Add to Search </a></li></ul></div></div></div><span class="period">. </span><span class="cit">2019 Aug 22;47(14):e83.</span> </div> <span class="citation-doi"> doi: 10.1093/nar/gkz418. </span> </div> <h1 class="heading-title"> FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences </h1> <div class="inline-authors"> <div class="authors"> <div class="authors-list"> <span class="authors-list-item "><a class="full-name" href="/?term=Quan+J&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Jenai Quan">Jenai Quan</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#full-view-affiliation-1" ref="linksrc=author_aff"> 1 </a><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA." href="#full-view-affiliation-2" ref="linksrc=author_aff"> 2 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Langelier+C&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Charles Langelier">Charles Langelier</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA." href="#full-view-affiliation-3" ref="linksrc=author_aff"> 3 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Kuchta+A&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Alison Kuchta">Alison Kuchta</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Pediatrics, University of California San Francisco, San Francisco, CA 94158, USA." href="#full-view-affiliation-4" ref="linksrc=author_aff"> 4 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Batson+J&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Joshua Batson">Joshua Batson</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#full-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Teyssier+N&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Noam Teyssier">Noam Teyssier</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA." href="#full-view-affiliation-3" ref="linksrc=author_aff"> 3 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Lyden+A&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Amy Lyden">Amy Lyden</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#full-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Caldera+S&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Saharai Caldera">Saharai Caldera</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA." href="#full-view-affiliation-3" ref="linksrc=author_aff"> 3 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=McGeever+A&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Aaron McGeever">Aaron McGeever</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#full-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Dimitrov+B&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Boris Dimitrov">Boris Dimitrov</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Initiative, Redwood City, CA 94063, USA." href="#full-view-affiliation-5" ref="linksrc=author_aff"> 5 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=King+R&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Ryan King">Ryan King</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Initiative, Redwood City, CA 94063, USA." href="#full-view-affiliation-5" ref="linksrc=author_aff"> 5 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Wilheim+J&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Jordan Wilheim">Jordan Wilheim</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA." href="#full-view-affiliation-6" ref="linksrc=author_aff"> 6 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Murphy+M&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Maxwell Murphy">Maxwell Murphy</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA." href="#full-view-affiliation-6" ref="linksrc=author_aff"> 6 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Ares+LP&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Lara Pesce Ares">Lara Pesce Ares</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#full-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Travisano+KA&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Katherine A Travisano">Katherine A Travisano</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#full-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Sit+R&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Rene Sit">Rene Sit</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#full-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Amato+R&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Roberto Amato">Roberto Amato</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Wellcome Sanger Institute, Hinxton CB10 1SA, UK." href="#full-view-affiliation-7" ref="linksrc=author_aff"> 7 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Mumbengegwi+DR&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Davis R Mumbengegwi">Davis R Mumbengegwi</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Multidisciplinary Research Centre, University of Namibia, Windhoek 93Q5+48, Namibia." href="#full-view-affiliation-8" ref="linksrc=author_aff"> 8 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Smith+JL&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Jennifer L Smith">Jennifer L Smith</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA." href="#full-view-affiliation-9" ref="linksrc=author_aff"> 9 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Bennett+A&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Adam Bennett">Adam Bennett</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA." href="#full-view-affiliation-9" ref="linksrc=author_aff"> 9 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Gosling+R&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Roly Gosling">Roly Gosling</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA." href="#full-view-affiliation-9" ref="linksrc=author_aff"> 9 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Mourani+PM&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Peter M Mourani">Peter M Mourani</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Section of Critical Care Medicine, Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO 80045, USA." href="#full-view-affiliation-10" ref="linksrc=author_aff"> 10 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Calfee+CS&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Carolyn S Calfee">Carolyn S Calfee</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA." href="#full-view-affiliation-11" ref="linksrc=author_aff"> 11 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Neff+NF&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Norma F Neff">Norma F Neff</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#full-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Chow+ED&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Eric D Chow">Eric D Chow</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA." href="#full-view-affiliation-2" ref="linksrc=author_aff"> 2 </a><span class="author-sup-separator"> </span><a class="affiliation-link" title="Center for Advanced Technology, University of California San Francisco, San Francisco, CA 94158, USA." href="#full-view-affiliation-12" ref="linksrc=author_aff"> 12 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Kim+PS&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Peter S Kim">Peter S Kim</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#full-view-affiliation-1" ref="linksrc=author_aff"> 1 </a><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA." href="#full-view-affiliation-13" ref="linksrc=author_aff"> 13 </a><span class="author-sup-separator"> </span><a class="affiliation-link" title="Stanford ChEM-H, Stanford, CA 94305, USA." href="#full-view-affiliation-14" ref="linksrc=author_aff"> 14 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Greenhouse+B&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Bryan Greenhouse">Bryan Greenhouse</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#full-view-affiliation-1" ref="linksrc=author_aff"> 1 </a><span class="author-sup-separator"> </span><a class="affiliation-link" title="Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA." href="#full-view-affiliation-6" ref="linksrc=author_aff"> 6 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=DeRisi+JL&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Joseph L DeRisi">Joseph L DeRisi</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#full-view-affiliation-1" ref="linksrc=author_aff"> 1 </a><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA." href="#full-view-affiliation-2" ref="linksrc=author_aff"> 2 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Crawford+ED&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Emily D Crawford">Emily D Crawford</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#full-view-affiliation-1" ref="linksrc=author_aff"> 1 </a><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94158, USA." href="#full-view-affiliation-15" ref="linksrc=author_aff"> 15 </a></sup></span> </div> </div> </div> <div class="short-article-details"> Affiliations <button class="more-details" id="toggle-authors" data-alt-text="Collapse" aria-controls="expanded-authors" aria-expanded="false" data-pinger-ignore data-fetch-url="/31114866/long-authors/" data-id-prefix=""> <span class="title"> Expand </span> </button> </div> <div class="extended-article-details" id="expanded-authors" aria-hidden="true"> <div class="expanded-authors" id="full-view-expanded-authors"> <div class="affiliations"> <h3 class="title"> Affiliations </h3> <ul class="item-list"> <li data-affiliation-id="full-view-affiliation-1" id="full-view-affiliation-1" ><sup class="key">1</sup> Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.</li> <li data-affiliation-id="full-view-affiliation-2" id="full-view-affiliation-2" ><sup class="key">2</sup> Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA.</li> <li data-affiliation-id="full-view-affiliation-3" id="full-view-affiliation-3" ><sup class="key">3</sup> Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA.</li> <li data-affiliation-id="full-view-affiliation-4" id="full-view-affiliation-4" ><sup class="key">4</sup> Department of Pediatrics, University of California San Francisco, San Francisco, CA 94158, USA.</li> <li data-affiliation-id="full-view-affiliation-5" id="full-view-affiliation-5" ><sup class="key">5</sup> Chan Zuckerberg Initiative, Redwood City, CA 94063, USA.</li> <li data-affiliation-id="full-view-affiliation-6" id="full-view-affiliation-6" ><sup class="key">6</sup> Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA.</li> <li data-affiliation-id="full-view-affiliation-7" id="full-view-affiliation-7" ><sup class="key">7</sup> Wellcome Sanger Institute, Hinxton CB10 1SA, UK.</li> <li data-affiliation-id="full-view-affiliation-8" id="full-view-affiliation-8" ><sup class="key">8</sup> Multidisciplinary Research Centre, University of Namibia, Windhoek 93Q5+48, Namibia.</li> <li data-affiliation-id="full-view-affiliation-9" id="full-view-affiliation-9" ><sup class="key">9</sup> Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA.</li> <li data-affiliation-id="full-view-affiliation-10" id="full-view-affiliation-10" ><sup class="key">10</sup> Section of Critical Care Medicine, Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO 80045, USA.</li> <li data-affiliation-id="full-view-affiliation-11" id="full-view-affiliation-11" ><sup class="key">11</sup> Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA.</li> <li data-affiliation-id="full-view-affiliation-12" id="full-view-affiliation-12" ><sup class="key">12</sup> Center for Advanced Technology, University of California San Francisco, San Francisco, CA 94158, USA.</li> <li data-affiliation-id="full-view-affiliation-13" id="full-view-affiliation-13" ><sup class="key">13</sup> Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.</li> <li data-affiliation-id="full-view-affiliation-14" id="full-view-affiliation-14" ><sup class="key">14</sup> Stanford ChEM-H, Stanford, CA 94305, USA.</li> <li data-affiliation-id="full-view-affiliation-15" id="full-view-affiliation-15" ><sup class="key">15</sup> Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94158, USA.</li> </ul> </div> </div> </div> <ul class="identifiers" id="full-view-identifiers"> <li> <span class="identifier pubmed"> <span class="id-label"> PMID: </span> <strong class="current-id" title="PubMed ID">31114866</strong> </span> </li> <li> <span class="identifier pmc"> <span class="id-label"> PMCID: </span> <a class="id-link" target="_blank" rel="noopener" ref="linksrc=article_id_link&article_id=PMC6698650&id_type=PMC" href="https://pmc.ncbi.nlm.nih.gov/articles/PMC6698650/" data-ga-category="full_text" data-ga-action="PMCID" > PMC6698650 </a> </span> </li> <li> <span class="identifier doi"> <span class="id-label"> DOI: </span> <a class="id-link" target="_blank" rel="noopener" ref="linksrc=article_id_link&article_id=10.1093/nar/gkz418&id_type=DOI" href="https://doi.org/10.1093/nar/gkz418" data-ga-category="full_text" data-ga-action="DOI" > 10.1093/nar/gkz418 </a> </span> </li> </ul> <div class="in-clipboard-label " hidden> Item in Clipboard </div> </div> <div class="short-view" id="short-view-heading"> <h1 class="heading-title"> FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences </h1> <div class="short-citation"> <span class="authors-list"> <span class="authors-list-item "><span class="full-name">Jenai Quan</span><span class="citation-separator"> et al.</span></span> </span> <span class="citation-journal"> Nucleic Acids Res<span class="citation-separator">.</span> </span> <span class="date"> <time class="citation-year" datetime="2019">2019</time><span class="citation-separator">.</span> </span> </div> <div class="more-article-details-section 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class="period">. </span><span class="cit">2019 Aug 22;47(14):e83.</span> </div> <span class="citation-doi"> doi: 10.1093/nar/gkz418. </span> </div> <div class="expanded-authors" id="short-view-expanded-authors"> <div class="authors"> <h3 class="title"> Authors </h3> <div class="authors-list"> <span class="authors-list-item "><a class="full-name" href="/?term=Quan+J&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Jenai Quan">Jenai Quan</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#short-view-affiliation-1" ref="linksrc=author_aff"> 1 </a><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA." href="#short-view-affiliation-2" ref="linksrc=author_aff"> 2 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Langelier+C&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Charles Langelier">Charles Langelier</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA." href="#short-view-affiliation-3" ref="linksrc=author_aff"> 3 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Kuchta+A&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Alison Kuchta">Alison Kuchta</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Pediatrics, University of California San Francisco, San Francisco, CA 94158, USA." href="#short-view-affiliation-4" ref="linksrc=author_aff"> 4 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Batson+J&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Joshua Batson">Joshua Batson</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#short-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Teyssier+N&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Noam Teyssier">Noam Teyssier</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA." href="#short-view-affiliation-3" ref="linksrc=author_aff"> 3 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Lyden+A&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Amy Lyden">Amy Lyden</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#short-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Caldera+S&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Saharai Caldera">Saharai Caldera</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA." href="#short-view-affiliation-3" ref="linksrc=author_aff"> 3 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=McGeever+A&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Aaron McGeever">Aaron McGeever</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#short-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Dimitrov+B&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Boris Dimitrov">Boris Dimitrov</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Initiative, Redwood City, CA 94063, USA." href="#short-view-affiliation-5" ref="linksrc=author_aff"> 5 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=King+R&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Ryan King">Ryan King</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Initiative, Redwood City, CA 94063, USA." href="#short-view-affiliation-5" ref="linksrc=author_aff"> 5 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Wilheim+J&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Jordan Wilheim">Jordan Wilheim</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA." href="#short-view-affiliation-6" ref="linksrc=author_aff"> 6 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Murphy+M&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Maxwell Murphy">Maxwell Murphy</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA." href="#short-view-affiliation-6" ref="linksrc=author_aff"> 6 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Ares+LP&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Lara Pesce Ares">Lara Pesce Ares</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#short-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Travisano+KA&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Katherine A Travisano">Katherine A Travisano</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#short-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Sit+R&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Rene Sit">Rene Sit</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#short-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Amato+R&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Roberto Amato">Roberto Amato</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Wellcome Sanger Institute, Hinxton CB10 1SA, UK." href="#short-view-affiliation-7" ref="linksrc=author_aff"> 7 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Mumbengegwi+DR&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Davis R Mumbengegwi">Davis R Mumbengegwi</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Multidisciplinary Research Centre, University of Namibia, Windhoek 93Q5+48, Namibia." href="#short-view-affiliation-8" ref="linksrc=author_aff"> 8 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Smith+JL&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Jennifer L Smith">Jennifer L Smith</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA." href="#short-view-affiliation-9" ref="linksrc=author_aff"> 9 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Bennett+A&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Adam Bennett">Adam Bennett</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA." href="#short-view-affiliation-9" ref="linksrc=author_aff"> 9 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Gosling+R&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Roly Gosling">Roly Gosling</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA." href="#short-view-affiliation-9" ref="linksrc=author_aff"> 9 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Mourani+PM&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Peter M Mourani">Peter M Mourani</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Section of Critical Care Medicine, Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO 80045, USA." href="#short-view-affiliation-10" ref="linksrc=author_aff"> 10 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Calfee+CS&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Carolyn S Calfee">Carolyn S Calfee</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA." href="#short-view-affiliation-11" ref="linksrc=author_aff"> 11 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Neff+NF&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Norma F Neff">Norma F Neff</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#short-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Chow+ED&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Eric D Chow">Eric D Chow</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA." href="#short-view-affiliation-2" ref="linksrc=author_aff"> 2 </a><span class="author-sup-separator"> </span><a class="affiliation-link" title="Center for Advanced Technology, University of California San Francisco, San Francisco, CA 94158, USA." href="#short-view-affiliation-12" ref="linksrc=author_aff"> 12 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Kim+PS&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Peter S Kim">Peter S Kim</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#short-view-affiliation-1" ref="linksrc=author_aff"> 1 </a><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA." href="#short-view-affiliation-13" ref="linksrc=author_aff"> 13 </a><span class="author-sup-separator"> </span><a class="affiliation-link" title="Stanford ChEM-H, Stanford, CA 94305, USA." href="#short-view-affiliation-14" ref="linksrc=author_aff"> 14 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Greenhouse+B&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Bryan Greenhouse">Bryan Greenhouse</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#short-view-affiliation-1" ref="linksrc=author_aff"> 1 </a><span class="author-sup-separator"> </span><a class="affiliation-link" title="Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA." href="#short-view-affiliation-6" ref="linksrc=author_aff"> 6 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=DeRisi+JL&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Joseph L DeRisi">Joseph L DeRisi</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#short-view-affiliation-1" ref="linksrc=author_aff"> 1 </a><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA." href="#short-view-affiliation-2" ref="linksrc=author_aff"> 2 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Crawford+ED&cauthor_id=31114866" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Emily D Crawford">Emily D Crawford</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Chan Zuckerberg Biohub, San Francisco, CA 94158, USA." href="#short-view-affiliation-1" ref="linksrc=author_aff"> 1 </a><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94158, USA." href="#short-view-affiliation-15" ref="linksrc=author_aff"> 15 </a></sup></span> </div> </div> <div class="affiliations"> <h3 class="title"> Affiliations </h3> <ul class="item-list"> <li data-affiliation-id="short-view-affiliation-1" id="short-view-affiliation-1" ><sup class="key">1</sup> Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.</li> <li data-affiliation-id="short-view-affiliation-2" id="short-view-affiliation-2" ><sup class="key">2</sup> Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA.</li> <li data-affiliation-id="short-view-affiliation-3" id="short-view-affiliation-3" ><sup class="key">3</sup> Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA.</li> <li data-affiliation-id="short-view-affiliation-4" id="short-view-affiliation-4" ><sup class="key">4</sup> Department of Pediatrics, University of California San Francisco, San Francisco, CA 94158, USA.</li> <li data-affiliation-id="short-view-affiliation-5" id="short-view-affiliation-5" ><sup class="key">5</sup> Chan Zuckerberg Initiative, Redwood City, CA 94063, USA.</li> <li data-affiliation-id="short-view-affiliation-6" id="short-view-affiliation-6" ><sup class="key">6</sup> Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA.</li> <li data-affiliation-id="short-view-affiliation-7" id="short-view-affiliation-7" ><sup class="key">7</sup> Wellcome Sanger Institute, Hinxton CB10 1SA, UK.</li> <li data-affiliation-id="short-view-affiliation-8" id="short-view-affiliation-8" ><sup class="key">8</sup> Multidisciplinary Research Centre, University of Namibia, Windhoek 93Q5+48, Namibia.</li> <li data-affiliation-id="short-view-affiliation-9" id="short-view-affiliation-9" ><sup class="key">9</sup> Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA.</li> <li data-affiliation-id="short-view-affiliation-10" id="short-view-affiliation-10" ><sup class="key">10</sup> Section of Critical Care Medicine, Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO 80045, USA.</li> <li data-affiliation-id="short-view-affiliation-11" id="short-view-affiliation-11" ><sup class="key">11</sup> Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA.</li> <li data-affiliation-id="short-view-affiliation-12" id="short-view-affiliation-12" ><sup class="key">12</sup> Center for Advanced Technology, University of California San Francisco, San Francisco, CA 94158, USA.</li> <li data-affiliation-id="short-view-affiliation-13" id="short-view-affiliation-13" ><sup class="key">13</sup> Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.</li> <li data-affiliation-id="short-view-affiliation-14" id="short-view-affiliation-14" ><sup class="key">14</sup> Stanford ChEM-H, Stanford, CA 94305, USA.</li> <li data-affiliation-id="short-view-affiliation-15" id="short-view-affiliation-15" ><sup class="key">15</sup> Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94158, USA.</li> </ul> </div> </div> <ul class="identifiers" id="short-view-identifiers"> <li> <span class="identifier pubmed"> <span class="id-label"> PMID: </span> <strong class="current-id" title="PubMed ID">31114866</strong> </span> </li> <li> <span class="identifier pmc"> <span class="id-label"> PMCID: </span> <a class="id-link" target="_blank" rel="noopener" ref="linksrc=article_id_link&article_id=PMC6698650&id_type=PMC" href="https://pmc.ncbi.nlm.nih.gov/articles/PMC6698650/" data-ga-category="full_text" data-ga-action="PMCID" > PMC6698650 </a> </span> </li> <li> <span class="identifier doi"> <span class="id-label"> DOI: </span> <a class="id-link" target="_blank" rel="noopener" ref="linksrc=article_id_link&article_id=10.1093/nar/gkz418&id_type=DOI" href="https://doi.org/10.1093/nar/gkz418" data-ga-category="full_text" data-ga-action="DOI" > 10.1093/nar/gkz418 </a> </span> </li> </ul> <div class="in-clipboard-label " hidden> Item in Clipboard </div> </div> </div> </header> <div class="actions-buttons inline"><div class="inner-wrap"><button class="full-text-links-button full-text-links-dialog-trigger" title="Open dialog with full text links" ref="linksrc=full_text_links"> Full text links </button><button class="citation-button citation-dialog-trigger" aria-label="Open dialog with citation text in different styles" data-ga-category="save_share" data-ga-action="cite" data-ga-label="open" data-all-citations-url="/31114866/citations/" data-citation-style="nlm" data-pubmed-format-link="/31114866/export/"><span 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<h2 class="title"> Abstract </h2> <div class="abstract-content selected" id="eng-abstract"> <p> The growing prevalence of deadly microbes with resistance to previously life-saving drug therapies is a dire threat to human health. Detection of low abundance pathogen sequences remains a challenge for metagenomic Next Generation Sequencing (NGS). We introduce FLASH (Finding Low Abundance Sequences by Hybridization), a next-generation CRISPR/Cas9 diagnostic method that takes advantage of the efficiency, specificity and flexibility of Cas9 to enrich for a programmed set of sequences. FLASH-NGS achieves up to 5 orders of magnitude of enrichment and sub-attomolar gene detection with minimal background. We provide an open-source software tool (FLASHit) for guide RNA design. Here we applied it to detection of antimicrobial resistance genes in respiratory fluid and dried blood spots, but FLASH-NGS is applicable to all areas that rely on multiplex PCR. </p> </div> </div> <p class="copyright" id="copyright"> © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. </p> <p class="disclaimer" id="disclaimer"> <a href="/disclaimer/" target="_blank" data-ga-category="literature_resources" data-ga-action="disclaimer_link" data-ga-label="under_abstract">PubMed Disclaimer</a> </p> <div class="figures" id="figures"> <h2 class="title"> Figures </h2> <div class="figures-list" id="slides-container" itemscope itemtype="http://schema.org/ImageGallery"> <figure class="figure-item " itemscope itemtype="http://schema.org/ImageObject" itemprop="associatedMedia" data-slide-index="0" data-label-slug="figure-1"> <a class="figure-link" href="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/027a/6698650/d0d4367fc2c2/gkz418fig1.jpg" itemprop="contentUrl" aria-describedby="figure-caption-0" role="button" data-image-width="747" data-image-height="259" data-image-alt="Figure 1." data-pmc-id="PMC6698650" data-figure-id="F1"> <img class="figure-thumb" itemprop="thumbnail" id="article-image-0" src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/027a/6698650/b90e5ce1c091/gkz418fig1.gif" alt="Figure 1." /> </a> <meta itemprop="width" itemtype="http://schema.org/ImageObject" content="747"> <meta itemprop="height" itemtype="http://schema.org/ImageObject" content="259"> <div class="figure-caption figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="caption" aria-hidden="true"> <div class="caption-wrap"> <strong class="figure-label"> <p> Figure 1. </p> </strong> <div class="figure-caption-contents"><p> Overview of the FLASH method.… </p></div> </div> </div> <div class="figure-caption-medium figure-caption-text" aria-hidden="true"> <strong class="figure-label"> <p> Figure 1. </p> </strong> <div class="figure-caption-contents"><p> Overview of the FLASH method. Genomic DNA or cDNA is first blocked with… </p></div> </div> <figcaption id="figure-caption-0" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description"> <strong class="figure-label"> Figure 1. </strong> <div class="figure-caption-contents">Overview of the FLASH method. Genomic DNA or cDNA is first blocked with phosphatase treatment and then digested with Cas9 complexed to a set of guide RNAs targeting genes of interest. Ligation of sequencing adaptors, amplification and sequencing follows.</div> </figcaption> </figure> <figure class="figure-item " itemscope itemtype="http://schema.org/ImageObject" itemprop="associatedMedia" data-slide-index="1" data-label-slug="figure-2"> <a class="figure-link" href="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/027a/6698650/075e0547e57a/gkz418fig2.jpg" itemprop="contentUrl" aria-describedby="figure-caption-1" role="button" data-image-width="614" data-image-height="469" data-image-alt="Figure 2." data-pmc-id="PMC6698650" data-figure-id="F2"> <img class="figure-thumb" itemprop="thumbnail" id="article-image-1" src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/027a/6698650/77d5ef6e96aa/gkz418fig2.gif" alt="Figure 2." /> </a> <meta itemprop="width" itemtype="http://schema.org/ImageObject" content="614"> <meta itemprop="height" itemtype="http://schema.org/ImageObject" content="469"> <div class="figure-caption figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="caption" aria-hidden="true"> <div class="caption-wrap"> <strong class="figure-label"> <p> Figure 2. </p> </strong> <div class="figure-caption-contents"><p> Results of FLASH on cultured… </p></div> </div> </div> <div class="figure-caption-medium figure-caption-text" aria-hidden="true"> <strong class="figure-label"> <p> Figure 2. </p> </strong> <div class="figure-caption-contents"><p> Results of FLASH on cultured isolates. ( <b> A </b> ) Proportion of targeted genes… </p></div> </div> <figcaption id="figure-caption-1" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description"> <strong class="figure-label"> Figure 2. </strong> <div class="figure-caption-contents">Results of FLASH on cultured isolates. (<b>A</b>) Proportion of targeted genes detected in FLASH-NGS and NGS libraries of six <i>S. aureus</i> isolates. Average of three replicates. chr: chromosomal gene; acq: acquired gene. Numbers in boxes represent, in order for each isolate: i. number of targets present (based on NGS); ii. number of expected targets observed in FLASH-NGS; iii. number of false-positive targets observed in FLASH-NGS (false positive not depicted in pie chart). (<b>B</b>) For isolate 1 with FLASH, <2000 sequencing reads were needed to achieve coverage of each targeted gene by at least 10 reads. Over 100 000 reads were needed to achieve the same coverage with NGS alone. (<b>C</b>) The fraction of targeted reads relative to background decreases substantially below 100 pg of DNA input; however, with as little as 100 fg input (∼35 copies of the <i>S. aureus</i> genome), the full set of targeted genes was detected at 10 rpM or greater. Bars and error bars represent mean and standard deviation of three replicates.</div> </figcaption> </figure> <figure class="figure-item " itemscope itemtype="http://schema.org/ImageObject" itemprop="associatedMedia" data-slide-index="2" data-label-slug="figure-3"> <a class="figure-link" href="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/027a/6698650/4122c434547e/gkz418fig3.jpg" itemprop="contentUrl" aria-describedby="figure-caption-2" role="button" data-image-width="752" data-image-height="743" data-image-alt="Figure 3." data-pmc-id="PMC6698650" data-figure-id="F3"> <img class="figure-thumb" itemprop="thumbnail" id="article-image-2" src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/027a/6698650/b99789a4fe05/gkz418fig3.gif" alt="Figure 3." /> </a> <meta itemprop="width" itemtype="http://schema.org/ImageObject" content="752"> <meta itemprop="height" itemtype="http://schema.org/ImageObject" content="743"> <div class="figure-caption figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="caption" aria-hidden="true"> <div class="caption-wrap"> <strong class="figure-label"> <p> Figure 3. </p> </strong> <div class="figure-caption-contents"><p> Results of FLASH on respiratory… </p></div> </div> </div> <div class="figure-caption-medium figure-caption-text" aria-hidden="true"> <strong class="figure-label"> <p> Figure 3. </p> </strong> <div class="figure-caption-contents"><p> Results of FLASH on respiratory samples. Number of reads aligning to targeted genes… </p></div> </div> <figcaption id="figure-caption-2" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description"> <strong class="figure-label"> Figure 3. </strong> <div class="figure-caption-contents">Results of FLASH on respiratory samples. Number of reads aligning to targeted genes in NGS and FLASH-NGS sequencing experiments on respiratory fluid samples from (<b>A</b>) patient 1, (<b>B</b>) patient 2, (<b>C</b>) patient 3 and (<b>D</b>) patient 4. Average of three or six replicates. Bars and error bars represent mean and standard deviation of three to six replicates (see Supplementary Table S5).</div> </figcaption> </figure> <figure class="figure-item " itemscope itemtype="http://schema.org/ImageObject" itemprop="associatedMedia" data-slide-index="3" data-label-slug="figure-4"> <a class="figure-link" href="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/027a/6698650/05394db03b11/gkz418fig4.jpg" itemprop="contentUrl" aria-describedby="figure-caption-3" role="button" data-image-width="743" data-image-height="870" data-image-alt="Figure 4." data-pmc-id="PMC6698650" data-figure-id="F4"> <img class="figure-thumb" itemprop="thumbnail" id="article-image-3" src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/027a/6698650/60aaceb8a9d0/gkz418fig4.gif" alt="Figure 4." /> </a> <meta itemprop="width" itemtype="http://schema.org/ImageObject" content="743"> <meta itemprop="height" itemtype="http://schema.org/ImageObject" content="870"> <div class="figure-caption figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="caption" aria-hidden="true"> <div class="caption-wrap"> <strong class="figure-label"> <p> Figure 4. </p> </strong> <div class="figure-caption-contents"><p> Results of FLASH on dried… </p></div> </div> </div> <div class="figure-caption-medium figure-caption-text" aria-hidden="true"> <strong class="figure-label"> <p> Figure 4. </p> </strong> <div class="figure-caption-contents"><p> Results of FLASH on dried blood spots. ( <b> A </b> ) Dried blood spots… </p></div> </div> <figcaption id="figure-caption-3" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description"> <strong class="figure-label"> Figure 4. </strong> <div class="figure-caption-contents">Results of FLASH on dried blood spots. (<b>A</b>) Dried blood spots (DBSs) from malaria lab strains were sequenced using either NGS or FLASH-NGS. Reads per million is plotted for each window for nine FLASH-NGS samples (three strain mixtures, each in triplicate, blue) and nine equivalent NGS samples (pink). Top panel indicates fold enrichment (average FLASH-NGS rpM divided by average NGS rpM). Light green bars in the upper panel represent windows for which no haplotype-determining read pairs were found. (<b>B</b>) Both lab strain mixtures and patient samples were evaluated for the presence of drug resistant haplotypes. Bars indicate mean of three replicates. (<b>C</b>) Target windows with sequences that distinguish the lab strains D10, HB3 and U659 were used to estimate strain ratios in the three mixtures. For the clinical DBS samples, the number of sequencing reads attributable to different haplotypes at each window was determined using SeekDeep. The average proportion of haplotypes at each of the maximum-haplotype containing windows is depicted. Bars indicate mean of three replicates.</div> </figcaption> </figure> </div>  <div class="pswp figures-dialog" id="figures-dialog" tabindex="-1" role="dialog" aria-hidden="true" data-image-gallery-uid="article-figures" aria-label="Figures Dialog">  <div class="pswp__bg"></div>  <div class="pswp__scroll-wrap">  <div class="pswp__container"> <div class="pswp__item"></div> <div class="pswp__item"></div> <div class="pswp__item"></div> </div>  <div class="pswp__ui pswp__ui--hidden"> <div class="pswp__top-bar">  <div class="pswp__counter"></div> <button class="pswp__button pswp__button--close" title="Close (Esc)"></button> <button class="pswp__button pswp__button--share" title="Share"></button> <button class="pswp__button pswp__button--fs" title="Toggle fullscreen"></button> <button class="pswp__button pswp__button--zoom" title="Zoom in/out"></button>   <div class="pswp__preloader"> <div class="pswp__preloader__icn"> <div class="pswp__preloader__cut"> <div class="pswp__preloader__donut"></div> </div> </div> </div> </div> <div class="pswp__share-modal pswp__share-modal--hidden pswp__single-tap"> <div class="pswp__share-tooltip"></div> </div> <button class="pswp__button pswp__button--arrow--left" title="Previous (arrow left)"> </button> <button class="pswp__button pswp__button--arrow--right" title="Next (arrow right)"> </button> <div class="pswp__caption"> <div class="pswp__caption__center"></div> </div> </div> </div> </div> <div class="figure-dialog-caption"> <div class="figure-caption-link-container"> <a class="figure-caption-link" href="#">See this image and copyright information in PMC</a> </div> <div class="figure-caption-center" data-expand-title="click to show full caption" data-collapse-title="click to hide full caption"> </div> <button class="figure-caption-toggle-btn" aria-label="show full caption" data-expand-text="show full caption" data-collapse-text="hide full caption">  </button> </div> </div> <div class="similar-articles" id="similar"> <h2 class="title"> Similar articles </h2> <ul class="articles-list" id="similar-articles-list"> <li class="full-docsum"> <div class="docsum-content" style="display:inline;"> <a class="docsum-title" href="/35818068/" ref="article_id=35818068&linksrc=similar_articles_link&ordinalpos=1" data-ga-category="similar_article" data-ga-action="35818068" data-ga-label=""> Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections. </a> <div class="docsum-citation full-citation"> <span class="docsum-authors full-authors">Serpa PH, Deng X, Abdelghany M, Crawford E, Malcolm K, Caldera S, Fung M, McGeever A, Kalantar KL, Lyden A, Ghale R, Deiss T, Neff N, Miller SA, Doernberg SB, Chiu CY, DeRisi JL, Calfee CS, Langelier CR.</span> <span class="docsum-authors short-authors">Serpa PH, et al.</span> <span class="docsum-journal-citation full-journal-citation">Genome Med. 2022 Jul 12;14(1):74. doi: 10.1186/s13073-022-01072-4.</span> <span class="docsum-journal-citation short-journal-citation">Genome Med. 2022.</span> <span class="citation-part">PMID: <span class="docsum-pmid">35818068</span></span> <span class="free-resources spaced-citation-item citation-part">Free PMC article.</span> </div> </div> </li> <li class="full-docsum"> <div class="docsum-content" style="display:inline;"> <a class="docsum-title" href="/35171007/" ref="article_id=35171007&linksrc=similar_articles_link&ordinalpos=2" data-ga-category="similar_article" data-ga-action="35171007" data-ga-label=""> Application of mNGS in the Etiological Analysis of Lower Respiratory Tract Infections and the Prediction of Drug Resistance. </a> <div class="docsum-citation full-citation"> <span class="docsum-authors full-authors">Liu H, Zhang Y, Yang J, Liu Y, Chen J.</span> <span class="docsum-authors short-authors">Liu H, et al.</span> <span class="docsum-journal-citation full-journal-citation">Microbiol Spectr. 2022 Feb 23;10(1):e0250221. doi: 10.1128/spectrum.02502-21. 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