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One genomic test can diagnose nearly any infection | University of California
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role="navigation" aria-label="Breadcrumb"> <ol> <li> <a href="/">Home</a> </li> <li> <a href="/news">News</a> </li> <li> One genomic test can diagnose nearly any infection </li> </ol> </nav> </div> <div id="block-uc-page-title" class="l-container block block-core block-page-title-block"> <h1 class="page-title"><span class="field field--name-title field--type-string field--label-hidden">One genomic test can diagnose nearly any infection</span> </h1> </div> <div id="block-addtoanybuttons" class="l-container share-links block block-addtoany block-addtoany-block"> <span class="a2a_kit a2a_kit_size_24 addtoany_list" data-a2a-url="https://www.universityofcalifornia.edu/news/one-genomic-test-can-diagnose-nearly-any-infection" data-a2a-title="One genomic test can diagnose nearly any infection"><a class="a2a_button_facebook"></a><a class="a2a_button_twitter"></a><a class="a2a_button_linkedin"></a><a class="a2a_button_reddit"></a></span> </div> <div id="block-uc-system-main" class="block block-system block-system-main-block"> <article data-history-node-id="11177" role="article" about="/news/one-genomic-test-can-diagnose-nearly-any-infection" class="node node--type-news-story node--view-mode-full article-section"> <div class="node__content byline-default field--name-field-image banner-style-0"> <div class="l-container content--meta"><span class="article-date">November 14, 2024</span><br><span class="byline article-byline">Levi Gadye</span>, <span class="source">UC San Francisco</span> </div> <div data-history-node-id="11177" class="l-container field--name-field-image banner-style-0" > <img src="/sites/default/files/styles/article_default_banner/public/charles-chiu-dna-extraction.jpg?h=2d3b4ecb&itok=Gfomo007" width="1680" height="940" alt="A researcher in a lab" /> </div> <div class="l-container"> <div class="field--name-field-image-credit">Credit: Noah Berger/UC San Francisco</div> <div class="field--name-field-image-caption">UC San Francisco infectious diseases physician and microbiologist Charles Chiu, M.D., Ph.D., watches as a robot extracts DNA from a sample. </div> </div> <div class="article-section-container"> <div class="field field--name-field-article-section field--type-entity-reference-revisions field--label-hidden field__items"> <div class="paragraph paragraph--type--article-section paragraph--view-mode--default display--"> <div class="l-container article-section"> <div class="section-content"> <div class="clearfix text-formatted field field--name-field-paragraph-body field--type-text-long field--label-hidden field__item"><p class="content-subheading"><strong>A genomic test developed at UC San Francisco to rapidly detect almost any kind of pathogen – virus, bacteria, fungus or parasite – has proved successful after a decade of use.</strong></p> <p>The test has the potential to vastly improve care for neurological infections that cause diseases like meningitis and encephalitis, as well as speed up the detection of new viral pandemic threats. It uses a powerful genomic sequencing technique, called metagenomic next-generation sequencing (mNGS).</p> </div> </div> <div class="section-image"> </div> </div> </div> <div class="paragraph paragraph--type--article-section paragraph--view-mode--default display--"> <div class="l-container article-section"> <div class="section-content"> <div class="clearfix text-formatted field field--name-field-paragraph-body field--type-text-long field--label-hidden field__item"><p>Rather than looking for one type of pathogen at a time, mNGS analyzes all the nucleic acids, RNA and DNA, that are present in a sample.</p> <p>“Our technology is deceptively simple,” said <a href="https://profiles.ucsf.edu/charles.chiu">Charles Chiu</a>, M.D., Ph.D., professor of laboratory medicine and infectious diseases at UCSF and senior author of the study. “By replacing multiple tests with a single test, we can take the lengthy guesswork out of diagnosing and treating infections.”</p> <p>The researchers originally developed a clinical mNGS test to analyze cerebrospinal fluid (CSF), the pristine liquid that bathes the brain and spinal cord.</p> <p>The test has now been performed on thousands of patients with unexplained neurological symptoms, both at UCSF and other hospitals across the country.</p> </div> </div> <div class="section-image"> <div class="field field--name-field-feature-image field--type-entity-reference field--label-hidden field__item"><div class="media media--type-image media--view-mode-default"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <img loading="lazy" src="/sites/default/files/2024-11/charles-chiu-square.jpg" width="800" height="800" alt="Headshot of Charles Chiu" typeof="foaf:Image" /> </div> </div> </div> <div class="field field--name-field-image-credit field--type-string field--label-hidden field__item">Image: UC San Francisco</div> <div class="clearfix text-formatted field field--name-field-image-caption field--type-text-long field--label-hidden field__item"><p>Charles Chiu, M.D., Ph.D.</p> </div> </div> <div class="section-quote bg-gradient-color__blue"> <div class="field field--name-field-quote field--type-string-long field--label-hidden field__item">Our goal was to have the entire process completed within 12 to 24 hours, giving a same-day or next-day result.</div> <div class="field field--name-field-quote-author field--type-string field--label-hidden field__item">Charles Chiu, M.D., Ph.D.</div> </div> </div> </div> <div class="paragraph paragraph--type--article-section paragraph--view-mode--default display--"> <div class="l-container article-section"> <div class="section-content"> <div class="clearfix text-formatted field field--name-field-paragraph-body field--type-text-long field--label-hidden field__item"><p>In a paper that appears Nov. 12 in <a href="https://www.nature.com/articles/s41591-024-03275-1">Nature Medicine</a>, the team demonstrated that the mNGS test correctly identified 86% of neurological infections.</p> <p>In a companion study published the same day in <a href="https://www.nature.com/articles/41467-024-51470-y">Nature Communications</a>, the team also used mNGS to identify pathogens in respiratory fluid that can cause pneumonia, and automated it to get results faster.</p> <p>They expect that the automated test will be able to detect novel viral pathogens that could cause respiratory pandemics like COVID-19.</p> </div> </div> <div class="section-image"> </div> <aside class="section-highlight bg-color__blue-pale" aria-labelledby="header-6376"> <h3 class="highlight-title field--name-field-highlight-title" id="header-6376">The types of infections that can threaten our brains and lungs</h3> <div class="clearfix text-formatted field field--name-field-highlight-body field--type-text-long field--label-hidden field__item"><p class="cta">Different types of pathogens — bacterial, fungal, parasitic or viral — can invade our bodies and cause life-threatening diseases, especially when they can’t be quickly diagnosed and properly treated. The mNGS test developed at UCSF correctly identified 86 percent of neurological infections, some of which are caused by the types of pathogens below.</p> <div class="media media--type-image media--view-mode-default" data-align="center"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <img loading="lazy" src="/sites/default/files/2024-11/pathogen-grid.jpg" width="1500" height="1503" alt="microscopic images of different types of pathogens" typeof="foaf:Image" /></div> </div> <p class="cta"><strong>1. Bacterial</strong><br /> Bacteria like Nocardia can cause pneumonia or encephalitis. <em>Image: Chiu Lab</em></p> <p class="cta"><strong>2. Fungal</strong><br /> Fungi such as Rhizopus can infect cerebrospinal fluid and respiratory fluid. <em>Image: Chiu Lab</em></p> <p class="cta"><strong>3. Parasitic</strong><br /> Here, Acanthamoeba parasites, known as the “brain eating amoeba,” carved a hole in the brain and are also ingesting red blood cells. <em>Image: Chiu Lab</em></p> <p class="cta"><strong>4. Viral</strong><br /> Adenoviruses in cerebrospinal fluid and respiratory fluid can cause diseases like bronchitis or pneumonia. <em>Image: Centers for Disease Control</em></p> </div> </aside> </div> </div> <div class="paragraph paragraph--type--article-section paragraph--view-mode--default display--"> <div class="l-container article-section"> <div class="section-content"> <div class="clearfix text-formatted field field--name-field-paragraph-body field--type-text-long field--label-hidden field__item"><p class="content-subheading"><strong>A breakthrough in diagnosing rare, infectious neurological disease</strong></p> <p>Neurological diseases can be very hard to diagnose, especially when the cause is a rare or previously unknown pathogen. In many cases, each day without a diagnosis means a continual worsening of a patient’s condition.</p> <p>In the early 2010s, Chiu, along with UCSF colleagues <a href="https://profiles.ucsf.edu/joe.derisi">Joe DeRisi</a>, PhD, and <a href="https://profiles.ucsf.edu/michael.r.wilson">Michael Wilson</a>, MD, developed a novel metagenomic sequencing method to test CSF for potential pathogens causing neurologic infections.</p> <p>The test works by sequencing all the genetic material in CSF, then running a computational analysis pipeline to separate human sequences from those that originate from bacteria, viruses, fungi or parasites.</p> <p>In 2014, the team used the technology to help doctors in Wisconsin <a data-entity-substitution="canonical" data-entity-type="node" data-entity-uuid="cc0d5afb-f459-42dc-97f3-79979d86098e" href="https://www.ucsf.edu/news/2014/06/115116/diagnosis-just-time" title="A Diagnosis Just in Time">treat a young boy</a> who was critically ill in the intensive care unit with an undiagnosed infection.</p> <p>A long series of tests had failed to find out what was wrong with him, but UCSF’s test took just 48 hours to reveal that the boy had leptospirosis, which is treatable with penicillin. His doctors gave it to him, and he fully recovered.</p> </div> </div> <div class="section-image"> </div> <div class="section-quote bg-gradient-color__blue"> <div class="field field--name-field-quote field--type-string-long field--label-hidden field__item">Our mNGS test performs better than any other category of test for neurologic infections.</div> <div class="field field--name-field-quote-author field--type-string field--label-hidden field__item">Charles Chiu, M.D., Ph.D.</div> </div> </div> </div> <div class="paragraph paragraph--type--article-section paragraph--view-mode--default display--"> <div class="l-container article-section"> <div class="section-content"> <div class="clearfix text-formatted field field--name-field-paragraph-body field--type-text-long field--label-hidden field__item"><p>The mNGS test soon became routine at UCSF, with hospitals and clinics nationwide sending samples to be processed by the UCSF Clinical Microbiology Laboratory, of which Chiu is the director.</p> <p>Between 2016 and 2023, the UCSF team analyzed nearly 5,000 CSF samples with the test, 14.4% of which turned out to have an infection. In those samples, the test accurately identified the pathogen 86% of the time.</p> <p>“Our mNGS test performs better than any other category of test for neurologic infections,” Chiu said, “The results support its use as a critical part of the diagnostic armamentarium for physicians who are working up patients with infectious diseases.”</p> <p>To increase access to this technology, Chiu, DeRisi, Wilson and others helped found Delve Bio, which is now the exclusive provider of the mNGS CSF test developed at UCSF.</p> <p>“These findings support including mNGS as a core tool in the clinical workup for CNS infections,” said Steve Miller, MD, PhD, chief medical officer of Delve Bio. “mNGS offers the single most unbiased, complete and definitive tool for pathogen detection. Thanks to its ability to quickly diagnose an infection, mNGS helps guide management decisions and treatment for patients with meningitis and encephalitis, potentially reducing healthcare costs down the line.”</p> <p class="content-subheading"><strong>Preparing for the next pandemic</strong></p> <p>If it is going to serve as an early-warning system for pandemics, the mNGS test must be fast. Chiu and his colleagues have adapted it to work with respiratory fluid and figured out how to automate it.</p> <p>Whereas the CSF test entails more than 100 separate steps and can take 2 to 7 days to process, the respiratory test requires just 30 minutes of hands-on time before robots and algorithms can take over.</p> <p>“Our goal was to have the entire process completed within 12 to 24 hours, giving a same-day or next-day result,” Chiu said.</p> <p>In the Nature Communications study, the researchers demonstrated that the test could detect respiratory viruses with pandemic potential, including SARS-CoV-2, influenza A and B, and RSV in less than a day, even when there were only small amounts of virus present in a sample.</p> <p>They also modeled the technology’s ability to detect divergent viruses – or newly-evolved strains – and found that it could hypothetically detect all of them, should they emerge in the future.</p> <p>Both the CSF and respiratory versions of the mNGS test have received breakthrough device designation from the U.S. Food and Drug Administration (FDA).</p> <figure role="group" class="caption caption-drupal-media"><div class="media media--type-image media--view-mode-default" data-align="center"> <div class="field field--name-field-media-image field--type-image field--label-hidden field__item"> <img loading="lazy" src="/sites/default/files/2024-11/charles-chiu-jenna-chiu.jpg" width="1800" height="1200" alt="Two researchers in a lab" typeof="foaf:Image" /></div> </div> <figcaption>Clinical research coordinator Jenna Chui loads DNA samples into a biorobot as Charles Chiu, M.D., Ph.D., looks on. <em>Image by Noah Berger</em></figcaption></figure></div> </div> <div class="section-image"> </div> </div> </div> </div> </div> <div class="l-container field--related-links"></div> </div> </article> </div> <div class="views-element-container l-container block block-views block-views-blockrelated-articles-block-1" id="block-views-block-related-articles-block-1"> <h2>Keep reading</h2> <div><div class="view view-related-articles view-id-related_articles view-display-id-block_1 js-view-dom-id-0a5d1b59cc29df833dc7a1d45b9cf9dc6779fc31c01815587ea2417aad293f94"> <div class="view-empty"> <div class="view view-related-articles view-id-related_articles view-display-id-block_4 js-view-dom-id-cea0081a812182912d4c921c7e1aadf39e2b65ea2a8628e181bdc7ae4a4e8891"> <div class="view-content"> <div class="views-row"><div class="views-field views-field-field-thumbnail"><div class="field-content views-field-field-image"> <img loading="lazy" src="/sites/default/files/styles/related_articles/public/iStock-1569033792.jpg?h=119335f7&itok=Ybu5w5FB" width="1320" height="1320" alt="A woman singing into an air microphone" typeof="Image" class="image-style-related-articles" /> </div></div><div class="views-field views-field-nid"><span class="field-content"><div class="content--meta"><time datetime="2024-08-22T19:27:17Z" class="datetime">Thursday, August 22, 2024</time> </div> <h3><a href="/news/singing-memory-unlocks-surprisingly-common-musical-superpower">Singing from memory unlocks a surprisingly common musical…</a> </h3> <p>Go ahead and sing in the shower — you might just have perfect pitch. </p></span></div></div> <div class="views-row"><div class="views-field views-field-field-thumbnail"><div class="field-content views-field-field-image"> <img loading="lazy" src="/sites/default/files/styles/related_articles/public/male-birth-control%20copy.jpg?h=c673cd1c&itok=sNdOtnD-" width="1320" height="1320" alt="A man with arm tattoos in a white t-shirt holds a white plastic bottle, standing in a well lit room with white walls." title="UC Davis Health Clinical Trial Tests Effectiveness of Hormonal Gel" typeof="Image" class="image-style-related-articles" /> </div></div><div class="views-field views-field-nid"><span class="field-content"><div class="content--meta"><time datetime="2023-12-21T19:01:52Z" class="datetime">Thursday, December 21, 2023</time> </div> <h3><a href="/news/unfold-podcast-episode-examines-hormonal-birth-control-men">‘Unfold’ podcast episode examines hormonal birth control…</a> </h3> <p>A clinical trial of birth control for males is underway at UC Davis. </p></span></div></div> </div> </div> </div> </div> </div> </div> </div> </div> </main> <footer role="contentinfo" class="bg-gradient__indigo"> <div class="l-container l-container--wide footer-wrapper"> <div class="footer-logo"><div class="logo"></div></div> <div class="footer-menu-wrapper"> <div class="region region-footer"> <div id="block-footercopy" class="block block-block-content block-block-contente5aa91c4-6de0-41f1-91e4-155daca7f701"> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>The University of California opened its doors in 1869 with just 10 faculty members and 40 students. 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