{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,25]],"date-time":"2026-10-25T02:38:09Z","timestamp":1792895889506,"version":"4.5.0"},"reference-count":77,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2020,10,30]],"date-time":"2020-10-30T00:00:00Z","timestamp":1604016000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"California Initiative to Advance Precision Medicine and Schwab Foundation to institution"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Metagenomic next generation sequencing (mNGS) is becoming increasingly available for pathogen detection directly from clinical specimens. These tests use target-independent, shotgun sequencing to detect potentially unlimited organisms. The promise of this methodology to aid infection diagnosis is demonstrated through early case reports and clinical studies. However, the optimal role of mNGS in clinical microbiology remains uncertain.<\/jats:p><\/jats:sec><jats:sec><jats:title>Content<\/jats:title><jats:p>We reviewed studies reporting clinical use of mNGS for pathogen detection from various specimen types, including cerebrospinal fluid, plasma, lower respiratory specimens, and others. Published clinical study data were critically evaluated and summarized to identify promising clinical indications for mNGS-based testing, to assess the clinical impact of mNGS for each indication, and to recognize test limitations. Based on these clinical studies, early testing recommendations are made to guide clinical utilization of mNGS for pathogen detection. Finally, current barriers to routine clinical laboratory implementation of mNGS tests are highlighted.<\/jats:p><\/jats:sec><jats:sec><jats:title>Summary<\/jats:title><jats:p>The promise of direct-from-specimen mNGS to enable challenging infection diagnoses has been demonstrated through early clinical studies of patients with meningitis or encephalitis, invasive fungal infections, community acquired pneumonia, and other clinical indications. However, the proportion of patient cases with positive clinical impact due to mNGS testing is low in published studies and the cost of testing is high, emphasizing the importance of improving our understanding of \u2018when to test\u2019 and for which patients mNGS testing is appropriate.<\/jats:p><\/jats:sec>","DOI":"10.1093\/clinchem\/hvaa183","type":"journal-article","created":{"date-parts":[[2020,7,22]],"date-time":"2020-07-22T19:16:50Z","timestamp":1595445410000},"page":"1381-1395","source":"Crossref","is-referenced-by-count":78,"title":["Navigating Clinical Utilization of Direct-from-Specimen Metagenomic Pathogen Detection: Clinical Applications, Limitations, and Testing Recommendations"],"prefix":"10.1093","volume":"66","author":[{"given":"Laura M","family":"Filkins","sequence":"first","affiliation":[{"name":"Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra L","family":"Bryson","sequence":"additional","affiliation":[{"name":"Department of Pathology, Virginia Commonwealth University Health System, Richmond, VA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steve A","family":"Miller","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie L","family":"Mitchell","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,10,30]]},"reference":[{"key":"2020120415571322200_hvaa183-B1","doi-asserted-by":"crossref","first-page":"1565","DOI":"10.1086\/509330","article-title":"Beyond viruses: clinical profiles and etiologies associated with encephalitis","volume":"43","author":"Glaser","year":"2006","journal-title":"Clin Infect Dis"},{"key":"2020120415571322200_hvaa183-B2","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1056\/NEJMoa1405870","article-title":"Community-acquired pneumonia requiring hospitalization among U.S. children","volume":"372","author":"Jain","year":"2015","journal-title":"N Engl J Med"},{"key":"2020120415571322200_hvaa183-B3","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1056\/NEJMoa1500245","article-title":"Community-acquired pneumonia requiring hospitalization among U.S. adults","volume":"373","author":"Jain","year":"2015","journal-title":"N Engl J Med"},{"key":"2020120415571322200_hvaa183-B4","doi-asserted-by":"crossref","first-page":"2547","DOI":"10.1001\/jama.2016.16477","article-title":"Prevalence of immunosuppression among US adults, 2013","volume":"316","author":"Harpaz","year":"2016","journal-title":"JAMA"},{"key":"2020120415571322200_hvaa183-B5","doi-asserted-by":"crossref","first-page":"e1002824","DOI":"10.1371\/journal.ppat.1002824","article-title":"Routine use of microbial whole genome sequencing in diagnostic and public health microbiology","volume":"8","author":"Koser","year":"2012","journal-title":"PLoS Pathog"},{"key":"2020120415571322200_hvaa183-B6","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1080\/14737159.2017.1283220","article-title":"Microbial genomics and antimicrobial susceptibility testing","volume":"17","author":"Dunne","year":"2017","journal-title":"Expert Rev Mol Diagn"},{"key":"2020120415571322200_hvaa183-B7","doi-asserted-by":"crossref","first-page":"1855","DOI":"10.1016\/j.mayocp.2017.10.004","article-title":"Microbiome at the frontier of personalized medicine","volume":"92","author":"Kashyap","year":"2017","journal-title":"Mayo Clin Proc"},{"key":"2020120415571322200_hvaa183-B8","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1038\/s41576-019-0113-7","article-title":"Clinical metagenomics","volume":"20","author":"Chiu","year":"2019","journal-title":"Nat Rev Genet"},{"key":"2020120415571322200_hvaa183-B9","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.jbiotec.2016.12.022","article-title":"Application of next generation sequencing in clinical microbiology and infection prevention","volume":"243","author":"Deurenberg","year":"2017","journal-title":"J Biotechnol"},{"key":"2020120415571322200_hvaa183-B10","doi-asserted-by":"crossref","first-page":"776","DOI":"10.5858\/arpa.2016-0539-RA","article-title":"Professional Practice Committee and Committee on Laboratory Practices of the American Society for Microbiology; Microbiology Resource Committee of the College of American Pathologists. 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