{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T23:14:12Z","timestamp":1793315652102,"version":"4.5.0"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,10,10]],"date-time":"2023-10-10T00:00:00Z","timestamp":1696896000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Karius Inc"},{"DOI":"10.13039\/100006513","name":"Duke Clinical Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006513","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Pneumonia is a common cause of morbidity and mortality, yet a causative pathogen is identified in a minority of cases. Plasma microbial cell-free DNA sequencing may improve diagnostic yield in immunocompromised patients with pneumonia.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>In this prospective, multicenter, observational study of immunocompromised adults undergoing bronchoscopy to establish a pneumonia etiology, plasma microbial cell-free DNA sequencing was compared to standardized usual care testing. Pneumonia etiology was adjudicated by a blinded independent committee. The primary outcome, additive diagnostic value, was assessed in the Per Protocol population (patients with complete testing results and no major protocol deviations) and defined as the percent of patients with an etiology of pneumonia exclusively identified by plasma microbial cell-free DNA sequencing. Clinical additive diagnostic value was assessed in the Per Protocol subgroup with negative usual care testing.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Of 257 patients, 173 met Per Protocol criteria. A pneumonia etiology was identified by usual care in 52\/173 (30.1%), plasma microbial cell-free DNA sequencing in 49\/173 (28.3%) and the combination of both in 73\/173 (42.2%) patients. Plasma microbial cell-free DNA sequencing exclusively identified an etiology of pneumonia in 21\/173 patients (additive diagnostic value 12.1%, 95% confidence interval [CI], 7.7% to 18.0%, P &amp;lt; .001). In the Per Protocol subgroup with negative usual care testing, plasma microbial cell-free DNA sequencing identified a pneumonia etiology in 21\/121 patients (clinical additive diagnostic value 17.4%, 95% CI, 11.1% to 25.3%).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Non-invasive plasma microbial cell-free DNA sequencing significantly increased diagnostic yield in immunocompromised patients with pneumonia undergoing bronchoscopy and extensive microbiologic and molecular testing.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Clinical Trials Registration<\/jats:title>\n                    <jats:p>NCT04047719.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/cid\/ciad599","type":"journal-article","created":{"date-parts":[[2023,9,29]],"date-time":"2023-09-29T16:38:17Z","timestamp":1696005497000},"page":"775-784","source":"Crossref","is-referenced-by-count":71,"title":["Plasma Microbial Cell-Free DNA Sequencing in Immunocompromised Patients With Pneumonia: A Prospective Observational Study"],"prefix":"10.1093","volume":"78","author":[{"given":"Stephen P","family":"Bergin","sequence":"first","affiliation":[{"name":"Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Duke University School of Medicine , Durham, North Carolina , USA"},{"name":"Duke Clinical Research Institute , Durham, North Carolina , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roy F","family":"Chemaly","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center , Houston, Texas , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanjeet S","family":"Dadwal","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Infectious Diseases, City of Hope National Medical Center , Duarte California, California , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua A","family":"Hill","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center , Seattle, Washington , USA"},{"name":"Department of Medicine, University of Washington School of Medicine , Seattle, Washington , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yeon Joo","family":"Lee","sequence":"additional","affiliation":[{"name":"Infectious Diseases Service, Memorial Sloan Kettering Cancer Center , NewYork, New York , USA"},{"name":"Department of Medicine, Weill Cornell Medicine , NewYork, New York , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ghady","family":"Haidar","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Infectious Diseases, University of Pittsburgh Medical Center , Pittsburgh, Pennsylvania , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alfred","family":"Luk","sequence":"additional","affiliation":[{"name":"Section of Infectious Diseases, John W. Deming Department of Medicine, Tulane University School of Medicine , New Orleans, Louisiana , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Drelick","sequence":"additional","affiliation":[{"name":"Department of Medicine, Weill Cornell Medicine , NewYork, New York , USA"},{"name":"Department of Medicine, NewYork-Presbyterian Hospital , New York, New York , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter V","family":"Chin-Hong","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, University of California San Francisco , San Francisco, California , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esther","family":"Benamu","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, University of Colorado , Aurora, Colorado , 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