{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T04:17:50Z","timestamp":1774757870492,"version":"3.50.1"},"reference-count":25,"publisher":"Cambridge University Press (CUP)","license":[{"start":{"date-parts":[[2023,10,27]],"date-time":"2023-10-27T00:00:00Z","timestamp":1698364800000},"content-version":"unspecified","delay-in-days":299,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000097","name":"National Center for Research Resources","doi-asserted-by":"publisher","award":["ULTR002649"],"award-info":[{"award-number":["ULTR002649"]}],"id":[{"id":"10.13039\/100000097","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cambridge.org"],"crossmark-restriction":true},"short-container-title":["Epidemiol. Infect."],"published-print":{"date-parts":[[2023]]},"abstract":"<jats:title>Abstract<\/jats:title>\n\t  <jats:p>Secondary pneumonia occurs in 8\u201324% of patients with Coronavirus 2019 (COVID-19) infection and is associated with increased morbidity and mortality. Diagnosis of secondary pneumonia can be challenging. The purpose of this study was to evaluate the use of plasma microbial cell free DNA sequencing (mcfNGS) in the evaluation of secondary pneumonia after COVID-19. We performed a single-center case series of patients with COVID-19 who underwent mcfNGS to evaluate secondary pneumonia and reported the organisms identified, concordance with available tests, clinical utility, and outcomes. In 8\/13 (61%) cases, mcfNGS detected 1\u20136 organisms, with clinically significant organisms identified in 4 cases, including <jats:italic>Pneumocystis jirovecii<\/jats:italic>, and <jats:italic>Legionella<\/jats:italic> spp. Management was changed in 85% (11\/13) of patients based on results, including initiation of targeted therapy, de-escalation of empiric antimicrobials, and avoiding contingent escalation of antifungals. mcfNGS may be helpful to identify pathogens causing secondary pneumonia, including opportunistic pathogens in immunocompromised patients with COVID-19. However, providers need to carefully interpret this test within the clinical context.<\/jats:p>","DOI":"10.1017\/s0950268823001711","type":"journal-article","created":{"date-parts":[[2023,10,27]],"date-time":"2023-10-27T08:57:56Z","timestamp":1698397076000},"update-policy":"https:\/\/doi.org\/10.1017\/policypage","source":"Crossref","is-referenced-by-count":5,"title":["Cell-free plasma next-generation sequencing assists in the evaluation of secondary pneumonia in patients with COVID-19: a case series"],"prefix":"10.1017","volume":"151","author":[{"given":"Joshua A.","family":"David","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bharadhwaj","family":"Kolipakkam","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Megan K.","family":"Morales","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7748-1215","authenticated-orcid":false,"given":"Nicole C.","family":"Vissichelli","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"56","published-online":{"date-parts":[[2023,10,27]]},"reference":[{"key":"S0950268823001711_r24","doi-asserted-by":"publisher","DOI":"10.1111\/tid.13954"},{"key":"S0950268823001711_r1","first-page":"2459","article-title":") Bacterial and fungal coinfection in individuals with coronavirus: a rapid review to support COVID-19 antimicrobial prescribing","volume":"71","author":"Rawson","year":"2020","journal-title":"Clinical Infectious Diseases"},{"key":"S0950268823001711_r9","doi-asserted-by":"publisher","DOI":"10.1378\/chest.121.5.1486"},{"key":"S0950268823001711_r23","first-page":"1","article-title":") Clinical impact of metagenomic next-generation sequencing of plasma cell-free DNA for the diagnosis of infectious diseases: a multicenter retrospective cohort study","volume":"94304","author":"Hogan","year":"2020","journal-title":"Clinical Infectious Diseases"},{"key":"S0950268823001711_r6","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-022-01172-2"},{"key":"S0950268823001711_r12","doi-asserted-by":"publisher","DOI":"10.1513\/AnnalsATS.201212-114FR"},{"key":"S0950268823001711_r15","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-018-0349-6"},{"key":"S0950268823001711_r14","doi-asserted-by":"publisher","DOI":"10.1086\/429921"},{"key":"S0950268823001711_r4","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0251170"},{"key":"S0950268823001711_r11","doi-asserted-by":"publisher","DOI":"10.1016\/j.infpip.2019.100029"},{"key":"S0950268823001711_r8","doi-asserted-by":"publisher","DOI":"10.1111\/tid.13407"},{"key":"S0950268823001711_r3","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens11040445"},{"key":"S0950268823001711_r13","doi-asserted-by":"publisher","DOI":"10.1016\/j.chest.2020.04.036"},{"key":"S0950268823001711_r18","doi-asserted-by":"publisher","DOI":"10.1186\/s12931-021-01623-0"},{"key":"S0950268823001711_r16","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciaa1639"},{"key":"S0950268823001711_r20","unstructured":"[20] COVID-19 Treatment Guidelines Panel. Coronavirus Disease 2019 (COVID-19) Treatment Guidelines. National Institutes of Health. Available at https:\/\/www.covid19treatmentguidelines.nih.gov\/ (accessed 18 April 2023)."},{"key":"S0950268823001711_r5","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2020.07.016"},{"key":"S0950268823001711_r17","doi-asserted-by":"publisher","DOI":"10.1002\/pbc.27734"},{"key":"S0950268823001711_r19","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.01859-22"},{"key":"S0950268823001711_r2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.01041"},{"key":"S0950268823001711_r21","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbi.2008.08.010"},{"key":"S0950268823001711_r10","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofx014"},{"key":"S0950268823001711_r7","doi-asserted-by":"publisher","DOI":"10.3201\/eid2701.202896"},{"key":"S0950268823001711_r22","doi-asserted-by":"publisher","DOI":"10.1016\/j.clinmicnews.2021.04.003"},{"key":"S0950268823001711_r25","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiad213"}],"container-title":["Epidemiology and Infection"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.cambridge.org\/core\/services\/aop-cambridge-core\/content\/view\/S0950268823001711","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,10]],"date-time":"2023-11-10T05:43:19Z","timestamp":1699594999000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.cambridge.org\/core\/product\/identifier\/S0950268823001711\/type\/journal_article"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023]]},"references-count":25,"alternative-id":["S0950268823001711"],"URL":"https:\/\/doi.org\/10.1017\/s0950268823001711","relation":{},"ISSN":["0950-2688","1469-4409"],"issn-type":[{"value":"0950-2688","type":"print"},{"value":"1469-4409","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023]]},"assertion":[{"value":"\u00a9 The Author(s), 2023. 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