{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,25]],"date-time":"2026-10-25T01:16:41Z","timestamp":1792891001368,"version":"4.5.0"},"reference-count":19,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,7,18]],"date-time":"2023-07-18T00:00:00Z","timestamp":1689638400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012151","name":"Sanming Project of Medicine in Shenzhen","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012151","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010002","name":"Ministry of Education","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Med."],"abstract":"<jats:p><jats:italic>Nocardia<\/jats:italic> species do not replicate as rapidly as other pyogenic bacteria and nocardial infections can be highly fatal, particularly in immunocompromised patients. Here, we present the first report of fatal <jats:italic>Nocardia kroppenstedtii<\/jats:italic> bacteremic pneumonia and empyema thoracis diagnosed by next-generation sequencing (NGS) using the Oxford Nanopore Technologies' MinION device. The bacterium was not identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Due to its low equipment cost, short turn-around-time, and portable size, the Oxford Nanopore Technologies' MinION device is a useful platform for NGS in routine clinical microbiology laboratories.<\/jats:p>","DOI":"10.3389\/fmed.2023.1226126","type":"journal-article","created":{"date-parts":[[2023,7,18]],"date-time":"2023-07-18T10:03:34Z","timestamp":1689674614000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["Rapid diagnosis of fatal Nocardia kroppenstedtii bacteremic pneumonia and empyema thoracis by next-generation sequencing: a case report"],"prefix":"10.3389","volume":"10","author":[{"given":"Fanfan","family":"Xing","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yao","family":"Xia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qianyun","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon K. F.","family":"Lo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susanna K. P.","family":"Lau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick C. Y.","family":"Woo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,7,18]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"908","DOI":"10.1111\/j.1469-0691.2008.02070.x","article-title":"Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories","volume":"14","author":"Woo","year":"2008","journal-title":"Clin Microbiol Infect."},{"key":"B2","doi-asserted-by":"publisher","first-page":"1346","DOI":"10.1080\/22221751.2022.2069514","article-title":"Identification of a novel drug-resistant community-acquired Nocardia spp. in a patient with bronchiectasis","volume":"11","author":"Li","year":"2022","journal-title":"Emerg Microbes Infect."},{"key":"B3","doi-asserted-by":"publisher","first-page":"1517","DOI":"10.3390\/microorganisms8101517","article-title":"Genomic virulence features of two novel species Nocardia barduliensis sp. nov and Nocardia gipuzkoensis sp nov, isolated from patients with chronic pulmonary diseases","volume":"8","author":"Nouioui","year":"2020","journal-title":"Microorganisms."},{"key":"B4","doi-asserted-by":"publisher","first-page":"751","DOI":"10.1099\/ijs.0.048330-0","article-title":"Nocardia kroppenstedtii sp. nov, an actinomycete isolated from a lung transplant patient with a pulmonary infection.","volume":"64","author":"Jones","year":"2014","journal-title":"Int J Syst Evol Microbiol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"4015","DOI":"10.1128\/JCM.01234-10","article-title":"Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of nocardia species","volume":"48","author":"Verroken","year":"2010","journal-title":"J Clin Microbiol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"3142","DOI":"10.1128\/JCM.01349-12","article-title":"Matrix-assisted laser desorption ionization-time of flight mass spectrometry for rapid identification of Burkholderia pseudomallei: importance of expanding databases with pathogens endemic to different localities","volume":"50","author":"Lau","year":"2012","journal-title":"J Clin Microbiol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"1081","DOI":"10.1136\/jclinpath-2013-201651","article-title":"Matrix-assisted laser desorption ionisation-time of flight mass spectrometry for rapid identification of Laribacter hongkongensis","volume":"66","author":"Tang","year":"2013","journal-title":"J Clin Pathol."},{"key":"B8","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/s13742-015-0051-z","article-title":"Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer","volume":"4","author":"Kilianski","year":"2015","journal-title":"Gigascience."},{"key":"B9","doi-asserted-by":"publisher","first-page":"bcr2016217337","DOI":"10.1136\/bcr-2016-217337","article-title":"First reported case of disseminated Nocardia kroppenstedtii sp nov. infection presenting with brain abscess and endocarditis in an immunocompromised patient with mantle cell lymphoma: challenges in diagnosis and treatment","volume":"2017","author":"Majeed","year":"2017","journal-title":"Br Med J Case Rep."},{"key":"B10","doi-asserted-by":"publisher","first-page":"53","DOI":"10.3928\/23258160-20181212-09","article-title":"A case report of endogenous endophthalmitis in the setting of Nocardia kroppenstedtii infection","volume":"50","author":"Venkat","year":"2019","journal-title":"Ophthalmic Surg Lasers Imaging Retina."},{"key":"B11","doi-asserted-by":"publisher","first-page":"605","DOI":"10.26355\/eurrev_202101_24618","article-title":"Nocardia kroppenstedtii: a rare pathogen isolated from the spinal vertebral abscess of a patient on long-term immunosuppressive therapy.","volume":"25","author":"Tay","year":"2021","journal-title":"Eur Rev Med Pharmacol Sci."},{"key":"B12","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1097\/IM9.0000000000000080","article-title":"Next-generation sequencing-based diagnosis of bacteremic Listeria monocytogenes meningitis in a patient with anti-interferon gamma autoantibodies: a case report","volume":"4","author":"Xing","year":"2022","journal-title":"Infect Microb Dis."},{"key":"B13","doi-asserted-by":"publisher","first-page":"e0010364","DOI":"10.1371\/journal.pntd.0010364","article-title":"Diverse and atypical manifestations of Q fever in a metropolitan city hospital: emerging role of next-generation sequencing for laboratory diagnosis of Coxiella burnetii","volume":"16","author":"Xing","year":"2022","journal-title":"PLoS Negl Trop Dis."},{"key":"B14","doi-asserted-by":"publisher","first-page":"636","DOI":"10.3390\/jof7080636","article-title":"Rapid genomic diagnosis of fungal infections in the age of next-generation sequencing","volume":"7","author":"Tsang","year":"2021","journal-title":"J Fungi."},{"key":"B15","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1016\/j.jinf.2022.08.026","article-title":"Clinical impact of next-generation sequencing on laboratory diagnosis of suspected culture-negative meningitis and encephalitis","volume":"85","author":"Xing","year":"2022","journal-title":"J Infect."},{"key":"B16","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1016\/j.jinf.2022.12.004","article-title":"Emergence of Tropheryma whipplei detection in respiratory samples by next-generation sequencing: pathogen or innocent bystander?","volume":"86","author":"Xing","year":"2023","journal-title":"J Infect."},{"key":"B17","doi-asserted-by":"publisher","first-page":"824122","DOI":"10.3389\/fmed.2022.824122","article-title":"Rapid diagnosis of Mycobacterium marinum infection by next-generation sequencing: a case report","volume":"9","author":"Xing","year":"2022","journal-title":"Front Med."},{"key":"B18","doi-asserted-by":"publisher","first-page":"1285","DOI":"10.1128\/JCM.02483-16","article-title":"Same-day diagnostic and surveillance data for tuberculosis via whole-genome sequencing of direct respiratory samples","volume":"55","author":"Votintseva","year":"2017","journal-title":"J Clin Microbiol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"3530","DOI":"10.1128\/JCM.01069-17","article-title":"Rapid nanopore sequencing of plasmids and resistance gene detection in clinical isolates","volume":"55","author":"Lemon","year":"2017","journal-title":"J Clin Microbiol."}],"container-title":["Frontiers in Medicine"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmed.2023.1226126\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,18]],"date-time":"2023-07-18T10:03:39Z","timestamp":1689674619000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmed.2023.1226126\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,7,18]]},"references-count":19,"alternative-id":["10.3389\/fmed.2023.1226126"],"URL":"https:\/\/doi.org\/10.3389\/fmed.2023.1226126","relation":{},"ISSN":["2296-858X"],"issn-type":[{"value":"2296-858X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,7,18]]},"article-number":"1226126"}}