{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T13:30:19Z","timestamp":1784122219282,"version":"3.55.0"},"reference-count":19,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2022,1,3]],"date-time":"2022-01-03T00:00:00Z","timestamp":1641168000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2022,1,3]],"date-time":"2022-01-03T00:00:00Z","timestamp":1641168000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Eur J Med Res"],"published-print":{"date-parts":[[2022,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Cryptococcal meningitis (CM) has a high morbidity and mortality due to the low detection of Cryptococcus in cerebrospinal fluid (CSF) during the early stage of the disease with traditional methods.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Case presentation<\/jats:title>\n                <jats:p>In addition to the traditional methods of India ink staining and cryptococcal antigen (CrAg), we used nanopore sequencing and next-generation sequencing (NGS) to detect pathogenic DNA in CSF samples of three patients with CM. The CSF samples of all three patients were positive by India ink staining and CrAg. NGS also detected Cryptococcus in all three CSF samples. Nanopore sequencing detected Cryptococcus in two CSF samples.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>Nanopore sequencing may be useful in assisting with the clinical diagnosis of CM. Further research is needed to determine the sensitivity and specificity of nanopore sequencing of CSF.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s40001-021-00625-4","type":"journal-article","created":{"date-parts":[[2022,1,3]],"date-time":"2022-01-03T07:03:20Z","timestamp":1641193400000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Nanopore sequencing of cerebrospinal fluid of three patients with cryptococcal meningitis"],"prefix":"10.1186","volume":"27","author":[{"given":"Ke","family":"Jin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaojuan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lingzhi","family":"Qin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yazhen","family":"Jia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keke","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yusu","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Milan","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengge","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weifeng","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lin","family":"Jia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongshi","family":"Teng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuhua","family":"Dai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3960-1749","authenticated-orcid":false,"given":"Wei","family":"li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,1,3]]},"reference":[{"key":"625_CR1","doi-asserted-by":"publisher","first-page":"459","DOI":"10.2217\/bmm-2019-0333","volume":"14","author":"V Poplin","year":"2020","unstructured":"Poplin V, Boulware DR, Bahr NC. Methods for rapid diagnosis of meningitis etiology in adults. Biomark Med. 2020;14:459\u201379.","journal-title":"Biomark Med"},{"key":"625_CR2","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1055\/s-0034-1372342","volume":"34","author":"T Makadzange Azure","year":"2014","unstructured":"Makadzange Azure T, McHugh G. New approaches to the diagnosis and treatment of cryptococcal meningitis. Semin Neurol. 2014;34:47\u201360.","journal-title":"Semin Neurol"},{"key":"625_CR3","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1097\/QAD.0b013e328322ffac","volume":"23","author":"J Park Benjamin","year":"2009","unstructured":"Park Benjamin J, Wannemuehler Kathleen A, Marston Barbara J, et al. Estimation of the current global burden of cryptococcal meningitis among persons living with HIV\/AIDS. AIDS. 2009;23:525\u201330.","journal-title":"AIDS"},{"key":"625_CR4","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1007\/s15010-018-1152-2","volume":"46","author":"K G\u00f3ralska","year":"2018","unstructured":"G\u00f3ralska K, Blaszkowska J, Dzikowiec M. Neuroinfections caused by fungi. Infection. 2018;46:443\u201359.","journal-title":"Infection"},{"key":"625_CR5","doi-asserted-by":"publisher","first-page":"144","DOI":"10.12688\/wellcomeopenres.15464.1","volume":"4","author":"MW Tenforde","year":"2019","unstructured":"Tenforde MW, Muthoga C, Callaghan A, et al. Cost-effectiveness of reflex laboratory-based cryptococcal antigen screening for the prevention and treatment of cryptococcal meningitis in Botswana. Wellcome Open Res. 2019;4:144.","journal-title":"Wellcome Open Res"},{"key":"625_CR6","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1016\/j.mmcr.2020.01.001","volume":"27","author":"S Tanu","year":"2020","unstructured":"Tanu S, Mi M, Rajeev S, et al. Neurological worsening during treatment of an immunocompetent adult with Cryptococcus neoformans meningitis. Med Mycol Case Rep. 2020;27:48\u201351.","journal-title":"Med Mycol Case Rep"},{"key":"625_CR7","doi-asserted-by":"publisher","first-page":"1204","DOI":"10.1099\/jmm.0.000994","volume":"68","author":"XW Xing","year":"2019","unstructured":"Xing XW, Zhang JT, Ma YB, et al. Apparent performance of metagenomic next-generation sequencing in the diagnosis of cryptococcal meningitis: a descriptive study.J. Med Microbiol. 2019;68:1204\u201310.","journal-title":"Med Microbiol"},{"key":"625_CR8","doi-asserted-by":"publisher","DOI":"10.3390\/jof5030071","author":"J Beardsley","year":"2019","unstructured":"Beardsley J, Sorrell TC, Chen SCA. Central Nervous System Cryptococcal infections in non-HIV infected patients. J Fungi (Basel). 2019. https:\/\/doi.org\/10.3390\/jof5030071.","journal-title":"J Fungi (Basel)"},{"key":"625_CR9","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/j.mib.2019.03.001","volume":"51","author":"J Trotter Alexander","year":"2019","unstructured":"Trotter Alexander J, Alp A, Strinden Michael J, et al. Recent and emerging technologies for the rapid diagnosis of infection and antimicrobial resistance. Curr Opin Microbiol. 2019;51:39\u201345.","journal-title":"Curr Opin Microbiol"},{"key":"625_CR10","doi-asserted-by":"publisher","first-page":"211","DOI":"10.3389\/fgene.2020.00211","volume":"11","author":"L Cozzuto","year":"2020","unstructured":"Cozzuto L, Liu H, Pryszcz LP, et al. MasterOfPores: a workflow for the analysis of oxford nanopore direct RNA sequencing datasets. Front Genet. 2020;11:211.","journal-title":"Front Genet"},{"key":"625_CR11","doi-asserted-by":"publisher","first-page":"1048","DOI":"10.3389\/fmicb.2020.01048","volume":"11","author":"W Kwak","year":"2020","unstructured":"Kwak W, Han YH, Seol D, et al. Complete genome of Lactobacillus iners KY using Flongle provides insight into the genetic background of optimal adaption to vaginal econiche. Front Microbiol. 2020;11:1048.","journal-title":"Front Microbiol"},{"key":"625_CR12","doi-asserted-by":"publisher","first-page":"4940","DOI":"10.1093\/nar\/gkaa206","volume":"48","author":"P Spealman","year":"2020","unstructured":"Spealman P, Burrell J, Gresham D. Inverted duplicate DNA sequences increase translocation rates through sequencing nanopores resulting in reduced base calling accuracy. Nucleic Acids Res. 2020;48:4940\u20135.","journal-title":"Nucleic Acids Res"},{"key":"625_CR13","doi-asserted-by":"publisher","first-page":"13501","DOI":"10.1038\/s41598-019-49700-1","volume":"9","author":"AS Gargis","year":"2019","unstructured":"Gargis AS, Cherney B, Conley AB, et al. Rapid detection of genetic engineering, structural variation, and antimicrobial resistance markers in bacterial biothreat pathogens by nanopore sequencing. Sci Rep. 2019;9:13501.","journal-title":"Sci Rep"},{"key":"625_CR14","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1111\/dgd.12608","volume":"61","author":"N Kono","year":"2019","unstructured":"Kono N, Arakawa K. Nanopore sequencing: review of potential applications in functional genomics. Dev Growth Differ. 2019;61:316\u201326.","journal-title":"Dev Growth Differ"},{"key":"625_CR15","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/j.meegid.2019.04.015","volume":"73","author":"MBB Oude","year":"2019","unstructured":"Oude MBB, Kik M, de Bruijn ND, et al. Towards high quality real-time whole genome sequencing during outbreaks using Usutu virus as example. Infect Genet Evol. 2019;73:49\u201354.","journal-title":"Infect Genet Evol"},{"key":"625_CR16","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1186\/s13742-016-0140-7","volume":"5","author":"CH Li","year":"2016","unstructured":"Li CH, Chng KR, Boey EJH, et al. INC-Seq: accurate single molecule reads using nanopore sequencing. Gigascience. 2016;5:34.","journal-title":"Gigascience"},{"key":"625_CR17","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0226234","volume":"15","author":"A Scheunert","year":"2020","unstructured":"Scheunert A, Dorfner M, Lingl T, et al. Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing. PLoS ONE. 2020;15: e0226234.","journal-title":"PLoS ONE"},{"key":"625_CR18","volume":"3","author":"RR Wick","year":"2017","unstructured":"Wick RR, Judd LM, Gorrie CL, et al. Completing bacterial genome assemblies with multiplex MinION sequencing. Microb Genom. 2017;3: e000132.","journal-title":"Microb Genom"},{"key":"625_CR19","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1016\/j.jinf.2019.12.011","volume":"80","author":"NTT Hong","year":"2020","unstructured":"Hong NTT, Nghia HDT, Thanh TT, et al. Cerebrospinal fluid MinION sequencing of 16S rRNA gene for rapid and accurate diagnosis of bacterial meningitis. J Infect. 2020;80:469\u201396.","journal-title":"J Infect"}],"container-title":["European Journal of Medical Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40001-021-00625-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s40001-021-00625-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40001-021-00625-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,3]],"date-time":"2022-01-03T19:15:22Z","timestamp":1641237322000},"score":1,"resource":{"primary":{"URL":"https:\/\/eurjmedres.biomedcentral.com\/articles\/10.1186\/s40001-021-00625-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1,3]]},"references-count":19,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2022,12]]}},"alternative-id":["625"],"URL":"https:\/\/doi.org\/10.1186\/s40001-021-00625-4","relation":{},"ISSN":["2047-783X"],"issn-type":[{"value":"2047-783X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,1,3]]},"assertion":[{"value":"29 August 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 December 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 January 2022","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"(a) The patient\u2019s written consent was obtained. (b) The design of the work has been approved by the ethical committees of the Henan Provincial People\u2019s Hospital.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"All presentations of case reports have consent for publication.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"1"}}