{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,26]],"date-time":"2026-06-26T15:26:09Z","timestamp":1782487569066,"version":"3.54.5"},"reference-count":40,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2020,1,31]],"date-time":"2020-01-31T00:00:00Z","timestamp":1580428800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2020,1,31]],"date-time":"2020-01-31T00:00:00Z","timestamp":1580428800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"name":"National Key Research and Development Plan Precision Medicine Project","award":["2016 YFC0904501"],"award-info":[{"award-number":["2016 YFC0904501"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Mol Neurosci"],"published-print":{"date-parts":[[2020,5]]},"DOI":"10.1007\/s12031-019-01472-z","type":"journal-article","created":{"date-parts":[[2020,1,31]],"date-time":"2020-01-31T00:04:40Z","timestamp":1580429080000},"page":"659-666","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":49,"title":["Reduction of Human DNA Contamination in Clinical Cerebrospinal Fluid Specimens Improves the Sensitivity of Metagenomic Next-Generation Sequencing"],"prefix":"10.1007","volume":"70","author":[{"given":"Xin-Chao","family":"Ji","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lin-Fu","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chao-Yang","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ya-Jun","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meng-Li","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao-Fei","family":"Fei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7679-8683","authenticated-orcid":false,"given":"Gang","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,1,31]]},"reference":[{"issue":"2","key":"1472_CR1","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1007\/s40475-015-0046-y","volume":"2","author":"M Abassi","year":"2015","unstructured":"Abassi M, Boulware DR, Rhein J (2015) Cryptococcal meningitis: diagnosis and management update. Curr Trop Med Rep 2(2):90\u201399","journal-title":"Curr Trop Med Rep"},{"issue":"7","key":"1472_CR2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0022213","volume":"6","author":"S Auburn","year":"2011","unstructured":"Auburn S, Campino S, Clark TG, Djimde AA, Zongo I, Pinches R, Manske M, Mangano V, Alcock D, Anastasi E, Maslen G, Macinnis B, Rockett K, Modiano D, Newbold CI, Doumbo OK, Ou\u00e9draogo JB, Kwiatkowski DP (2011) An effective method to purify plasmodium falciparum DNA directly from clinical blood samples for whole genome high-throughput sequencing. PLoS One 6(7):e22213","journal-title":"PLoS One"},{"issue":"1","key":"1472_CR3","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1016\/S1473-3099(17)30474-7","volume":"18","author":"NC Bahr","year":"2018","unstructured":"Bahr NC, Nuwagira E, Evans EE, Cresswell FV, Bystrom PV, Byamukama A, Bridge SC, Bangdiwala AS, Meya DB, Denkinger CM, Muzoora C, Boulware DR, ASTRO-CM Trial Team (2018) Diagnostic accuracy of Xpert MTB\/RIF ultra for tuberculous meningitis in HIV-infected adults: a prospective cohort study. Lancet Infect Dis 18(1):68\u201375","journal-title":"Lancet Infect Dis"},{"key":"1472_CR4","first-page":"180352","volume":"2011","author":"S Bhagwan","year":"2011","unstructured":"Bhagwan S, Naidoo K (2011) Aetiology, clinical presentation, and outcome of meningitis in patients coinfected with human immunodeficiency virus and tuberculosis. AIDS Res Treat 2011:180352","journal-title":"AIDS Res Treat"},{"issue":"3","key":"1472_CR5","doi-asserted-by":"publisher","first-page":"276","DOI":"10.5588\/ijtld.14.0805","volume":"19","author":"TH Boyles","year":"2015","unstructured":"Boyles TH, Thwaites GE (2015) Appropriate use of the Xpert(R) MTB\/RIF assay in suspected tuberculous meningitis. Int J Tuberc Lung Dis 19(3):276\u2013277","journal-title":"Int J Tuberc Lung Dis"},{"key":"1472_CR6","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1186\/1471-2164-13-262","volume":"13","author":"AT Bright","year":"2012","unstructured":"Bright AT, Tewhey R, Abeles S, Chuquiyauri R, Llanos-Cuentas A, Ferreira MU et al (2012) Whole genome sequencing analysis of plasmodium vivax using whole genome capture. BMC Genomics 13:262","journal-title":"BMC Genomics"},{"key":"1472_CR7","volume-title":"Sensitivity of next-generation sequencing metagenomic analysis for detection of RNA and DNA viruses in cerebrospinal fluid: the confounding effect of background contamination","author":"I Bukowska-Osko","year":"2016","unstructured":"Bukowska-Osko I, Perlejewski K, Nakamura S, Motooka D, Stokowy T, Kosinska J et al (2016) Sensitivity of next-generation sequencing metagenomic analysis for detection of RNA and DNA viruses in cerebrospinal fluid: the confounding effect of background contamination. Biol, Adv Exp Med"},{"issue":"8","key":"1472_CR8","doi-asserted-by":"publisher","first-page":"2753","DOI":"10.1128\/JCM.00840-15","volume":"53","author":"C Conde-Pereira","year":"2015","unstructured":"Conde-Pereira C, Rodas-Rodriguez L, Diaz-Paz M, Palacios-Rivera H, Firacative C, Meyer W et al (2015) Fatal case of polymicrobial meningitis caused by Cryptococcus liquefaciens and Mycobacterium tuberculosis complex in a human immunodeficiency virus-infected patient. J Clin Microbiol 53(8):2753\u20132755","journal-title":"J Clin Microbiol"},{"issue":"2","key":"1472_CR9","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1016\/S0891-5520(05)70160-4","volume":"15","author":"BA Cunha","year":"2001","unstructured":"Cunha BA (2001) Central nervous system infections in the compromised host: a diagnostic approach. Infect Dis Clin N Am 15(2):567\u2013590","journal-title":"Infect Dis Clin N Am"},{"issue":"8","key":"1472_CR10","volume":"6","author":"W Fang","year":"2017","unstructured":"Fang W, Zhang L, Liu J, Denning DW, Hagen F, Jiang W, Hong N, Deng S, Lei X, Deng D, Liao W, Xu J, Boekhout T, Chen M, Pan W (2017) Tuberculosis\/cryptococcosis co-infection in China between 1965 and 2016. Emerg Microbes Infect 6(8):e73","journal-title":"Emerg Microbes Infect"},{"issue":"1","key":"1472_CR11","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1002\/ana.24833","volume":"81","author":"A Foutz","year":"2017","unstructured":"Foutz A, Appleby BS, Hamlin C, Liu X, Yang S, Cohen Y, Chen W, Blevins J, Fausett C, Wang H, Gambetti P, Zhang S, Hughson A, Tatsuoka C, Schonberger LB, Cohen ML, Caughey B, Safar JG (2017) Diagnostic and prognostic value of human prion detection in cerebrospinal fluid. Ann Neurol 81(1):79\u201392","journal-title":"Ann Neurol"},{"issue":"4","key":"1472_CR12","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1099\/mic.0.000601","volume":"164","author":"SV Gordon","year":"2018","unstructured":"Gordon SV, Parish T (2018) Microbe profile: mycobacterium tuberculosis: humanity's deadly microbial foe. Microbiology 164(4):437\u2013439","journal-title":"Microbiology"},{"key":"1472_CR13","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1186\/s13073-015-0235-2","volume":"7","author":"AL Greninger","year":"2015","unstructured":"Greninger AL, Messacar K, Dunnebacke T, Naccache SN, Federman S, Bouquet J et al (2015) Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing. Genome Med 7:113","journal-title":"Genome Med"},{"issue":"4","key":"1472_CR14","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1128\/JCM.03050-15","volume":"54","author":"MR Hasan","year":"2016","unstructured":"Hasan MR, Rawat A, Tang P, Jithesh PV, Thomas E, Tan R, Tilley P (2016) Depletion of human DNA in spiked clinical specimens for improvement of sensitivity of pathogen detection by next-generation sequencing. J Clin Microbiol 54(4):919\u2013927","journal-title":"J Clin Microbiol"},{"issue":"4","key":"1472_CR15","doi-asserted-by":"publisher","first-page":"363","DOI":"10.4103\/aian.AIAN_219_17","volume":"20","author":"R Jipa","year":"2017","unstructured":"Jipa R, Olaru ID, Manea E, Merisor S, Hristea A (2017) Rapid clinical score for the diagnosis of tuberculous meningitis: a retrospective cohort study. Ann Indian Acad Neurol 20(4):363\u2013366","journal-title":"Ann Indian Acad Neurol"},{"issue":"Suppl 3","key":"1472_CR16","doi-asserted-by":"publisher","first-page":"S331","DOI":"10.1097\/QAI.0000000000000484","volume":"68","author":"JE Kaplan","year":"2015","unstructured":"Kaplan JE, Vallabhaneni S, Smith RM, Chideya-Chihota S, Chehab J, Park B (2015) Cryptococcal antigen screening and early antifungal treatment to prevent cryptococcal meningitis: a review of the literature. J Acquir Immune Defic Syndr 68(Suppl 3):S331\u2013S339","journal-title":"J Acquir Immune Defic Syndr"},{"issue":"3","key":"1472_CR17","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1016\/j.ijtb.2017.01.005","volume":"64","author":"JE Kaviyil","year":"2017","unstructured":"Kaviyil JE, Ravikumar R (2017) Diagnosis of tuberculous meningitis: current scenario from a tertiary Neurocare Centre in India. Indian J Tuberc 64(3):183\u2013188","journal-title":"Indian J Tuberc"},{"key":"1472_CR18","doi-asserted-by":"publisher","first-page":"33452","DOI":"10.1038\/srep33452","volume":"6","author":"J Kawada","year":"2016","unstructured":"Kawada J, Okuno Y, Torii Y, Okada R, Hayano S, Ando S et al (2016) Identification of viruses in cases of pediatric acute encephalitis and encephalopathy using next-generation sequencing. Sci Rep 6:33452","journal-title":"Sci Rep"},{"issue":"3","key":"1472_CR19","first-page":"144","volume":"9","author":"VM Kozko","year":"2017","unstructured":"Kozko VM, Bondarenko AV, Gavrylov AV, Shevchenko OS, Gargin VV (2017) Pathomorphological peculiarities of tuberculous meningoencephalitis associated with HIV infection. Interv Med Appl Sci 9(3):144\u2013149","journal-title":"Interv Med Appl Sci"},{"key":"1472_CR20","doi-asserted-by":"crossref","unstructured":"Leonard JM (2017) Central nervous system tuberculosis. Microbiol Spectr 5(2)","DOI":"10.1128\/microbiolspec.TNMI7-0044-2017"},{"issue":"6","key":"1472_CR21","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1080\/14787210.2017.1309974","volume":"15","author":"K Li","year":"2017","unstructured":"Li K, Tang H, Yang Y, Li Q, Zhou Y, Ren M, Long X, Shen W, Hu R, Wang X, Zeng K (2017a) Clinical features, long-term clinical outcomes, and prognostic factors of tuberculous meningitis in West China: a multivariate analysis of 154 adults. Expert Rev Anti-Infect Ther 15(6):629\u2013635","journal-title":"Expert Rev Anti-Infect Ther"},{"issue":"9","key":"1472_CR22","first-page":"681","volume":"30","author":"XL Li","year":"2017","unstructured":"Li XL, Xie N, Wang SW, Wu QH, Ma Y, Shu W, Chen HM, Zhang LQ, Wu XG, Ma LP, Che NY, Gao MQ (2017b) Diagnostic value of cerebrospinal fluid T-SPOT.TB for tuberculosis meningitis in China. Biomed Environ Sci 30(9):681\u2013684","journal-title":"Biomed Environ Sci"},{"key":"1472_CR23","first-page":"4417","volume":"9","author":"A Liu","year":"2015","unstructured":"Liu A, Wang C, Liang Z, Zhou ZW, Wang L, Ma Q et al (2015) High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in cerebrospinal fluid samples from patients with purulent meningitis. Drug Des Devel Ther 9:4417\u20134429","journal-title":"Drug Des Devel Ther"},{"issue":"1","key":"1472_CR24","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1055\/s-0034-1372342","volume":"34","author":"AT Makadzange","year":"2014","unstructured":"Makadzange AT, McHugh G (2014) New approaches to the diagnosis and treatment of cryptococcal meningitis. Semin Neurol 34(1):47\u201360","journal-title":"Semin Neurol"},{"issue":"1\u20132","key":"1472_CR25","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1016\/S0378-1119(02)00759-X","volume":"293","author":"CA Malloff","year":"2002","unstructured":"Malloff CA, Fernandez RC, Dullaghan EM, Stokes RW, Lam WL (2002) Two-dimensional display and whole genome comparison of bacterial pathogen genomes of high G+C DNA content. Gene 293(1\u20132):205\u2013211","journal-title":"Gene"},{"issue":"4","key":"1472_CR26","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1016\/j.ijid.2007.09.009","volume":"12","author":"R Manfredi","year":"2008","unstructured":"Manfredi R, Calza L (2008) Severe brain co-infection with Cryptococcus neoformans and Mycobacterium tuberculosis in a young, otherwise healthy student recently immigrated from China. Int J Infect Dis 12(4):438\u2013441","journal-title":"Int J Infect Dis"},{"issue":"11","key":"1472_CR27","doi-asserted-by":"publisher","first-page":"803","DOI":"10.1016\/S1473-3099(10)70138-9","volume":"10","author":"S Marais","year":"2010","unstructured":"Marais S, Thwaites G, Schoeman JF, Torok ME, Misra UK, Prasad K et al (2010) Tuberculous meningitis: a uniform case definition for use in clinical research. Lancet Infect Dis 10(11):803\u2013812","journal-title":"Lancet Infect Dis"},{"issue":"8","key":"1472_CR28","doi-asserted-by":"publisher","first-page":"R73","DOI":"10.1186\/gb-2011-12-8-r73","volume":"12","author":"A Melnikov","year":"2011","unstructured":"Melnikov A, Galinsky K, Rogov P, Fennell T, Van Tyne D, Russ C et al (2011) Hybrid selection for sequencing pathogen genomes from clinical samples. Genome Biol 12(8):R73","journal-title":"Genome Biol"},{"issue":"3","key":"1472_CR29","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1128\/JCM.02507-12","volume":"51","author":"SO Oyola","year":"2013","unstructured":"Oyola SO, Gu Y, Manske M, Otto TD, O'Brien J, Alcock D, Macinnis B, Berriman M, Newbold CI, Kwiatkowski DP, Swerdlow HP, Quail MA (2013) Efficient depletion of host DNA contamination in malaria clinical sequencing. J Clin Microbiol 51(3):745\u2013751","journal-title":"J Clin Microbiol"},{"issue":"3","key":"1472_CR30","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1385\/MB:13:3:191","volume":"13","author":"T Parish","year":"1999","unstructured":"Parish T, Stoker NG (1999) Mycobacteria: bugs and bugbears (two steps forward and one step back). Mol Biotechnol 13(3):191\u2013200","journal-title":"Mol Biotechnol"},{"issue":"7","key":"1472_CR31","first-page":"1122","volume":"66","author":"E Pasquier","year":"2018","unstructured":"Pasquier E, Kunda J, De Beaudrap P, Loyse A, Temfack E, Molloy SF et al (2018) Long-term mortality and disability in Cryptococcal meningitis: a systematic literature review. Clin Infect Dis 66(7):1122\u20131132","journal-title":"Clin Infect Dis"},{"key":"1472_CR32","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1007\/5584_2016_25","volume":"935","author":"K Perlejewski","year":"2016","unstructured":"Perlejewski K, Bukowska-Osko I, Nakamura S, Motooka D, Stokowy T, Ploski R et al (2016) Metagenomic analysis of cerebrospinal fluid from patients with multiple sclerosis. Adv Exp Med Biol 935:89\u201398","journal-title":"Adv Exp Med Biol"},{"issue":"4","key":"1472_CR33","first-page":"349","volume":"77","author":"A Pormohammad","year":"2018","unstructured":"Pormohammad A, Nasiri MJ (2018) Diagnostic test accuracy of adenosine deaminase for tuberculous meningitis: a systematic review and meta-analysis - an update. J Inf Secur 77(4):349\u2013356","journal-title":"J Inf Secur"},{"issue":"1","key":"1472_CR34","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1038\/nmeth.1814","volume":"9","author":"MA Quail","year":"2011","unstructured":"Quail MA, Otto TD, Gu Y, Harris SR, Skelly TF, McQuillan JA et al (2011) Optimal enzymes for amplifying sequencing libraries. Nat Methods 9(1):10\u201311","journal-title":"Nat Methods"},{"issue":"3","key":"1472_CR35","doi-asserted-by":"publisher","first-page":"226","DOI":"10.4103\/0028-3886.35683","volume":"55","author":"P Satishchandra","year":"2007","unstructured":"Satishchandra P, Mathew T, Gadre G, Nagarathna S, Chandramukhi A, Mahadevan A et al (2007) Cryptococcal meningitis: clinical, diagnostic and therapeutic overviews. Neurol India 55(3):226\u2013232","journal-title":"Neurol India"},{"issue":"9","key":"1472_CR36","doi-asserted-by":"publisher","first-page":"542","DOI":"10.1111\/myc.12496","volume":"59","author":"SA Schmalzle","year":"2016","unstructured":"Schmalzle SA, Buchwald UK, Gilliam BL, Riedel DJ (2016) Cryptococcus neoformans infection in malignancy. Mycoses 59(9):542\u2013552","journal-title":"Mycoses"},{"issue":"12","key":"1472_CR37","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.1016\/S1473-3099(17)30639-4","volume":"17","author":"S Singh","year":"2017","unstructured":"Singh S, Sankar MM (2017) Diagnostic algorithm for low-volume CSF samples in tuberculous meningitis. Lancet Infect Dis 17(12):1236\u20131237","journal-title":"Lancet Infect Dis"},{"key":"1472_CR38","doi-asserted-by":"publisher","first-page":"169","DOI":"10.2147\/CLEP.S38850","volume":"6","author":"DJ Sloan","year":"2014","unstructured":"Sloan DJ, Parris V (2014) Cryptococcal meningitis: epidemiology and therapeutic options. Clin Epidemiol 6:169\u2013182","journal-title":"Clin Epidemiol"},{"key":"1472_CR39","doi-asserted-by":"crossref","unstructured":"Smith M, Campino S, Gu Y, Clark TG, Otto TD, Maslen G et al (2012) An in-solution hybridisation method for the isolation of pathogen DNA from human DNA-rich clinical samples for analysis by NGS. Open Genomics J 5","DOI":"10.2174\/1875693X01205010018"},{"issue":"10","key":"1472_CR40","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nrneurol.2017.120","volume":"13","author":"RJ Wilkinson","year":"2017","unstructured":"Wilkinson RJ, Rohlwink U, Misra UK, van Crevel R, Mai NTH, Dooley KE, Caws M, Figaji A, Savic R, Solomons R, Thwaites GE, Tuberculous Meningitis International Research Consortium (2017) Tuberculous meningitis. Nat Rev Neurol 13(10):581\u2013598","journal-title":"Nat Rev Neurol"}],"container-title":["Journal of Molecular Neuroscience"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s12031-019-01472-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s12031-019-01472-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s12031-019-01472-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,1,30]],"date-time":"2021-01-30T00:30:59Z","timestamp":1611966659000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s12031-019-01472-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,1,31]]},"references-count":40,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2020,5]]}},"alternative-id":["1472"],"URL":"https:\/\/doi.org\/10.1007\/s12031-019-01472-z","relation":{},"ISSN":["0895-8696","1559-1166"],"issn-type":[{"value":"0895-8696","type":"print"},{"value":"1559-1166","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,1,31]]},"assertion":[{"value":"21 May 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 December 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 January 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Compliance with Ethical Standards"}},{"value":"The authors declare that they have no conflict of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of Interest"}}]}}