{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,6]],"date-time":"2026-11-06T07:12:03Z","timestamp":1793949123684,"version":"4.8.0"},"reference-count":58,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,12,1]],"date-time":"2015-12-01T00:00:00Z","timestamp":1448928000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2015,12,1]],"date-time":"2015-12-01T00:00:00Z","timestamp":1448928000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000050","name":"National Heart, Lung, and Blood Institute","doi-asserted-by":"publisher","award":["R01-HL105704"],"award-info":[{"award-number":["R01-HL105704"]}],"id":[{"id":"10.13039\/100000050","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","award":["UL1-TR001082"],"award-info":[{"award-number":["UL1-TR001082"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000030","name":"Centers for Disease Control and Prevention","doi-asserted-by":"publisher","award":["U50\/CCU915546-09"],"award-info":[{"award-number":["U50\/CCU915546-09"]}],"id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"publisher"}]},{"name":"University of California Discovery Award"},{"DOI":"10.13039\/100001316","name":"Abbott Laboratories","doi-asserted-by":"publisher","award":["Pathogen Discovery Award"],"award-info":[{"award-number":["Pathogen Discovery Award"]}],"id":[{"id":"10.13039\/100001316","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Genome Med"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/s13073-015-0235-2","type":"journal-article","created":{"date-parts":[[2015,11,3]],"date-time":"2015-11-03T06:26:55Z","timestamp":1446532015000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":117,"title":["Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing"],"prefix":"10.1186","volume":"7","author":[{"given":"Alexander L.","family":"Greninger","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin","family":"Messacar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thelma","family":"Dunnebacke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samia N.","family":"Naccache","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scot","family":"Federman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jerome","family":"Bouquet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Mirsky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yosuke","family":"Nomura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shigeo","family":"Yagi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carol","family":"Glaser","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Vollmer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Craig A.","family":"Press","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bette K.","family":"Kleinschmidt-DeMasters","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel R.","family":"Dominguez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles Y.","family":"Chiu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2015,12,1]]},"reference":[{"key":"235_CR1","first-page":"283","volume":"60","author":"GS Visvesvara","year":"1993","unstructured":"Visvesvara GS. Epidemiology of infections with free-living amebas and laboratory diagnosis of microsporidiosis. Mt Sinai J Med. 1993;60:283\u20138.","journal-title":"Mt Sinai J Med."},{"key":"235_CR2","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1128\/CMR.00056-07","volume":"21","author":"A Matin","year":"2008","unstructured":"Matin A, Siddiqui R, Jayasekera S, Khan NA. Increasing importance of Balamuthia mandrillaris. Clin Microbiol Rev. 2008;21:435\u201348.","journal-title":"Clin Microbiol Rev."},{"key":"235_CR3","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1111\/j.1550-7408.2005.00082.x","volume":"53","author":"FL Schuster","year":"2006","unstructured":"Schuster FL, Guglielmo BJ, Visvesvara GS. In-vitro activity of miltefosine and voriconazole on clinical isolates of free-living amebas: Balamuthia mandrillaris, Acanthamoeba spp., and Naegleria fowleri. J Eukaryot Microbiol. 2006;53:121\u20136.","journal-title":"J Eukaryot Microbiol"},{"key":"235_CR4","doi-asserted-by":"crossref","first-page":"2750","DOI":"10.1128\/JCM.28.12.2750-2756.1990","volume":"28","author":"GS Visvesvara","year":"1990","unstructured":"Visvesvara GS, Martinez AJ, Schuster FL, Leitch GJ, Wallace SV, Sawyer TK, et al. Leptomyxid ameba, a new agent of amebic meningoencephalitis in humans and animals. J Clin Microbiol. 1990;28:2750\u20136.","journal-title":"J Clin Microbiol."},{"key":"235_CR5","doi-asserted-by":"publisher","first-page":"3175","DOI":"10.1128\/JCM.41.7.3175-3180.2003","volume":"41","author":"FL Schuster","year":"2003","unstructured":"Schuster FL, Dunnebacke TH, Booton GC, Yagi S, Kohlmeier CK, Glaser C, et al. Environmental isolation of Balamuthia mandrillaris associated with a case of amebic encephalitis. J Clin Microbiol. 2003;41:3175\u201380.","journal-title":"J Clin Microbiol."},{"key":"235_CR6","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1111\/jeu.12062","volume":"60","author":"AF Ahmad","year":"2013","unstructured":"Ahmad AF, Heaselgrave W, Andrew PW, Kilvington S. The in vitro efficacy of antimicrobial agents against the pathogenic free-living amoeba Balamuthia mandrillaris. J Eukaryot Microbiol. 2013;60:539\u201343.","journal-title":"J Eukaryot Microbiol."},{"key":"235_CR7","doi-asserted-by":"publisher","first-page":"1304","DOI":"10.1086\/379020","volume":"37","author":"TR Deetz","year":"2003","unstructured":"Deetz TR, Sawyer MH, Billman G, Schuster FL, Visvesvara GS. Successful treatment of Balamuthia amoebic encephalitis: presentation of 2 cases. Clin Infect Dis. 2003;37:1304\u201312.","journal-title":"Clin Infect Dis."},{"key":"235_CR8","doi-asserted-by":"publisher","first-page":"1977","DOI":"10.2169\/internalmedicine.52.0299","volume":"52","author":"H Kato","year":"2013","unstructured":"Kato H, Mitake S, Yuasa H, Hayashi S, Hara T, Matsukawa N. Successful treatment of granulomatous amoebic encephalitis with combination antimicrobial therapy. Intern Med. 2013;52:1977\u201381.","journal-title":"Intern Med."},{"key":"235_CR9","doi-asserted-by":"publisher","first-page":"e7","DOI":"10.1086\/653609","volume":"51","author":"DY Martinez","year":"2010","unstructured":"Martinez DY, Seas C, Bravo F, Legua P, Ramos C, Cabello AM, et al. Successful treatment of Balamuthia mandrillaris amoebic infection with extensive neurological and cutaneous involvement. Clin Infect Dis. 2010;51:e7\u2013e11.","journal-title":"Clin Infect Dis."},{"key":"235_CR10","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1128\/JCM.34.2.385-388.1996","volume":"34","author":"FL Schuster","year":"1996","unstructured":"Schuster FL, Visvesvara GS. Axenic growth and drug sensitivity studies of Balamuthia mandrillaris, an agent of amebic meningoencephalitis in humans and other animals. J Clin Microbiol. 1996;34:385\u20138.","journal-title":"J Clin Microbiol."},{"key":"235_CR11","doi-asserted-by":"publisher","first-page":"3589","DOI":"10.1128\/JCM.00875-06","volume":"44","author":"Y Qvarnstrom","year":"2006","unstructured":"Qvarnstrom Y, Visvesvara GS, Sriram R, da Silva AJ. Multiplex real-time PCR assay for simultaneous detection of Acanthamoeba spp., Balamuthia mandrillaris, and Naegleria fowleri. J Clin Microbiol. 2006;44:3589\u201395.","journal-title":"J Clin Microbiol"},{"key":"235_CR12","doi-asserted-by":"publisher","first-page":"3192","DOI":"10.1128\/JCM.43.7.3192-3197.2005","volume":"43","author":"S Yagi","year":"2005","unstructured":"Yagi S, Booton GC, Visvesvara GS, Schuster FL. Detection of Balamuthia mitochondrial 16S rRNA gene DNA in clinical specimens by PCR. J Clin Microbiol. 2005;43:3192\u20137.","journal-title":"J Clin Microbiol."},{"key":"235_CR13","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1016\/j.anndiagpath.2006.04.003","volume":"11","author":"MT Perez","year":"2007","unstructured":"Perez MT, Bush LM. Fatal amebic encephalitis caused by Balamuthia mandrillaris in an immunocompetent host: a clinicopathological review of pathogenic free-living amebae in human hosts. Ann Diagn Pathol. 2007;11:440\u20137.","journal-title":"Ann Diagn Pathol."},{"key":"235_CR14","doi-asserted-by":"publisher","first-page":"1510","DOI":"10.3201\/eid1008.040139","volume":"10","author":"FL Schuster","year":"2004","unstructured":"Schuster FL, Glaser C, Honarmand S, Maguire JH, Visvesvara GS. Balamuthia amebic encephalitis risk, Hispanic Americans. Emerg Infect Dis. 2004;10:1510\u20132.","journal-title":"Emerg Infect Dis."},{"key":"235_CR15","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1093\/cid\/ciu912","volume":"60","author":"SN Naccache","year":"2015","unstructured":"Naccache SN, Peggs KS, Mattes FM, Phadke R, Garson JA, Grant P, et al. Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing. Clin Infect Dis. 2015;60:919\u201323.","journal-title":"Clin Infect Dis."},{"key":"235_CR16","doi-asserted-by":"publisher","first-page":"2408","DOI":"10.1056\/NEJMoa1401268","volume":"370","author":"MR Wilson","year":"2014","unstructured":"Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med. 2014;370:2408\u201317.","journal-title":"N Engl J Med."},{"key":"235_CR17","doi-asserted-by":"publisher","first-page":"1180","DOI":"10.1101\/gr.171934.113","volume":"24","author":"SN Naccache","year":"2014","unstructured":"Naccache SN, Federman S, Veeraraghavan N, Zaharia M, Lee D, Samayoa E, et al. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res. 2014;24:1180\u201392.","journal-title":"Genome Res."},{"key":"235_CR18","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1097\/WCO.0000000000000198","volume":"28","author":"RD Schubert","year":"2015","unstructured":"Schubert RD, Wilson MR. A tale of two approaches: how metagenomics and proteomics are shaping the future of encephalitis diagnostics. Curr Opin Neurol. 2015;28:283\u20137.","journal-title":"Curr Opin Neurol."},{"key":"235_CR19","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1038\/nrg3624","volume":"15","author":"WF Fricke","year":"2014","unstructured":"Fricke WF, Rasko DA. Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions. Nat Rev Genet. 2014;15:49\u201355.","journal-title":"Nat Rev Genet."},{"key":"235_CR20","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1016\/S1473-3099(15)70093-9","volume":"15","author":"AL Greninger","year":"2015","unstructured":"Greninger AL, Naccache SN, Messacar K, Clayton A, Yu G, Somasekar S, et al. A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012\u201314): a retrospective cohort study. Lancet Infect Dis. 2015;15:671\u201382.","journal-title":"Lancet Infect Dis."},{"key":"235_CR21","first-page":"5572","volume":"1111","author":"M Zaharia","year":"2011","unstructured":"Zaharia M, Bolosky W, Curtis K, Fox A, Patterson D, Shenker S, et al. Faster and more accurate sequence alignment with SNAP. arXivorg. 2011;1111:5572.","journal-title":"arXivorg."},{"key":"235_CR22","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1016\/j.diagmicrobio.2015.04.007","volume":"82","author":"LF Lares-Jimenez","year":"2015","unstructured":"Lares-Jimenez LF, Gamez-Gutierrez RA, Lares-Villa F. Novel culture medium for the axenic growth of Balamuthia mandrillaris. Diagn Microbiol Infect Dis. 2015;82:286\u20138.","journal-title":"Diagn Microbiol Infect Dis."},{"key":"235_CR23","doi-asserted-by":"publisher","first-page":"2035","DOI":"10.1093\/bioinformatics\/btv057","volume":"31","author":"J O'Connell","year":"2015","unstructured":"O'Connell J, Schulz-Trieglaff O, Carlson E, Hims MM, Gormley NA, Cox AJ. NxTrim: optimized trimming of Illumina mate pair reads. Bioinformatics. 2015;31:2035\u20137.","journal-title":"Bioinformatics."},{"key":"235_CR24","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","volume":"19","author":"A Bankevich","year":"2012","unstructured":"Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455\u201377.","journal-title":"J Comput Biol."},{"key":"235_CR25","first-page":"3","volume":"3","author":"AL Greninger","year":"2015","unstructured":"Greninger AL, Chorny I, Knowles S, Ng VL, Chaturvedi V. Draft genome sequences of four NDM-1-Producing Klebsiella pneumoniae strains from a health care facility in northern California. Genome Announc. 2015;3:3.","journal-title":"Genome Announc."},{"key":"235_CR26","doi-asserted-by":"publisher","first-page":"3100","DOI":"10.1093\/nar\/gkm160","volume":"35","author":"K Lagesen","year":"2007","unstructured":"Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35:3100\u20138.","journal-title":"Nucleic Acids Res."},{"key":"235_CR27","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1093\/nar\/25.5.0955","volume":"25","author":"TM Lowe","year":"1997","unstructured":"Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955\u201364.","journal-title":"Nucleic Acids Res."},{"key":"235_CR28","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403\u201310.","journal-title":"J Mol Biol."},{"key":"235_CR29","doi-asserted-by":"publisher","first-page":"W244","DOI":"10.1093\/nar\/gki408","volume":"33","author":"J Soding","year":"2005","unstructured":"Soding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005;33:W244\u20138.","journal-title":"Nucleic Acids Res."},{"key":"235_CR30","doi-asserted-by":"publisher","first-page":"1","DOI":"10.14806\/ej.17.1.200","volume":"17","author":"M Martin","year":"2011","unstructured":"Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:1.","journal-title":"EMBnet J."},{"key":"235_CR31","doi-asserted-by":"publisher","first-page":"1384","DOI":"10.1101\/gr.170720.113","volume":"24","author":"R Kajitani","year":"2014","unstructured":"Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, et al. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res. 2014;24:1384\u201395.","journal-title":"Genome Res."},{"key":"235_CR32","doi-asserted-by":"publisher","first-page":"522","DOI":"10.1006\/jmbi.1994.0043","volume":"245","author":"G Burger","year":"1995","unstructured":"Burger G, Plante I, Lonergan KM, Gray MW. The mitochondrial DNA of the amoeboid protozoon, Acanthamoeba castellanii: complete sequence, gene content and genome organization. J Mol Biol. 1995;245:522\u201337.","journal-title":"J Mol Biol."},{"key":"235_CR33","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1111\/jeu.12022","volume":"60","author":"EK Herman","year":"2013","unstructured":"Herman EK, Greninger AL, Visvesvara GS, Marciano-Cabral F, Dacks JB, Chiu CY. The mitochondrial genome and a 60-kb nuclear DNA segment from Naegleria fowleri, the causative agent of primary amoebic meningoencephalitis. J Eukaryot Microbiol. 2013;60:179\u201391.","journal-title":"J Eukaryot Microbiol."},{"key":"235_CR34","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1007\/s00239-006-0279-4","volume":"64","author":"H Fukami","year":"2007","unstructured":"Fukami H, Chen CA, Chiou CY, Knowlton N. Novel group I introns encoding a putative homing endonuclease in the mitochondrial cox1 gene of Scleractinian corals. J Mol Evol. 2007;64:591\u2013600.","journal-title":"J Mol Evol."},{"key":"235_CR35","doi-asserted-by":"publisher","first-page":"371","DOI":"10.1007\/s11274-011-0829-9","volume":"28","author":"Z Zheng","year":"2012","unstructured":"Zheng Z, Jiang K, Huang C, Mei C, Han R. Cordyceps militaris (Hypocreales: Cordycipitaceae): transcriptional analysis and molecular characterization of cox1 and group I intron with putative LAGLIDADG endonuclease. World J Microbiol Biotechnol. 2012;28:371\u201380.","journal-title":"World J Microbiol Biotechnol."},{"key":"235_CR36","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1093\/oxfordjournals.molbev.a026126","volume":"16","author":"J Laroche","year":"1999","unstructured":"Laroche J, Bousquet J. Evolution of the mitochondrial rps3 intron in perennial and annual angiosperms and homology to nad5 intron 1. Mol Biol Evol. 1999;16:441\u201352.","journal-title":"Mol Biol Evol."},{"key":"235_CR37","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1007\/s00239-004-0098-4","volume":"60","author":"TM Regina","year":"2005","unstructured":"Regina TM, Picardi E, Lopez L, Pesole G, Quagliariello C. A novel additional group II intron distinguishes the mitochondrial rps3 gene in gymnosperms. J Mol Evol. 2005;60:196\u2013206.","journal-title":"J Mol Evol."},{"key":"235_CR38","doi-asserted-by":"crossref","first-page":"65","DOI":"10.4269\/ajtmh.2003.68.65","volume":"68","author":"GC Booton","year":"2003","unstructured":"Booton GC, Carmichael JR, Visvesvara GS, Byers TJ, Fuerst PA. Genotyping of Balamuthia mandrillaris based on nuclear 18S and mitochondrial 16S rRNA genes. Am J Trop Med Hyg. 2003;68:65\u20139.","journal-title":"Am J Trop Med Hyg."},{"key":"235_CR39","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1128\/genomeA.01013-15","volume":"3","author":"H Detering","year":"2015","unstructured":"Detering H, Aebischer T, Dabrowski PW, Radonic A, Nitsche A, Renard BY, et al. First draft genome sequence of Balamuthia mandrillaris, the causative agent of amoebic encephalitis. Genome Announc. 2015;3:5.","journal-title":"Genome Announc."},{"key":"235_CR40","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1016\/j.gene.2004.12.017","volume":"347","author":"D Kordis","year":"2005","unstructured":"Kordis D. A genomic perspective on the chromodomain-containing retrotransposons: Chromoviruses. Gene. 2005;347:161\u201373.","journal-title":"Gene."},{"key":"235_CR41","first-page":"666","volume":"62","author":"Centers for Disease C, Prevention","year":"2013","unstructured":"Centers for Disease C, Prevention. Investigational drug available directly from CDC for the treatment of infections with free-living amebae. MMWR Morb Mortal Wkly Rep. 2013;62:666.","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"235_CR42","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1186\/1471-2180-8-210","volume":"8","author":"AF Kiderlen","year":"2008","unstructured":"Kiderlen AF, Radam E, Lewin A. Detection of Balamuthia mandrillaris DNA by real-time PCR targeting the RNase P gene. BMC Microbiol. 2008;8:210.","journal-title":"BMC Microbiol."},{"key":"235_CR43","first-page":"447","volume":"22","author":"A Bakardjiev","year":"2003","unstructured":"Bakardjiev A, Azimi PH, Ashouri N, Ascher DP, Janner D, Schuster FL, et al. Amebic encephalitis caused by Balamuthia mandrillaris: report of four cases. Pediatr Infect Dis J. 2003;22:447\u201353.","journal-title":"Pediatr Infect Dis J."},{"key":"235_CR44","doi-asserted-by":"publisher","first-page":"468","DOI":"10.1016\/j.mib.2013.05.001","volume":"16","author":"CY Chiu","year":"2013","unstructured":"Chiu CY. Viral pathogen discovery. Curr Opin Microbiol. 2013;16:468\u201378.","journal-title":"Curr Opin Microbiol."},{"key":"235_CR45","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","volume":"12","author":"B Buchfink","year":"2015","unstructured":"Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59\u201360.","journal-title":"Nat Methods."},{"key":"235_CR46","doi-asserted-by":"publisher","first-page":"e69","DOI":"10.1093\/nar\/gkv180","volume":"43","author":"TA Freitas","year":"2015","unstructured":"Freitas TA, Li PE, Scholz MB, Chain PS. Accurate read-based metagenome characterization using a hierarchical suite of unique signatures. Nucleic Acids Res. 2015;43:e69.","journal-title":"Nucleic Acids Res."},{"key":"235_CR47","doi-asserted-by":"publisher","first-page":"R46","DOI":"10.1186\/gb-2014-15-3-r46","volume":"15","author":"DE Wood","year":"2014","unstructured":"Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014;15:R46.","journal-title":"Genome Biol."},{"key":"235_CR48","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1186\/s13059-014-0538-4","volume":"15","author":"YH Grad","year":"2014","unstructured":"Grad YH, Lipsitch M. Epidemiologic data and pathogen genome sequences: a powerful synergy for public health. Genome Biol. 2014;15:538.","journal-title":"Genome Biol."},{"key":"235_CR49","doi-asserted-by":"publisher","first-page":"e1000455","DOI":"10.1371\/journal.ppat.1000455","volume":"5","author":"T Briese","year":"2009","unstructured":"Briese T, Paweska JT, McMullan LK, Hutchison SK, Street C, Palacios G, et al. Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa. PLoS Pathog. 2009;5:e1000455.","journal-title":"PLoS Pathog."},{"key":"235_CR50","doi-asserted-by":"publisher","first-page":"11966","DOI":"10.1128\/JVI.02323-13","volume":"87","author":"SN Naccache","year":"2013","unstructured":"Naccache SN, Greninger AL, Lee D, Coffey LL, Phan T, Rein-Weston A, et al. The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns. J Virol. 2013;87:11966\u201377.","journal-title":"J Virol."},{"key":"235_CR51","doi-asserted-by":"publisher","first-page":"e1004437","DOI":"10.1371\/journal.ppat.1004437","volume":"10","author":"MJ Strong","year":"2014","unstructured":"Strong MJ, Xu G, Morici L, Splinter Bon-Durant S, Baddoo M, Lin Z, et al. Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples. PLoS Pathog. 2014;10:e1004437.","journal-title":"PLoS Pathog."},{"key":"235_CR52","doi-asserted-by":"publisher","unstructured":"Wilson MR, Shanbhag NM, Reid MJ, Singhal NS, Gelfand JM, Sample HA, et al. Diagnosing Balamuthia mandrillaris encephalitis with metagenomic deep sequencing. Ann Neurol. 2015. doi: \n                    10.1002\/ana.24499\n                    \n                  . [Epub ahead of print]","DOI":"10.1002\/ana.24499"},{"key":"235_CR53","doi-asserted-by":"publisher","first-page":"1108","DOI":"10.1086\/512818","volume":"44","author":"CA Petti","year":"2007","unstructured":"Petti CA. Detection and identification of microorganisms by gene amplification and sequencing. Clin Infect Dis. 2007;44:1108\u201314.","journal-title":"Clin Infect Dis."},{"key":"235_CR54","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1186\/1471-2164-15-496","volume":"15","author":"DC Zysset-Burri","year":"2014","unstructured":"Zysset-Burri DC, Muller N, Beuret C, Heller M, Schurch N, Gottstein B, et al. Genome-wide identification of pathogenicity factors of the free-living amoeba Naegleria fowleri. BMC Genomics. 2014;15:496.","journal-title":"BMC Genomics."},{"key":"235_CR55","doi-asserted-by":"crossref","unstructured":"Bakardjiev A, Azimi PH, Ashouri N, Ascher DP, Janner D, Schuster FL, et al. Amebic. encephalitis caused by Balamuthia mandrillaris: report of four cases. Pediatr Infect Dis J 2003, 22:447\u2013453.","DOI":"10.1097\/01.inf.0000066540.18671.f8"},{"key":"235_CR56","doi-asserted-by":"crossref","unstructured":"Dunnebacke TH, Schuster FL, Yagi S, Booton GC. Balamuthia mandrillaris from soil samples. Microbiology. 2004, 150:2837\u20132842.","DOI":"10.1099\/mic.0.27218-0"},{"key":"235_CR57","doi-asserted-by":"crossref","unstructured":"Gordon SM, Steinberg JP, DuPuis MH, Kozarsky PE, Nickerson JF, Visvesvara GS et al. Culture isolation of Acanthamoeba species and leptomyxid amebas from patients with amebic meningoencephalitis, including two patients with AIDS. Clin Infect Dis 1992, 15:1024\u20131030.","DOI":"10.1093\/clind\/15.6.1024"},{"key":"235_CR58","first-page":"556","volume":"60","author":"XH Yang","year":"2001","unstructured":"Yang XH, Jones D, Kaeppen A, Qian J: Amebic meningoencephalitis in a 6 year-old girl caused by Balamuthia mandrsillaris. J Neuropathol Exp Neurol 2001, 60:556.","journal-title":"J Neuropathol Exp Neurol"}],"updated-by":[{"DOI":"10.1186\/s13073-015-0257-9","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2016,1,11]],"date-time":"2016-01-11T00:00:00Z","timestamp":1452470400000}}],"container-title":["Genome Medicine"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13073-015-0235-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s13073-015-0235-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13073-015-0235-2","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13073-015-0235-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,15]],"date-time":"2020-05-15T08:42:59Z","timestamp":1589532179000},"score":1,"resource":{"primary":{"URL":"https:\/\/genomemedicine.biomedcentral.com\/articles\/10.1186\/s13073-015-0235-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,12]]},"references-count":58,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["235"],"URL":"https:\/\/doi.org\/10.1186\/s13073-015-0235-2","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/024455","asserted-by":"object"}]},"ISSN":["1756-994X"],"issn-type":[{"value":"1756-994X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,12]]},"assertion":[{"value":"18 August 2015","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 October 2015","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 December 2015","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"113"}}