)
23.WilsonMR,SuanD,DugginsA,et?al.Anovelcauseofchronicviralmeningoen-39.AfshinnekooE,MeydanC,ChowdhuryS,et?al.Geospatialresolutionof
cephalitis:CacheValleyvirus.AnnNeurol2017;82:105–14.humanandbacterialdiversitywithcity-scalemetagenomics.CellSyst2015;
24.WylieKM,WeinstockGM,StorchGA.Viromegenomics:atoolfordefiningthe1:97–97.e3.
humanvirome.CurrOpinMicrobiol2013;16:479–84.40.USFoodandDrugAdministration.DatabaseforReferenceGradeMicrobial
25.PendletonKM,Erb-DownwardJR,BaoY,et?al.RapidpathogenidentificationinSequences(FDA-ARGOS).Availableat:https://www.fda.gov/MedicalDevices/
bacterialpneumoniausingreal-timemetagenomics.AmJRespirCritCareMedScienceandResearch/DatabaseforReferenceGradeMicrobialSequences/default.
2017.doi:10.1164/rccm.201703-0537LE.htm.Accessed17July2017.
26.St?mmlerF,Gl?snerJ,HiergeistA,et?al.Adjustingmicrobiomeprofilesfordiffer-41.GreningerAL,NaccacheSN,FedermanS,et?al.Rapidmetagenomicidentification
encesinmicrobialloadbyspike-inbacteria.Microbiome2016;4:28.ofviralpathogensinclinicalsamplesbyreal-timenanoporesequencinganalysis.
27.NaccacheSN,GreningerAL,LeeD,et?al.Theperilsofpathogendiscovery:originGenomeMed2015;7:99.
ofanovelparvovirus-likehybridgenometracedtonucleicacidextractionspin42.KujiraokaM,KurodaM,AsaiK,et?al.Comprehensivediagnosisofbacterial
columns.JVirol2013;87:11966–77.infectionassociatedwithacutecholecystitisusingmetagenomicapproach.Front
28.SalterSJ,CoxMJ,TurekEM,et?al.ReagentandlaboratorycontaminationcanMicrobiol2017;8:685.
criticallyimpactsequence-basedmicrobiomeanalyses.BMCBiol2014;12:87.43.HoffmannB,TappeD,H?perD,et?al.Avariegatedsquirrelbornavirusassociated
29.BreitwieserFP,SalzbergSL.Pavian:interactiveanalysisofmetagenomicsdatawithfatalhumanencephalitis.NEnglJMed2015;373:154–62.
formicrobiomicsandpathogenidentification.bioRxiv2016.doi:https://doi.44.GreningerAL,MessacarK,DunnebackeT,et?al.Clinicalmetagenomiciden-
org/10.1101/084715.tificationofBalamuthiamandrillarisencephalitisandassemblyofthedraft
30.HartML,MeyerA,JohnsonPJ,EricssonAC.ComparativeevaluationofDNAgenome:thecontinuingcaseforreferencegenomesequencing.GenomeMed
extractionmethodsfromfecesofmultiplehostspeciesfordownstreamnext-gen-2015;7:113.
erationsequencing.PLoSOne2015;10:e0143334.45.MurkeyJA,ChewKW,CarlsonM,et?al.HepatitisEvirus-associatedmeningo-
31.LeberAL,EverhartK,Balada-LlasatJM,et?al.MulticenterevaluationofBioFireencephalitisinalungtransplantrecipientdiagnosedbyclinicalmetagenomic
FilmArraymeningitis/encephalitispanelfordetectionofbacteria,viruses,andsequencing.OpenFourmInfectDis2017;4:ofx121.
yeastincerebrospinalfluidspecimens.JClinMicrobiol2016;54:2251–61.46.ChiuCY,CoffeyLL,MurkeyJ,et?al.Diagnosisoffatalhumancaseofmosqui-
32.KandathilAJ,BreitwieserFP,SachithanandhamJ,et?al.Presenceofhumanhepegi-to-borneSt.Louisencephalitisvirusinfectiondiagnosedbymetagenomic
virus-1inacohortofpeoplewhoinjectdrugs.AnnInternMed2017;167:1–7.sequencing,California,2016.EmergInfectDis2017;23:1964–68.
33.ErlichY,NarayananA.Routesforbreachingandprotectinggeneticprivacy.Nat47.DoanT,WilsonMR,CrawfordED,et?al.Illuminatinguveitis:metagenomic
RevGenet2014;15:409–21.deepsequencingidentifiescommonandrarepathogens.GenomeMed2016;
34.CallawayE.Microbiomeprivacyrisk.Nature2015;521:136.8:90.
35.NaccacheSN,PeggsKS,MattesFM,et?al.Diagnosisofneuroinvasiveastrovi-48.SardiSI,SomasekarS,NaccacheSN,et?al.CoinfectionsofZikaandChikungunya
rusinfectioninanimmunocompromisedadultwithencephalitisbyunbiasedvirusesinBahia,Brazil,identifiedbymetagenomicnext-generationsequencing.J
next-generationsequencing.ClinInfectDis2015;60:919–23.ClinMicrobiol2016;54:2348–53.
36.NaccacheSN,FedermanS,VeeraraghavanN,et?al.Acloud-compatiblebio-49.FukuiY,AokiK,OkumaS,SatoT,IshiiY,TatedaK.Metagenomicanalysis
informaticspipelineforultrarapidpathogenidentificationfromnext-generationfordetectingpathogensinculture-negativeinfectiveendocarditis.JInfect
sequencingofclinicalsamples.GenomeRes2014;24:1180–92.Chemother2015;21:882–4.
37.WoodDE,SalzbergSL.Kraken:ultrafastmetagenomicsequenceclassification50.GrardG,FairJN,LeeD,et?al.Anovelrhabdovirusassociatedwithacutehemor-
usingexactalignments.GenomeBiol2014;15:R46.rhagicfeverincentralAfrica.PLoSPathog2012;8:e1002924.
38.WestbladeLF,vanBelkumA,GrundhoffA,et?al.Roleofclinicogenomicsin51.ZhouY,WylieKM,ElFeghalyRE,et?al.Metagenomicapproachforidentification
infectiousdiseasediagnosticsandpublichealthmicrobiology.JClinMicrobiolofthepathogensassociatedwithdiarrheainstoolspecimens.JClinMicrobiol
2016;54:1686–93.2016;54:368–75.
788?CID2018:66(1March?Simneret?al
Downloadedfromhttps://academic.oup.com/cid/article-abstract/66/5/778/4460112
byDTULibrary-TechnicalInformationCenterofDenmarkuser
on02March2018 |
|
