1 / 18
文档名称:

Extensive microbiological respiratory tract specimen characterization in critically ill COVID‐19 patients 2021 Kim Thomsen.pdf

格式:pdf   大小:7,602KB   页数:18页
下载后只包含 1 个 PDF 格式的文档,没有任何的图纸或源代码,查看文件列表

如果您已付费下载过本站文档,您可以点这里二次下载

Extensive microbiological respiratory tract specimen characterization in critically ill COVID‐19 patients 2021 Kim Thomsen.pdf

上传人:tiros009 2023/1/28 文件大小:7.42 MB

下载得到文件列表

Extensive microbiological respiratory tract specimen characterization in critically ill COVID‐19 patients 2021 Kim Thomsen.pdf

相关文档

文档介绍

文档介绍:该【Extensive microbiological respiratory tract specimen characterization in critically ill COVID‐19 patients 2021 Kim Thomsen 】是由【tiros009】上传分享,文档一共【18】页,该文档可以免费在线阅读,需要了解更多关于【Extensive microbiological respiratory tract specimen characterization in critically ill COVID‐19 patients 2021 Kim Thomsen 】的内容,可以使用淘豆网的站内搜索功能,选择自己适合的文档,以下文字是截取该文章内的部分文字,如需要获得完整电子版,请下载此文档到您的设备,方便您编辑和打印。:.
Title:Extensivemicrobiologicalrespiratorytractspecimencharacterizationincriticallyill
COVID-19patients
Authors:KimThomsen1,HenrikPlanckPedersen2,SusanneIversen3,LotharWiese4,Kurt
Fuursted5,HenrikVedelNielsen5,JensJørgenElmerChristensen1,6,XiaohuiChenNielsen1
Affiliations:
,ZealandUniversityHospital,
Denmark
,ZealandUniversityHospitalRoskilde,Denmark
,Slagelsehospital,Denmark
,ZealandUniversityHospitalRoskilde,Denmark
,ParasitesandFungi,StatensSerumInstitut,Copenhagen,
Denmark
,UniversityofCopenhagen,Denmark
Runninghead:CharacterizationofCOVID-19co-infections
Correspondingauthor:XiaohuiChenNielsen
Address:TheRegionalDepartmentofClinicalMicrobiology,ZealandUniversityHospital
Ingemannsvej46,4200Slagelse,Denmark
Email:******@
Tel:004558559404
Fax:004558559410
Abstract
Thisarticlehasbeenacceptedforpublicationandundergonefullpeerreviewbuthasnotbeen
AcceptedArticle
throughthecopyediting,typesetting,paginationandproofreadingprocess,whichmayleadto
:

:.
Background:Microbialco-infectionsmaycontributetothepulmonarydeteriorationinCOVID-19
-infectionsin
COVID-19ICUpatients.
Methods:Conventionalculture,moleculardetectionsforatypicalaetiologies,QiaStat-Dx®
respiratorypanelV2detecting21respiratorypathogensandribosomalDNAgenes16S/18S
amplicon-basedmicrobiomeanalyseswereperformedonrespiratorysamplesfrom34COVID-19
patientsadmittedtotheICU.
Results:Potentialpathogensweredetectedinsevenpatients(21%)byculturing,infourpatients
(12%)bymicrobiomeanalysis,andinonepatient(3%)
receivingantibioticspriortoICUadmission,fungi(3Candidaalbicans,,1C.
dubliniensis)wereculturedin5(15%)
antibiotic-naiveatICUadmission,twopatients(6%)hadbacterialrespiratorypathogens
(Staphylococcusaureus,Streptococcuspseudopneumoniae)culturedintheirendotracheal
(3Haemophilus
influenza,1Fusobacteriumnecrophorum)isolatedinsamplesfromfourotherpatients(12%).
QiaStat-Dx®respiratorypanelV2detectedadenovirusinonepatient(3%).
Conclusion:Theprevalenceofpulmonarymicrobialco-infectionsismodestamongCOVID-19

diagnosticsincharacterizationofrespiratoryco-infections.
Keywords
SARS-CoV-2;COVID-19;co-infections;microbiome;microbiologicalcharacterization
Abbreviations
SARS-CoV-2:SevereAcuteRespiratorySyndromeCoronavirus2
COVID-19:CoronavirusDisease2019
AcceptedArticle
:.
ICU:IntensiveCareUnit
LRT:LowerRespiratoryTract
PCR:Polymerase-Chain-Reaction
ARDS:AcuteRespiratoryDistressSyndrome
Introduction
CoronavirusDisease2019(COVID-19),arespiratorytractdiseasewithrelativelyhighcase
fatalityrate,iscausedbyanovelcoronavirus,theSevereAcuteRespiratorySyndrome
Coronavirus2(SARS-CoV-2)(1).SARS-CoV-2canleadtoabroadspectrumofdisease,ranging
fromverymildsymptomsofupperrespiratorytractinfectiontolife-
pneumoniacausedbySARS-CoV-2ischaracterizedbyaresilientinflammatoryresponse
triggeringapotentialdeleteriouspulmonarydisease(2)andthepresenceofrespiratoryco-
,criticalCOVID-19diseaseis
associatedwithhighinflammationmarkerlevelsuponadmission,whichchallengethewarinessof
respiratoryco-infectionasitisdifficulttodistinguishbetweensevereCOVID-19andbacterialor
fungalco-,criticallyillCOVID-19patientsarepronetoreceivebroad
spectrumantibioticsuponhospitalization(3).AsCOVID-19patientsoftenneedprolonged
hospitalizationandintensivecare,redundantantibioticsuponhospitalizationmayincreasetherisk
ofsubsequenthospital-acquiredinfectionsandotheradverseevents(4,5).Thuspromptsampling
ofrespiratorysecretionsandsubsequentmicrobialdiagnosticsaredemandedinordertovalidate
thelikelihoodofbacterialco-infectionsandtheconsequentrequirementforantibiotictreatment.
Identificationofrespiratorypathogensbyconventionalcultureischallengedbythecomprehensive
useofantimicrobialtherapypriortoICUadmissionandthefastidiousnatureofsomerespiratory

anduncultivablerespiratorypathogens(6)asamplificationandsubsequentsequencingofthe
highlyconserved16SrRNAgeneinbacteriaandtheeukaryoticcytosolichomologue18Sinfungi

weperformedacomprehensivemicrobiologicalcharacterizationofrespiratorysamplesfrom
criticallyillCOVID-19patientsinordertoexaminethecontributionofamplicon-based
microbiomeanalysisonthediagnosisofrespiratoryco-infections.
AcceptedArticle
:.
Methods
ThisisanobservationalcohortstudyconductedonlaboratoryconfirmedCOVID-19patientswho
wereadmittedtoICUsattwohospitalsinRegionZealandinDenmarkbetweenMarch11thand
April10th,
17municipalities,
periodofMarch11thtoApril10thatotalof826patientshadapositiveSARS-CoV-2PCRtestin
RegionZealandand254COVID-19patientswereadmittedtoahospital(n=6)intheregionof
-
confirmedSARS-CoV-2infection,referredtohospitalsinRegionZealand,andsubsequently
-19wasdefinedasapositiveresult
onreal-timereverse-transcriptase–polymerase-chain-reaction(RT-PCR)assayofnasaland
-confirmedcaseswere
includedinthestudy.
Datacollection
Epidemiological,clinicalandlaboratorydatawereobtainedfrompatientselectronicmedical

demographicdata,medicalhistory,underlyingcomorbidities,laboratoryfindingsandtreatment
measures(.,antiviraltherapy,antibacterialtherapy,respiratorysupport,kidneyreplacement
therapy).ThedurationfromonsetofdiseasetohospitaladmissionandICUadmissionwere
(ARDS)wasdefinedaccordingtotheBerlin
definition.
Microbiologicalmethodsandsampling
Lowerrespiratorytract(LRT)sampleswereroutinelyobtaineduponadmissiontotheICU.
Endotrachealaspiratesweresubjectedtoroutinecultureandantimicrobialsusceptibilitytesting
accordingtoEuropeanCommitteeonAntimicrobialSusceptibilityTesting(EUCAST)
-timePCRbaseddetectionofLegionellapneumophila,Mycoplasma
pneumoniae,ChlamydophilapneumoniaeandChlamydophilapsittaciwasperformedbya
AcceptedArticle
:.
commercialkit,b-CAPassay(Biolegio,Nijmegen,TheNetherlands),accompanyingtheBD
MAXsystemaccordingtothemanufacturer’sprotocol.
Inaddition,QiaStat-Dx®respiratorypanelV2(Qiagen,Hilden,Germany)detecting21
respiratorypathogens(includingsubtypes):InfluenzaA,
InfluenzaAsubtypeH1N1/2009,subtypeH1andH3,InfluenzaB,Coronavirus229E,
CoronavirusHKU1,CoronavirusNL63,CoronavirusOC43,Parainfluenzavirus1,2,3,and4,
RespiratorySyncytialvirusA/B,humanMetapneumovirusA/B,Adenovirus,Bocavirus,
Rhinovirus/Enterovirus,Mycoplasmapneumoniae,LegionellapneumophilaandBordetella
pertussis.
MicrobiomeAnalysis(16S/18SrRNAGeneAmpliconSequencing).
Residualmaterialfromtheendotrachealaspirateswereanalysedusingcombined16S/18SDNA
geneamplicon-basedmicrobiomeanalysistoevaluatethepresenceofspecies-specificsequences
(7).Briefly,DNAwasextractedbyQIAamp®DNAminiKit(Qiagen,Hilden,Germany)
accordingtothemanufacturer`,anegativecontrol

atwo-stepPCRusingamodifiedversionofthepublisheduniversalprokaryoticprimers341F
(ACTCCTAYGGGRBGCASCAG)and806R(ACTCCTAYGGGRBGCASCAG)targetingthe
V3-
sequencer(IlluminaInc.,SanDiego,CA,USA),usingtheV2ReagentKit.
Thesubsequentinter-samplevariablesequencereadoutputcompromisestheuseofastandardized
absolutenumberofsequencestodeterminethedetectionofpotentialclinicalimportantorganisms.
Insteadwerationalizedthatitwouldbevaluabletodefineacut-offthresholdbasedona

insampleswhere>50%ofthetotalsequenceoutputexhibitingnon-vertebrateDNA(host-DNA)
couldbeconsignedtoabacterialorfungalgenus/species,thisgenus/specieswasconsidered

themajorityofthesequencesproducedforanygivensamplecouldbeattributedtoasingle
prevailingmicroorganism,thepossibilityofthisorganismbeinginvolvedinrespiratorytract
infectionmightbeconsideredsignificant.
AcceptedArticle
:.
Results
Table1summarizesthedemographicalandclinicalcharacteristicsofCOVID-19patientsatthe
,4%(n=34)ofallhospitalizedCOVID-
(IQR
59y–74y)and6patients(18%)(27[79%])hadatleast1comorbidity,
however7patients(21%)
III(SAPS3)isanICUscoringsystemandisusedtopredictthemortalityriskforpatients
,themedianSAPSIIIscorewas72(–
)correspondingtoapredictedmortality>40%.Thelaboratorymeasuresdemonstratedan
elevatedC-reactiveprotein(CRP)at145(118–233)mg/L,whereasprocalcitoninwasgenerally
(–)ug/(arterialpartialpressureofoxygen)/FiO2(fractionof
inspiredoxygen)(–)with50%ofthepatientshavingPaO2/FiO2ratio
≤(mean2,7days[0-
16])priortoICUadmissionandstayedameanof15days(range2–49)
ofpatients(20[59%])receivedantimicrobialtherapypriortoICUadmission.
Table2summarizesthemicrobiologicalresultsfromtheanalysesperformedonLRTsamplesand
comparespatientsreceivingantibioticspriortoICUadmissionwithantibiotic-naïvepatients.
Pathogensweredetectedinsevenpatients(21%)
patientsreceivingantibioticspriortoICUadmission,fungi(3Candidaalbicans,,1
)wereculturedin5(15%)endotrachealaspirates;however,bacterialpathogens
-naiveatICU
admission,twopatients(6%)hadbacterialrespiratorypathogens(Staphylococcusaureus,
Streptococcuspseudopneumoniae)culturedintheirendotrachealaspirates.
Co-infectionofviralaetiologywasevaluatedbytheQiaStat-Dx®respiratorypanelV2which
detectedadenovirusinonepatient(3%).ThecommercialPCRtargetingLegionellapneumophila,
Mycoplasmapneumoniae,ChlamydophilapneumoniaeandChlamydophilapsittaciwereunableto
detectanyofthesebacteriaofatypicalaetiologytoLRTinfectionsinthesamples.
AcceptedArticle
:.
Byapplyingthestandardizedthresholdfordetectingpotentialclinicalimportantmi