2025
Rapid Metagenomic Sequencing (RaMSes) of Bronchoalveolar Lavage Fluid for Diagnosis of Infection in Patients with Hematologic Malignancies and Pulmonary Complications
Hensley M, Sayed K, Haidar G, Wang X, Benos P, Ito S, Im A, Geramita E, Shlomchik W, Methé B, Dela Cruz C, Morris A, Kitsios G. Rapid Metagenomic Sequencing (RaMSes) of Bronchoalveolar Lavage Fluid for Diagnosis of Infection in Patients with Hematologic Malignancies and Pulmonary Complications. CHEST Pulmonary 2025, 100173. DOI: 10.1016/j.chpulm.2025.100173.Peer-Reviewed Original ResearchPulmonary complicationsHematologic malignanciesRespiratory pathogensCulture-independent sequencing approachesDetection of fungal pathogensNon-infectious pulmonary complicationsSuspected lower respiratory tract infectionLower respiratory tract infectionsCulture-independent sequencing methodsRespiratory tract infectionsBronchoalveolar lavage fluidDiagnosis of infectionEmpirical antimicrobialsPCR-based testsTract infectionsFungal pathogensMetagenomic sequencingClinical manifestationsSequencing approachLavage fluidMicrobial communitiesCohort studySequencing methodsPatientsComplications
2024
Vaccination Against Influenza and Pneumococcus During Pretravel Health Consultations in the United States: Interventions and Missed Opportunities
Kakoullis L, Rao S, Ryan E, Walker A, Chen L, LaRocque R. Vaccination Against Influenza and Pneumococcus During Pretravel Health Consultations in the United States: Interventions and Missed Opportunities. Open Forum Infectious Diseases 2024, 12: ofae761. PMID: 39817035, PMCID: PMC11733775, DOI: 10.1093/ofid/ofae761.Peer-Reviewed Original ResearchInfluenza vaccinePretravel health consultationPretravel visitGlobal TravEpiNetMultivariate logistic regression modelStreptococcus pneumoniae</i>Influenza virusNonacademic centersLogistic regression modelsPneumococcal vaccineRespiratory pathogensVaccine-preventable diseasesAcademic centersInfluenzaRoutine vaccinationUS healthcare facilitiesVaccineVaccination practicesMissed opportunitiesVisitsRegression modelsHealthcare facilitiesIncreased awarenessInternational travelStructured questionnaireAssessment and mitigation of bias in influenza and COVID-19 vaccine effectiveness analyses — IVY Network, September 1, 2022–March 30, 2023
Lewis N, Harker E, Leis A, Zhu Y, Talbot H, Grijalva C, Halasa N, Chappell J, Johnson C, Rice T, Casey J, Lauring A, Gaglani M, Ghamande S, Columbus C, Steingrub J, Shapiro N, Duggal A, Felzer J, Prekker M, Peltan I, Brown S, Hager D, Gong M, Mohamed A, Exline M, Khan A, Wilson J, Mosier J, Qadir N, Chang S, Ginde A, Mohr N, Mallow C, Harris E, Johnson N, Srinivasan V, Gibbs K, Kwon J, Vaughn I, Ramesh M, Safdar B, DeCuir J, Surie D, Dawood F, Ellington S, Self W, Martin E. Assessment and mitigation of bias in influenza and COVID-19 vaccine effectiveness analyses — IVY Network, September 1, 2022–March 30, 2023. Vaccine 2024, 43: 126492. PMID: 39515195, DOI: 10.1016/j.vaccine.2024.126492.Peer-Reviewed Original ResearchCo-circulating virusesRespiratory syncytial virusCOVID-19-associated hospitalizationVaccine effectivenessControl groupRespiratory pathogensInfluenza-associated hospitalizationsExclusion of patientsStudies of vaccine effectivenessAcute respiratory illnessTest-negative studySentinel Surveillance NetworkEstimates of VEInfluenza VEInfluenza-associatedVE controlsReal-world analysisSyncytial virusVE estimatesOverall VEVE analysisPatientsInfluenzaRespiratory illnessVaccine-preventableRapid Metagenomic Sequencing (RaMSes) for Comprehensive Detection of Respiratory Pathogens in Patients With Hematologic Malignancy
Hensley M, Sayed K, Haidar G, Wang X, Benos P, Ito S, Im A, Geramita E, Dela Cruz C, Morris A, Kitsios G. Rapid Metagenomic Sequencing (RaMSes) for Comprehensive Detection of Respiratory Pathogens in Patients With Hematologic Malignancy. 2024, a2915-a2915. DOI: 10.1164/ajrccm-conference.2024.209.1_meetingabstracts.a2915.Peer-Reviewed Original Research
2023
1387. Vaccination against respiratory pathogens during pretravel consultations at US Global TravEpiNet Sites: interventions and missed opportunities.
Kakoullis L, Rao S, Ryan E, LaRocque R, Chen L. 1387. Vaccination against respiratory pathogens during pretravel consultations at US Global TravEpiNet Sites: interventions and missed opportunities. Open Forum Infectious Diseases 2023, 10: ofad500.1224. PMCID: PMC10676970, DOI: 10.1093/ofid/ofad500.1224.Peer-Reviewed Original ResearchGlobal TravEpiNetGlobal TravEpiNet sitesPneumococcal vaccinePretravel visitInfluenza vaccineGlobal TravEpiNet clinicsTravel-related characteristicsInfluenza transmissionAnalyzed prospectively-collected dataRespiratory pathogensCases of influenzaProspectively-collected dataEligible travelersIssues of insurance coverageYear-round transmissionTravelInfluenza seasonInfluenza exposureExpiration datePretravel consultationInfluenzaRoutine vaccinationCDC recommendationsDestinationNon-administration881. Saliva-Based, Extraction-Free PCR Testing For The Detection Of Key Respiratory Pathogens
Allicock O, Lin T, Fajardo K, Yolda-Carr D, Hislop M, Wang J, Zuniga D, Platt W, Tuohy B, Peno C, Wyllie A. 881. Saliva-Based, Extraction-Free PCR Testing For The Detection Of Key Respiratory Pathogens. Open Forum Infectious Diseases 2023, 10: ofad500.926. PMCID: PMC10677551, DOI: 10.1093/ofid/ofad500.926.Peer-Reviewed Original ResearchSARS-CoV-2Saliva samplesRespiratory virusesRespiratory pathogensSARS-CoV-2 PCR testInfluenza A/BSARS-CoV-2 testingUpper respiratory tract pathogensAdditional respiratory virusesDetection of hMPVMass testing strategyPCR testCommon respiratory virusesCommon respiratory pathogensRespiratory tract pathogensKey respiratory pathogensYears of ageSARS-CoV-2 detectionGrant/research supportTransmissible infectious diseasesUse of salivaYale HealthRespiratory symptomsInfluenza B.Nasopharyngeal swabsThe emergence of influenza B as a major respiratory pathogen in the absence of COVID-19 during the 2021–2022 flu season in China
Chang D, Lin M, Song N, Zhu Z, Gao J, Li S, Liu H, Liu D, Zhang Y, Sun W, Zhou X, Yang B, Li Y, Wang L, Xiao Z, Li K, Xing L, Xie L, Sharma L. The emergence of influenza B as a major respiratory pathogen in the absence of COVID-19 during the 2021–2022 flu season in China. Virology Journal 2023, 20: 189. PMID: 37620959, PMCID: PMC10463403, DOI: 10.1186/s12985-023-02115-x.Peer-Reviewed Original ResearchConceptsInfluenza BAverage ageCOVID-19Influenza-like illnessNumber of patientsMajor respiratory pathogenCOVID-19 testCOVID-19-related restrictionsCell death markersClinical characteristicsFever clinicYounger patientsAppropriate vaccinationPatient characteristicsSubstantial morbidityRespiratory virusesSeasonal virusesLaboratory findingsPositivity rateInfluenza ARespiratory pathogensPreventive strategiesSecondary infectionSevere casesFlu seasonThe potential of saliva as an accessible and sensitive sample type for the detection of respiratory pathogens and host immunity
Laxton C, Peno C, Hahn A, Allicock O, Perniciaro S, Wyllie A. The potential of saliva as an accessible and sensitive sample type for the detection of respiratory pathogens and host immunity. The Lancet Microbe 2023, 4: e837-e850. PMID: 37516121, DOI: 10.1016/s2666-5247(23)00135-0.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsSARS-CoV-2Respiratory pathogensPotential of salivaUsefulness of salivaUse of salivaRespiratory specimenRespiratory secretionsDisease burdenImmunological componentsImmunity surveillanceClinical utilityHost immunityClinical useDiagnostic testsNon-invasive natureSalivaCOVID-19 pandemicSample typesMethodological factorsPathogensImmunitySecretion
2022
Respiratory pandemic preparedness learnings from the June 2020 COVID-19 outbreak at San Quentin California State Prison
Kwan A, Sklar R, Cameron DB, Schell RC, Bertozzi SM, McCoy SI, Williams B, Sears DA. Respiratory pandemic preparedness learnings from the June 2020 COVID-19 outbreak at San Quentin California State Prison. International Journal Of Prison Health 2022, 19: 306-321. PMID: 35678718, PMCID: PMC10231421, DOI: 10.1108/ijph-12-2021-0116.Peer-Reviewed Original ResearchConceptsCalifornia state prisonsGeneral populationCOVID-19 outbreakStates general populationCOVID-19 infection ratesPublic health crisisEffective vaccineRespiratory pathogensRespiratory pandemicInfection rateHealth harmsState prisonsCarceral settingsCOVID-19 pandemicAdministrative dataHealth crisisEpidemic measuresOutbreakUncontrolled transmissionPandemicSettingRisk assessmentUnique challengesVaccineStudy
2021
Palliative Care During a Pandemic
Feder S, Schulman-Green D, Akgün K. Palliative Care During a Pandemic. Respiratory Medicine 2021, 345-372. DOI: 10.1007/978-3-030-81788-6_18.Peer-Reviewed Original ResearchCare deliveryLung diseasePalliative careSevere acute respiratory syndromeChronic lung diseasePalliative care deliveryAcute respiratory syndromeDisease careRespiratory pathogensRespiratory syndromeFamily caregiversHealthcare providersPrevious pandemicsCarePatient autonomyDiseasePalliative communicationVirus pandemicPandemicDeliveryPatientsProvidersSyndromeCaregiversA Prospective Study of the Effects of Sex Hormones on Lung Function and Inflammation in Women with Cystic Fibrosis.
Holtrop M, Heltshe S, Shabanova V, Keller A, Schumacher L, Fernandez L, Jain R. A Prospective Study of the Effects of Sex Hormones on Lung Function and Inflammation in Women with Cystic Fibrosis. Annals Of The American Thoracic Society 2021, 18: 1158-1166. PMID: 33544657, PMCID: PMC12039855, DOI: 10.1513/annalsats.202008-1064oc.Peer-Reviewed Original ResearchConceptsLung functionSex hormonesCystic fibrosisInflammatory markersProinflammatory cytokinesHormone concentrationsEthinyl estradiol/norethindroneRegular menstrual cyclesSubset of subjectsHormone contraceptionPeak estrogenAirway inflammationPulmonary exacerbationsInflammatory biomarkersRespiratory symptomsHormonal contraceptivesHormonal contraceptionProspective studyContraceptive pillsMenstrual cycleSymptom questionnaireWorse outcomesStudy visitRespiratory pathogensClinical impact
2020
Acute encephalopathy with elevated CSF inflammatory markers as the initial presentation of COVID-19
Farhadian S, Glick LR, Vogels CBF, Thomas J, Chiarella J, Casanovas-Massana A, Zhou J, Odio C, Vijayakumar P, Geng B, Fournier J, Bermejo S, Fauver JR, Alpert T, Wyllie AL, Turcotte C, Steinle M, Paczkowski P, Dela Cruz C, Wilen C, Ko AI, MacKay S, Grubaugh ND, Spudich S, Barakat LA. Acute encephalopathy with elevated CSF inflammatory markers as the initial presentation of COVID-19. BMC Neurology 2020, 20: 248. PMID: 32552792, PMCID: PMC7301053, DOI: 10.1186/s12883-020-01812-2.Peer-Reviewed Original ResearchConceptsInitial presentationCentral nervous system inflammationSARS-CoV-2 infectionCSF inflammatory markersNervous system inflammationCerebrospinal fluid (CSF) cytokinesSeizure-like activityCOVID-19 infectionVirus SARS-CoV-2COVID-19SARS-CoV-2BackgroundCOVID-19Inflammatory markersNeurologic complicationsSystem inflammationImmunocompromised womanNeurologic manifestationsNeurologic symptomsViral neuroinvasionCase presentationWeInfected patientsMental statusRespiratory pathogensConclusionOur findingsInflammation
2019
Clinical characteristics and outcomes of patients with Escherichia coli in airway samples
Schneer S, Khoury J, Adir Y, Stein N, Mishan P, Ken‐Dror S, Weber G, Meler R, Khateeb A, Shteinberg M. Clinical characteristics and outcomes of patients with Escherichia coli in airway samples. The Clinical Respiratory Journal 2019, 14: 205-213. PMID: 31799802, DOI: 10.1111/crj.13116.Peer-Reviewed Original ResearchMeSH KeywordsAgedAged, 80 and overAnti-Bacterial AgentsBronchiectasisCase-Control StudiesCommunity-Acquired InfectionsCross InfectionCystic FibrosisDrug Resistance, BacterialEscherichia coliEscherichia coli InfectionsFemaleHospitalizationHumansMaleMicrobial Sensitivity TestsMiddle AgedRespiratory Tract InfectionsSputumConceptsRespiratory secretionsResistant E. coliE. coli positive culturesResistant strainsMore hospitalization daysOutcomes of patientsGroup of patientsCommunity-acquired infectionsClinical characteristicsHospital daysPulmonary infectionHospitalization daysAmbulatory patientsPrevious hospitalizationAirway samplesPrognostic valueRespiratory pathogensCommon pathogensPositive culturesPatientsNosocomial pathogenAntibiotic classesAntimicrobial classesSecretionElevated mortality
2016
Clinical Utility of On-Demand Multiplex Respiratory Pathogen Testing among Adult Outpatients
Green DA, Hitoaliaj L, Kotansky B, Campbell SM, Peaper DR. Clinical Utility of On-Demand Multiplex Respiratory Pathogen Testing among Adult Outpatients. Journal Of Clinical Microbiology 2016, 54: 2950-2955. PMID: 27654334, PMCID: PMC5121384, DOI: 10.1128/jcm.01579-16.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overAmbulatory Care FacilitiesAnti-Bacterial AgentsAsthmaEmergency Service, HospitalFemaleHumansInfluenza, HumanMaleMiddle AgedOrthomyxoviridaeOseltamivirPractice Patterns, Physicians'Pulmonary Disease, Chronic ObstructiveRespiratory Tract InfectionsRetrospective StudiesConceptsNon-influenza virusesRespiratory pathogen testingInfluenza virusAntibiotic prescriptionsPrescription ratesAdult outpatientsLarge Veterans Administration Medical CenterVeterans Administration Medical CenterAntibiotic prescription ratesPathogen testingRespiratory tract infectionsUnnecessary antibiotic useFilmArray Respiratory PanelPatients' medical recordsSpecific therapeutic interventionsTract infectionsRespiratory panelOutpatient centerAntibiotic useAntimicrobial prescriptionsMedical recordsRespiratory pathogensMedical CenterClinical utilityCommon pathogens
2014
An ENU-induced splicing mutation reveals a role for Unc93b1 in early immune cell activation following influenza A H1N1 infection
Lafferty EI, Flaczyk A, Angers I, Homer R, d'Hennezel E, Malo D, Piccirillo CA, Vidal SM, Qureshi ST. An ENU-induced splicing mutation reveals a role for Unc93b1 in early immune cell activation following influenza A H1N1 infection. Genes & Immunity 2014, 15: 320-332. PMID: 24848930, PMCID: PMC4978536, DOI: 10.1038/gene.2014.22.Peer-Reviewed Original ResearchMeSH KeywordsAlternative SplicingAnimalsCD8-Positive T-LymphocytesChemokine CXCL10EndosomesEthylnitrosoureaImmunity, InnateInfluenza A Virus, H1N1 SubtypeInterferon Type IInterferon-gammaL-SelectinLungLymphocyte ActivationMacrophage ActivationMembrane Transport ProteinsMiceMice, Inbred C57BLMutationOrthomyxoviridae InfectionsToll-Like ReceptorsConceptsEndosomal TLRsImmune responseEndosomal Toll-like receptorsInfluenza A/PR/8/34Expression of CXCL10Toll-like receptorsImmune cell activationCD69 activation markerInnate immune responseHuman infectious diseasesViral clearanceActivation markersInfected lungsRespiratory pathogensTLR responsesT cellsLymphoid cellsCell activationTissue pathologyInfectious diseasesMouse strainsInfectionExudate macrophagesReduced expressionUNC93B1
2013
Short Palate, Lung, and Nasal Epithelial Clone–1 Is a Tightly Regulated Airway Sensor in Innate and Adaptive Immunity
Britto CJ, Liu Q, Curran DR, Patham B, Dela Cruz CS, Cohn L. Short Palate, Lung, and Nasal Epithelial Clone–1 Is a Tightly Regulated Airway Sensor in Innate and Adaptive Immunity. American Journal Of Respiratory Cell And Molecular Biology 2013, 48: 717-724. PMID: 23470624, PMCID: PMC3727874, DOI: 10.1165/rcmb.2012-0072oc.Peer-Reviewed Original ResearchMeSH KeywordsAdaptive ImmunityAnimalsCell Line, TumorGene Expression RegulationGlycoproteinsHumansImmunity, InnateImmunohistochemistryInflammationInfluenza A virusInterferon-gammaLipopolysaccharidesLungMiceMice, Inbred C57BLPhosphoproteinsPneumonia, BacterialPseudomonas aeruginosaRespiratory MucosaRespiratory Tract InfectionsStreptococcus pneumoniaeConceptsNasal epithelial clone 1Lower respiratory tractRespiratory tractAirway inflammationShort palateTh2-induced airway inflammationHost defenseAllergic airway inflammationCommon respiratory pathogensAirway epithelial cellsModel of pneumoniaAirway surface liquidPathogen-associated molecular patternsGreatest environmental exposureClone 1Mucociliary clearanceRespiratory pathogensAirway sensorsRespiratory epitheliumAdaptive immunitySPLUNC1IFN-γ actBasal conditionsMRNA expressionMolecular patterns
2012
Baby bottle steam sterilizers disinfect home nebulizers inoculated with bacterial respiratory pathogens
Towle D, Callan DA, Farrel PA, Egan ME, Murray TS. Baby bottle steam sterilizers disinfect home nebulizers inoculated with bacterial respiratory pathogens. Journal Of Cystic Fibrosis 2012, 12: 512-516. PMID: 23267773, DOI: 10.1016/j.jcf.2012.11.013.Peer-Reviewed Original ResearchConceptsHome nebulizersMethicillin-resistant Staphylococcus aureusBacterial respiratory pathogensResistant Staphylococcus aureusNon-mucoid Pseudomonas aeruginosaMucoid Pseudomonas aeruginosaRespiratory pathogensHaemophilus influenzaeBacterial infectionsClinical settingAdditional studiesBacterial growthStaphylococcus aureusStenotrophomonas maltophiliaPseudomonas aeruginosaViable bacteriaTreatmentNebulizerBurkholderia cepaciaInfectionInfluenzae
2011
Are We Ready for Novel Detection Methods to Treat Respiratory Pathogens in Hospital-Acquired Pneumonia?
Endimiani A, Hujer K, Hujer A, Kurz S, Jacobs M, Perlin D, Bonomo R. Are We Ready for Novel Detection Methods to Treat Respiratory Pathogens in Hospital-Acquired Pneumonia? Clinical Infectious Diseases 2011, 52: s373-s383. PMID: 21460299, PMCID: PMC3106236, DOI: 10.1093/cid/cir054.Peer-Reviewed Original ResearchConceptsHospital-acquired pneumoniaGenetic determinants of antimicrobial resistanceDeterminants of antimicrobial resistanceAntimicrobial susceptibility testingAntibiotic-resistant pathogensHospital-acquired bacterial pneumoniaPathogen-directed therapyDifficult treatment challengeCharacterize pathogensResults of cultureSusceptibility testingDiagnosis of pneumoniaEmpirical therapyAntimicrobial resistancePathogensHospital-AcquiredPulmonary microbiomeBacterial pneumoniaMolecular diagnosticsPolymerase chain reactionTreatment challengesMolecular testingRespiratory pathogensPneumoniaChain reaction
2009
Rhinoviruses Are a Major Cause of Wheezing and Hospitalization in Children Less Than 2 Years of Age
Piotrowska Z, Vázquez M, Shapiro ED, Weibel C, Ferguson D, Landry ML, Kahn JS. Rhinoviruses Are a Major Cause of Wheezing and Hospitalization in Children Less Than 2 Years of Age. The Pediatric Infectious Disease Journal 2009, 28: 25-29. PMID: 19057454, PMCID: PMC4639321, DOI: 10.1097/inf.0b013e3181861da0.Peer-Reviewed Original ResearchConceptsRespiratory syncytial virusHRV-positive childrenHuman rhinovirusSyncytial virusAge groupsDiagnostic laboratoriesRespiratory tract diseaseMajor respiratory pathogenRate of infectionYears of ageSimilar age groupAsymptomatic childrenRespiratory specimenAsymptomatic groupRespiratory infectionsHRV infectionHospitalization ratesPolymerase chain reactionTract diseaseRespiratory pathogensHRV isolatesMajor causeStudy periodSymptomsInfection
2004
A 1-Year Experience with Human Metapneumovirus in Children Aged <5 Years
Esper F, Martinello RA, Boucher D, Weibel C, Ferguson D, Landry ML, Kahn JS. A 1-Year Experience with Human Metapneumovirus in Children Aged <5 Years. The Journal Of Infectious Diseases 2004, 189: 1388-1396. PMID: 15073675, PMCID: PMC7109939, DOI: 10.1086/382482.Peer-Reviewed Original ResearchConceptsHuman metapneumovirusPresence of hMPVStudy periodHMPV-positive childrenRespiratory syncytial virusParainfluenza virus 1Respiratory tract diseaseReverse transcription-polymerase chain reactionDirect fluorescent antibody testFluorescent antibody testSyncytial virusRespiratory specimensPolymerase chain reactionChildren AgedCommon findingInfluenza ARespiratory pathogensChest wallAntibody testVirus 1Chain reactionNegative resultsMetapneumovirusSignificant proportionChildren
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