2023
Saliva as an alternative sample type for detection of pneumococcal carriage in young children
Wyllie A, Rots N, Wijmenga-Monsuur A, van Houten M, Sanders E, Trzciński K. Saliva as an alternative sample type for detection of pneumococcal carriage in young children. Microbiology 2023, 169: 001394. PMID: 37819029, PMCID: PMC10634364, DOI: 10.1099/mic.0.001394.Peer-Reviewed Original ResearchConceptsNasopharyngeal swabsCarriage detectionPneumococcal carriageSaliva samplesSubset of serotypesOlder age groupsConventional cultureAlternative sample typePneumococcal colonizationPneumococcal detectionPolymicrobial growthAge groupsStudy participantsSaliva samplingSwabsDiagnostic culturesGold standardLongitudinal studyYoung childrenSalivaCarriageChildrenInfantsMolecular detection methodsPneumococciPooled RNA-extraction-free testing of saliva for the detection of SARS-CoV-2
Allicock O, Yolda-Carr D, Todd J, Wyllie A. Pooled RNA-extraction-free testing of saliva for the detection of SARS-CoV-2. Scientific Reports 2023, 13: 7426. PMID: 37156888, PMCID: PMC10165292, DOI: 10.1038/s41598-023-34662-2.Peer-Reviewed Original ResearchConceptsSARS-CoV-2RT-qPCR assaysSARS-CoV-2 testingVirus-infected individualsAged care facilitiesSelf-collected salivaSARS-CoV-2 spreadActionable time frameAsymptomatic individualsTest turnaround timeHealthcare workersGeneral populationCare facilitiesTest availabilityWeekly testingFree testingClinical salivaPositive agreementClinical laboratoriesSalivaCT valuesSuch testingTesting workflowIndividual testingTesting protocolHigh Levels of Detection of Nonpneumococcal Species of Streptococcus in Saliva from Adults in the United States
Hislop M, Allicock O, Thammavongsa D, Mbodj S, Nelson A, Shaw A, Weinberger D, Wyllie A. High Levels of Detection of Nonpneumococcal Species of Streptococcus in Saliva from Adults in the United States. Microbiology Spectrum 2023, 11: e05207-22. PMID: 37067447, PMCID: PMC10269540, DOI: 10.1128/spectrum.05207-22.Peer-Reviewed Original ResearchPersistence of Pneumococcal Carriage among Older Adults in the Community despite COVID-19 Mitigation Measures
Wyllie A, Mbodj S, Thammavongsa D, Hislop M, Yolda-Carr D, Waghela P, Nakahata M, Stahlfeld A, Vega N, York A, Allicock O, Wilkins G, Ouyang A, Siqueiros L, Strong Y, Anastasio K, Alexander-Parrish R, Arguedas A, Gessner B, Weinberger D. Persistence of Pneumococcal Carriage among Older Adults in the Community despite COVID-19 Mitigation Measures. Microbiology Spectrum 2023, 11: e04879-22. PMID: 37036377, PMCID: PMC10269788, DOI: 10.1128/spectrum.04879-22.Peer-Reviewed Original ResearchConceptsInvasive pneumococcal diseasePneumococcal diseaseSchool-aged childrenOlder adultsPneumococcal carriageSaliva samplesCOVID-19 pandemicRate of carriageCOVID-19-related disruptionsUpper respiratory tractRegular contactNew Haven areaFirst yearCarriage prevalencePre-pandemic levelsMedical historyRespiratory tractHigh prevalenceStreptococcus pneumoniaeCOVID-19 mitigation measuresStudy participantsPneumococciPrevalenceDiseaseCarriage
2022
Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19
Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C, Deng W, Chen M, Raredon MSB, Hoehn KB, Wang G, Wang Z, DeIuliis G, Ravindra NG, Li N, Castaldi C, Wong P, Fournier J, Bermejo S, Sharma L, Casanovas-Massana A, Vogels CBF, Wyllie AL, Grubaugh ND, Melillo A, Meng H, Stein Y, Minasyan M, Mohanty S, Ruff WE, Cohen I, Raddassi K, Niklason L, Ko A, Montgomery R, Farhadian S, Iwasaki A, Shaw A, van Dijk D, Zhao H, Kleinstein S, Hafler D, Kaminski N, Dela Cruz C. Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19. Nature Communications 2022, 13: 440. PMID: 35064122, PMCID: PMC8782894, DOI: 10.1038/s41467-021-27716-4.Peer-Reviewed Original ResearchMeSH KeywordsAdaptive ImmunityAgedAntibodies, Monoclonal, HumanizedCD4-Positive T-LymphocytesCD8-Positive T-LymphocytesCells, CulturedCOVID-19COVID-19 Drug TreatmentFemaleGene Expression ProfilingGene Expression RegulationHumansImmunity, InnateMaleReceptors, Antigen, B-CellReceptors, Antigen, T-CellRNA-SeqSARS-CoV-2Single-Cell AnalysisConceptsProgressive COVID-19B cell clonesSingle-cell analysisT cellsImmune responseMulti-omics single-cell analysisCOVID-19Cell clonesAdaptive immune interactionsSevere COVID-19Dynamic immune responsesGene expressionSARS-CoV-2 virusAdaptive immune systemSomatic hypermutation frequenciesCellular effectsProtein markersEffector CD8Immune signaturesProgressive diseaseHypermutation frequencyProgressive courseClassical monocytesClonesImmune interactions
2021
Longitudinal Immune Profiling of a Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection in a Solid Organ Transplant Recipient
Klein J, Brito AF, Trubin P, Lu P, Wong P, Alpert T, Peña-Hernández MA, Haynes W, Kamath K, Liu F, Vogels CBF, Fauver JR, Lucas C, Oh J, Mao T, Silva J, Wyllie AL, Muenker MC, Casanovas-Massana A, Moore AJ, Petrone ME, Kalinich CC, Dela Cruz C, Farhadian S, Ring A, Shon J, Ko AI, Grubaugh ND, Israelow B, Iwasaki A, Azar MM, Team F. Longitudinal Immune Profiling of a Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection in a Solid Organ Transplant Recipient. The Journal Of Infectious Diseases 2021, 225: 374-384. PMID: 34718647, PMCID: PMC8807168, DOI: 10.1093/infdis/jiab553.Peer-Reviewed Original ResearchConceptsSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfectionLongitudinal immune profilingTransplant recipientsImmune profilingPrimary SARS-CoV-2 infectionCD4 T cell poolMale renal transplant recipientSolid organ transplant recipientsSARS-CoV-2 reinfectionSARS-CoV-2 antibodiesSARS-CoV-2 infectionWhole viral genome sequencingRenal transplant recipientsImmune escape mutationsOrgan transplant recipientsT cell poolTime of reinfectionCoronavirus disease 2019Lower neutralization titersHumoral memory responsesViral genome sequencingInitial diagnosisImmunologic deficiencyHumoral responseImmunologic investigationsDelayed production of neutralizing antibodies correlates with fatal COVID-19
Lucas C, Klein J, Sundaram ME, Liu F, Wong P, Silva J, Mao T, Oh JE, Mohanty S, Huang J, Tokuyama M, Lu P, Venkataraman A, Park A, Israelow B, Vogels CBF, Muenker MC, Chang CH, Casanovas-Massana A, Moore AJ, Zell J, Fournier JB, Wyllie A, Campbell M, Lee A, Chun H, Grubaugh N, Schulz W, Farhadian S, Dela Cruz C, Ring A, Shaw A, Wisnewski A, Yildirim I, Ko A, Omer S, Iwasaki A. Delayed production of neutralizing antibodies correlates with fatal COVID-19. Nature Medicine 2021, 27: 1178-1186. PMID: 33953384, PMCID: PMC8785364, DOI: 10.1038/s41591-021-01355-0.Peer-Reviewed Original ResearchConceptsDeceased patientsAntibody levelsAntibody responseDisease severityAnti-S IgG levelsCOVID-19 disease outcomesFatal COVID-19Impaired viral controlWorse clinical progressionWorse disease severitySevere COVID-19Length of hospitalizationImmunoglobulin G levelsHumoral immune responseCoronavirus disease 2019COVID-19 mortalityCOVID-19Domain (RBD) IgGSeroconversion kineticsDisease courseIgG levelsClinical parametersClinical progressionHumoral responseDisease onset
2020
Longitudinal analyses reveal immunological misfiring in severe COVID-19
Lucas C, Wong P, Klein J, Castro TBR, Silva J, Sundaram M, Ellingson MK, Mao T, Oh JE, Israelow B, Takahashi T, Tokuyama M, Lu P, Venkataraman A, Park A, Mohanty S, Wang H, Wyllie AL, Vogels CBF, Earnest R, Lapidus S, Ott IM, Moore AJ, Muenker MC, Fournier JB, Campbell M, Odio CD, Casanovas-Massana A, Herbst R, Shaw A, Medzhitov R, Schulz W, Grubaugh N, Dela Cruz C, Farhadian S, Ko A, Omer S, Iwasaki A. Longitudinal analyses reveal immunological misfiring in severe COVID-19. Nature 2020, 584: 463-469. PMID: 32717743, PMCID: PMC7477538, DOI: 10.1038/s41586-020-2588-y.Peer-Reviewed Original ResearchConceptsSevere COVID-19Moderate COVID-19Immune signaturesDisease outcomeCOVID-19Disease trajectoriesInterleukin-5Early immune signaturesInnate cell lineagesType 2 effectorsT cell numbersPoor clinical outcomeWorse disease outcomesImmune response profileCoronavirus disease 2019Distinct disease trajectoriesCytokine levelsImmunological correlatesImmune profileClinical outcomesEarly elevationImmune profilingIL-13Immunoglobulin EDisease 2019Acute 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
Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis
Lees JA, Ferwerda B, Kremer PHC, Wheeler NE, Serón MV, Croucher NJ, Gladstone RA, Bootsma HJ, Rots NY, Wijmega-Monsuur AJ, Sanders EAM, Trzciński K, Wyllie AL, Zwinderman AH, van den Berg LH, van Rheenen W, Veldink JH, Harboe ZB, Lundbo LF, de Groot LCPGM, van Schoor NM, van der Velde N, Ängquist LH, Sørensen TIA, Nohr EA, Mentzer AJ, Mills TC, Knight JC, du Plessis M, Nzenze S, Weiser JN, Parkhill J, Madhi S, Benfield T, von Gottberg A, van der Ende A, Brouwer MC, Barrett JC, Bentley SD, van de Beek D. Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis. Nature Communications 2019, 10: 2176. PMID: 31092817, PMCID: PMC6520353, DOI: 10.1038/s41467-019-09976-3.Peer-Reviewed Original ResearchConceptsGenetic variationGenome-wide association studiesCommon nasopharyngeal colonizerPathogen genomesHalf of variationPneumococcal factorsPneumococcal genesAssociation studiesJoint sequencingHuman variationInvasive potentialLife-threatening invasive diseasesGenesPathogensInteraction analysisInvasivenessGenomeZmpDGeneticsSequencingColonizersHumansVariationHostSusceptibility
2015
Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients
de Steenhuijsen Piters WA, Huijskens EG, Wyllie AL, Biesbroek G, van den Bergh MR, Veenhoven RH, Wang X, Trzciński K, Bonten MJ, Rossen JW, Sanders EA, Bogaert D. Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients. The ISME Journal: Multidisciplinary Journal Of Microbial Ecology 2015, 10: 97-108. PMID: 26151645, PMCID: PMC4681870, DOI: 10.1038/ismej.2015.99.Peer-Reviewed Original ResearchConceptsElderly pneumonia patientsAdult pneumonia patientsPneumonia patientsMicrobiota profilesUpper respiratory tract microbiomeUpper respiratory tract microbiotaRespiratory tract microbiomeDevelopment of pneumoniaRespiratory tract microbiotaYoung healthy adultsURT microbiomeBacterial overgrowthBacterial pneumoniaPathogen overgrowthHealthy controlsOropharyngeal microbiotaHealthy individualsPatientsHealthy adultsPneumoniaDisease statusPrevotella melaninogenicaMicrobiome changesURT microbiotaDysbiosisCarriage of Streptococcus pneumoniae in Aged Adults with Influenza-Like-Illness
Krone CL, Wyllie AL, van Beek J, Rots NY, Oja AE, Chu ML, Bruin JP, Bogaert D, Sanders EA, Trzciński K. Carriage of Streptococcus pneumoniae in Aged Adults with Influenza-Like-Illness. PLOS ONE 2015, 10: e0119875. PMID: 25789854, PMCID: PMC4366201, DOI: 10.1371/journal.pone.0119875.Peer-Reviewed Original ResearchConceptsS. pneumoniaeStreptococcus pneumoniaeCarriage detectionSaliva samplesPneumococcal conjugated vaccineStudy time pointsPCV13 serotypesPneumococcal diseaseCarriage prevalenceNasopharyngeal colonisationNasopharyngeal swabsConjugated vaccineNasopharyngealAged adultsPneumococciTime pointsPneumoniaeCarriageInfantsConventional cultureIllnessSalivaInfluenzaDiseaseSerotypes