2023
Persistence 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
Impact of Temporary Storage Conditions on the Viability of Streptococcus pneumoniae in Saliva
Allicock O, York A, Waghela P, Yolda-Carr D, Weinberger D, Wyllie A. Impact of Temporary Storage Conditions on the Viability of Streptococcus pneumoniae in Saliva. MSphere 2022, 7: e00331-22. PMID: 36409104, PMCID: PMC9769876, DOI: 10.1128/msphere.00331-22.Peer-Reviewed Original ResearchAssociation of Upper Respiratory Streptococcus pneumoniae Colonization With Severe Acute Respiratory Syndrome Coronavirus 2 Infection Among Adults
Parker A, Jackson N, Awasthi S, Kim H, Alwan T, Wyllie A, Baldwin A, Brennick N, Moehle E, Giannikopoulos P, Kogut K, Holland N, Mora-Wyrobek A, Eskenazi B, Riley L, Lewnard J. Association of Upper Respiratory Streptococcus pneumoniae Colonization With Severe Acute Respiratory Syndrome Coronavirus 2 Infection Among Adults. Clinical Infectious Diseases 2022, 76: 1209-1217. PMID: 36401872, DOI: 10.1093/cid/ciac907.Peer-Reviewed Original ResearchMeSH KeywordsAdultCOVID-19HumansNasopharynxPneumococcal InfectionsSARS-CoV-2Streptococcus pneumoniaeConceptsSARS-CoV-2 infectionSARS-CoV-2Upper airwayAcute respiratory syndrome coronavirus 2 infectionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectionSevere acute respiratory syndrome coronavirus 2Syndrome coronavirus 2 infectionAcute respiratory syndrome coronavirus 2Respiratory syndrome coronavirus 2SARS-CoV-2 molecular testingCoronavirus 2 infectionStreptococcus pneumoniae colonizationViral respiratory pathogensSyndrome coronavirus 2Conditional logistic regressionWorking-age adultsQuantitative polymerase chain reactionPneumococcal carriersPneumococcal carriagePneumoniae colonizationOutpatient clinicCoronavirus 2Polymerase chain reactionRespiratory pathogensSaliva specimensPneumococcal genetic variability in age-dependent bacterial carriage
Kremer P, Ferwerda B, Bootsma HJ, Rots NY, Wijmenga-Monsuur AJ, Sanders E, Trzciński K, Wyllie AL, Turner P, van der Ende A, Brouwer MC, Bentley SD, van de Beek D, Lees JA. Pneumococcal genetic variability in age-dependent bacterial carriage. ELife 2022, 11: e69244. PMID: 35881438, PMCID: PMC9395192, DOI: 10.7554/elife.69244.Peer-Reviewed Original ResearchConceptsSecond cohortImproved vaccine formulationsFirst cohortFuture vaccination strategiesSingle nucleotide polymorphismsHost immune factorsAge-specific differencesPneumococcal carriageImmune factorsVaccination strategiesBacterial carriageCarriage studiesVaccine formulationsCohortGenetic factorsAdult hostsSerotypesHost ageAdultsCarriageChildrenGenetic backgroundWeak evidenceInfantsPopulationSaliva as a sample type for SARS-CoV-2 detection: implementation successes and opportunities around the globe
Tobik ER, Kitfield-Vernon LB, Thomas RJ, Steel SA, Tan SH, Allicock OM, Choate BL, Akbarzada S, Wyllie AL. Saliva as a sample type for SARS-CoV-2 detection: implementation successes and opportunities around the globe. Expert Review Of Molecular Diagnostics 2022, 22: 519-535. PMID: 35763281, DOI: 10.1080/14737159.2022.2094250.Peer-Reviewed Original Research
2021
Saliva for Detection of SARS-CoV-2. Reply.
Wyllie AL, Vogels CBF, Grubaugh ND. Saliva for Detection of SARS-CoV-2. Reply. New England Journal Of Medicine 2021, 384: e31. PMID: 33534974, DOI: 10.1056/nejmc2032165.Peer-Reviewed Original Research
2020
Detection of SARS-CoV-2 RNA by multiplex RT-qPCR
Kudo E, Israelow B, Vogels CBF, Lu P, Wyllie AL, Tokuyama M, Venkataraman A, Brackney DE, Ott IM, Petrone ME, Earnest R, Lapidus S, Muenker MC, Moore AJ, Casanovas-Massana A, Team Y, Omer SB, Dela Cruz CS, Farhadian SF, Ko AI, Grubaugh ND, Iwasaki A. Detection of SARS-CoV-2 RNA by multiplex RT-qPCR. PLOS Biology 2020, 18: e3000867. PMID: 33027248, PMCID: PMC7571696, DOI: 10.1371/journal.pbio.3000867.Peer-Reviewed Original ResearchMeSH KeywordsBetacoronavirusCase-Control StudiesClinical Laboratory TechniquesCoronavirus InfectionsCOVID-19COVID-19 TestingDNA PrimersHEK293 CellsHumansLimit of DetectionMultiplex Polymerase Chain ReactionNasopharynxPandemicsPneumonia, ViralReagent Kits, DiagnosticReverse Transcriptase Polymerase Chain ReactionRNA, ViralSARS-CoV-2United StatesConceptsSARS-CoV-2 RNAMultiplex RT-qPCRRT-qPCRSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testingSARS-CoV-2Quantitative reverse transcription PCRCycle threshold valuesReverse transcription-PCRRT-qPCR assaysDisease controlMultiplex RT-qPCR assayTranscription-PCRAssaysSingle assayLow copy numberSaliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2
Wyllie AL, Fournier J, Casanovas-Massana A, Campbell M, Tokuyama M, Vijayakumar P, Warren JL, Geng B, Muenker MC, Moore AJ, Vogels CBF, Petrone ME, Ott IM, Lu P, Venkataraman A, Lu-Culligan A, Klein J, Earnest R, Simonov M, Datta R, Handoko R, Naushad N, Sewanan LR, Valdez J, White EB, Lapidus S, Kalinich CC, Jiang X, Kim DJ, Kudo E, Linehan M, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takahashi T, Taura M, Weizman OE, Wong P, Yang Y, Bermejo S, Odio CD, Omer SB, Dela Cruz CS, Farhadian S, Martinello RA, Iwasaki A, Grubaugh ND, Ko AI. Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2. New England Journal Of Medicine 2020, 383: 1283-1286. PMID: 32857487, PMCID: PMC7484747, DOI: 10.1056/nejmc2016359.Peer-Reviewed Original ResearchUpper respiratory tract colonization with Streptococcus pneumoniae in adults
Arguedas A, Trzciński K, O’Brien K, Ferreira DM, Wyllie AL, Weinberger D, Danon L, Pelton SI, Azzari C, Hammitt LL, Sá-Leão R, Brandileone MC, Saha S, Suaya J, Isturiz R, Jodar L, Gessner BD. Upper respiratory tract colonization with Streptococcus pneumoniae in adults. Expert Review Of Vaccines 2020, 19: 353-366. PMID: 32237926, DOI: 10.1080/14760584.2020.1750378.Peer-Reviewed Original ResearchConceptsPediatric approachPneumococcal colonizationPneumococcal detectionRespiratory sitesUpper respiratory tract colonizationAdult respiratory tractRespiratory tract colonizationHigh disease burdenPneumococcal carriage studiesRespiratory carriageNasal washesPeer-reviewed journalsRespiratory colonizationCarriage prevalencePneumococcal transmissionTract colonizationDisease burdenRespiratory tractCarriage studiesCurrent evidenceStreptococcus pneumoniaeMolecular diagnostic methodsRoutine cultureAdultsRecent evidence
2016
Molecular surveillance of nasopharyngeal carriage of Streptococcus pneumoniae in children vaccinated with conjugated polysaccharide pneumococcal vaccines
Wyllie AL, Wijmenga-Monsuur AJ, van Houten MA, Bosch AATM, Groot JA, van Engelsdorp Gastelaars J, Bruin JP, Bogaert D, Rots NY, Sanders EAM, Trzciński K. Molecular surveillance of nasopharyngeal carriage of Streptococcus pneumoniae in children vaccinated with conjugated polysaccharide pneumococcal vaccines. Scientific Reports 2016, 6: 23809. PMID: 27046258, PMCID: PMC4820691, DOI: 10.1038/srep23809.Peer-Reviewed Original ResearchConceptsPneumococcal conjugate vaccinePolysaccharide pneumococcal vaccineVaccine-targeted serotypesStreptococcus pneumoniae carriageCross-sectional surveillanceVaccine serotypes 4Number of serotypesPneumococcal surveillancePneumococcal vaccinePneumoniae carriageUnvaccinated individualsConjugate vaccineNasopharyngeal carriagePneumococcal diseaseVaccine effectsNasopharyngeal samplesConventional diagnostic methodsSurveillance studyS. pneumoniaeStreptococcus pneumoniaeSerotype detectionMolecular surveillanceHidden circulationSerotypesDiagnostic methodsDevelopment of the Nasopharyngeal Microbiota in Infants with Cystic Fibrosis
Prevaes SM, de Winter-de Groot KM, Janssens HM, de Steenhuijsen Piters WA, Tramper-Stranders GA, Wyllie AL, Hasrat R, Tiddens HA, van Westreenen M, van der Ent CK, Sanders EA, Bogaert D. Development of the Nasopharyngeal Microbiota in Infants with Cystic Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2016, 193: 504-515. PMID: 26492486, DOI: 10.1164/rccm.201509-1759oc.Peer-Reviewed Original ResearchMeSH KeywordsAnti-Bacterial AgentsBurkholderiaBurkholderia InfectionsCarrier StateCase-Control StudiesCohort StudiesCorynebacteriumCorynebacterium InfectionsCystic FibrosisDNA, BacterialEnterobacteriaceaeEnterobacteriaceae InfectionsFemaleHaemophilus InfectionsHaemophilus influenzaeHumansInfantInfant, NewbornMaleMicrobiotaMoraxellaMoraxellaceae InfectionsNasopharynxProspective StudiesReal-Time Polymerase Chain ReactionRNA, Ribosomal, 16SStaphylococcal InfectionsStaphylococcus aureusStreptococcal InfectionsStreptococcus mitisConceptsHealthy control subjectsControl subjectsMonths of lifeMonths of ageCystic fibrosisAntibiotic useMicrobiota profilesAge-matched healthy control subjectsEarly structural lung diseaseNasopharyngeal microbiota profilesNasopharynx of infantsProspective cohort studyStructural lung diseaseTime of diagnosisMoraxella sppPotential respiratory pathogensRespiratory symptomsAntibiotic therapyCohort studyPulmonary infectionLung diseaseNasopharyngeal microbiotaRespiratory pathogensHaemophilus influenzaeNasopharynx samples
2013
Superiority of Trans-Oral over Trans-Nasal Sampling in Detecting Streptococcus pneumoniae Colonization in Adults
Trzciński K, Bogaert D, Wyllie A, Chu ML, van der Ende A, Bruin JP, van den Dobbelsteen G, Veenhoven RH, Sanders EA. Superiority of Trans-Oral over Trans-Nasal Sampling in Detecting Streptococcus pneumoniae Colonization in Adults. PLOS ONE 2013, 8: e60520. PMID: 23555985, PMCID: PMC3610877, DOI: 10.1371/journal.pone.0060520.Peer-Reviewed Original ResearchConceptsS. pneumoniaeLive pneumococciDiagnostic stepsTrans-nasal approachStreptococcus pneumoniae colonizationInitial diagnostic stepPneumoniae colonizationNasopharyngeal samplesPneumococcal colonizationNasopharyngeal colonizationStreptococcus pneumoniaeHuman nasopharynxPneumococciPneumoniaeCell harvestAdultsQPCRQPCR resultsMain reservoirMolecular methods