2023
The 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 factorsPathogensImmunitySecretionMethod versatility in RNA extraction-free PCR detection of SARS-CoV-2 in saliva samples
Allicock O, Yolda-Carr D, Earnest R, Breban M, Vega N, Ott I, Kalinich C, Alpert T, Petrone M, Wyllie A. Method versatility in RNA extraction-free PCR detection of SARS-CoV-2 in saliva samples. Progress In Biophysics And Molecular Biology 2023, 182: 103-108. PMID: 37369293, PMCID: PMC10290768, DOI: 10.1016/j.pbiomolbio.2023.06.004.Peer-Reviewed Original ResearchPooled 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 participantsPneumococciPrevalenceDiseaseCarriageDeficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS
Guo C, Che X, Briese T, Ranjan A, Allicock O, Yates R, Cheng A, March D, Hornig M, Komaroff A, Levine S, Bateman L, Vernon S, Klimas N, Montoya J, Peterson D, Lipkin W, Williams B. Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS. Cell Host & Microbe 2023, 31: 288-304.e8. PMID: 36758522, PMCID: PMC10183837, DOI: 10.1016/j.chom.2023.01.004.Peer-Reviewed Original ResearchConceptsME/CFSFaecalibacterium prausnitziiMyalgic encephalomyelitis/chronic fatigue syndromeFecal short-chain fatty acidsChronic fatigue syndromeShort-chain fatty acidsGut microbiome diversityGut dysbiosisGastrointestinal disturbancesTherapeutic trialsFatigue severityFatigue syndromeOrthostatic intoleranceValidation cohortHealthy controlsCognitive dysfunctionFatigue symptomsGut microbiomeDiverse cohortButyrate producersHuman gutPossible targetsEubacterium rectaleCohortMulti-omics analysis
2022
Saliva-based methods for SARS-CoV-2 testing in low- and middle-income countries
Tan S, Allicock O, Katamba A, Carrington C, Wyllie A, Armstrong-Hough M. Saliva-based methods for SARS-CoV-2 testing in low- and middle-income countries. Bulletin Of The World Health Organization 2022, 100: 808-814. PMID: 36466209, PMCID: PMC9706358, DOI: 10.2471/blt.22.288526.Peer-Reviewed Original ResearchImpact 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 ResearchSaliva 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 ResearchEvaluation of saliva self-collection devices for SARS-CoV-2 diagnostics
Allicock OM, Petrone ME, Yolda-Carr D, Breban M, Walsh H, Watkins AE, Rothman JE, Farhadian SF, Grubaugh ND, Wyllie AL. Evaluation of saliva self-collection devices for SARS-CoV-2 diagnostics. BMC Infectious Diseases 2022, 22: 284. PMID: 35337266, PMCID: PMC8953967, DOI: 10.1186/s12879-022-07285-7.Peer-Reviewed Original Research
2021
Saliva as a gold-standard sample for SARS-CoV-2 detection
Tan SH, Allicock O, Armstrong-Hough M, Wyllie AL. Saliva as a gold-standard sample for SARS-CoV-2 detection. The Lancet Respiratory Medicine 2021, 9: 562-564. PMID: 33887248, PMCID: PMC8055204, DOI: 10.1016/s2213-2600(21)00178-8.Peer-Reviewed Original Research
2018
BacCapSeq: a Platform for Diagnosis and Characterization of Bacterial Infections
Allicock O, Guo C, Uhlemann A, Whittier S, Chauhan L, Garcia J, Price A, Morse S, Mishra N, Briese T, Lipkin W. BacCapSeq: a Platform for Diagnosis and Characterization of Bacterial Infections. MBio 2018, 9: 10.1128/mbio.02007-18. PMID: 30352937, PMCID: PMC6199491, DOI: 10.1128/mbio.02007-18.Peer-Reviewed Original ResearchConceptsHigh-throughput sequencingVirulence Factor DatabaseComprehensive Antibiotic Resistance DatabaseBacterial infectionsResistance genesAntimicrobial resistance genesHealth care costsHuman pathogenic speciesUnbiased high-throughput sequencingAntimicrobial sensitivity profileCharacterization of bacteriaDifferential diagnosisReal-time PCRBlood samplesCare costsCenter databaseTotal readsInappropriate useBacterial readsCapture sequencingBacterial speciesAntimicrobial resistanceVirulence determinantsVirulence factorsFactor database
2015
Molecular Characterisation of Chikungunya Virus Infections in Trinidad and Comparison of Clinical and Laboratory Features with Dengue and Other Acute Febrile Cases
Sahadeo N, Mohammed H, Allicock O, Auguste A, Widen S, Badal K, Pulchan K, Foster J, Weaver S, Carrington C. Molecular Characterisation of Chikungunya Virus Infections in Trinidad and Comparison of Clinical and Laboratory Features with Dengue and Other Acute Febrile Cases. PLOS Neglected Tropical Diseases 2015, 9: e0004199. PMID: 26580074, PMCID: PMC4651505, DOI: 10.1371/journal.pntd.0004199.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAgedAged, 80 and overChikungunya FeverChikungunya virusDengueDiagnosis, DifferentialFemaleFever of Unknown OriginGenotypeHumansMaleMiddle AgedMolecular Diagnostic TechniquesMolecular Sequence DataPhylogenyRNA, ViralSequence Analysis, DNASequence HomologyTrinidad and TobagoYoung AdultConceptsAcute undifferentiated febrile illnessChikungunya feverChikungunya virusCHIKV infectionDengue virusDengue feverRT-qPCRExact testLower white blood cell countWhite blood cell countPearson χ2Undifferentiated febrile illnessCharacteristics of patientsChikungunya virus infectionSymptoms of peopleBlood cell countComparison of ClinicalConfidence intervalsFisher's exact testT-testStudent's t-testMann-Whitney UFebrile illnessJoint painLaboratory features
2012
Phylogeography and Population Dynamics of Dengue Viruses in the Americas
Allicock O, Lemey P, Tatem A, Pybus O, Bennett S, Mueller B, Suchard M, Foster J, Rambaut A, Carrington C. Phylogeography and Population Dynamics of Dengue Viruses in the Americas. Molecular Biology And Evolution 2012, 29: 1533-1543. PMID: 22319149, PMCID: PMC3529620, DOI: 10.1093/molbev/msr320.Peer-Reviewed Original Research