2020
Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences
Walter KS, Colijn C, Cohen T, Mathema B, Liu Q, Bowers J, Engelthaler DM, Narechania A, Lemmer D, Croda J, Andrews JR. Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences. Microbial Genomics 2020, 6: mgen000418. PMID: 32735210, PMCID: PMC7641424, DOI: 10.1099/mgen.0.000418.Peer-Reviewed Original Research
2019
Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions
Stimson J, Gardy J, Mathema B, Crudu V, Cohen T, Colijn C. Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions. Molecular Biology And Evolution 2019, 36: 587-603. PMID: 30690464, PMCID: PMC6389316, DOI: 10.1093/molbev/msy242.Peer-Reviewed Original Research
2018
Accurate quantification of uncertainty in epidemic parameter estimates and predictions using stochastic compartmental models
Zimmer C, Leuba SI, Cohen T, Yaesoubi R. Accurate quantification of uncertainty in epidemic parameter estimates and predictions using stochastic compartmental models. Statistical Methods In Medical Research 2018, 28: 3591-3608. PMID: 30428780, PMCID: PMC6517086, DOI: 10.1177/0962280218805780.Peer-Reviewed Original ResearchConceptsFilter degeneracyParameter estimatesPosterior distributionStochastic transmission-dynamic modelParameter posterior distributionsEpidemic compartmental modelKey epidemic parametersStochastic compartmental modelStochastic systemsPrediction intervalsCompartmental modelMultiple shootingArt calibration methodsEpidemic parametersDegeneracyDynamic modelInfluenza modelMSS approachLong-term predictionTransmission dynamic modelSimulation experimentsCalibration methodUncertaintyEstimatesCompetitive performance
2017
Antimicrobial Resistance Risks of Cholera Prophylaxis for United Nations Peacekeepers
Kunkel A, Lewnard JA, Pitzer VE, Cohen T. Antimicrobial Resistance Risks of Cholera Prophylaxis for United Nations Peacekeepers. Antimicrobial Agents And Chemotherapy 2017, 61: 10.1128/aac.00026-17. PMID: 28533237, PMCID: PMC5527623, DOI: 10.1128/aac.00026-17.Peer-Reviewed Original ResearchConceptsDrug-resistant infectionsAntimicrobial chemoprophylaxisDrug-sensitive infectionsDrug resistance generationCholera importationChemoprophylaxisDrug resistanceImportation eventsInfectionAntibiotic resistanceAntimicrobial resistance risksRiskRelative benefitsResistance generationCholeraPotential resistance risksPotential benefitsResistance riskProphylaxisPrevalence
2015
Evaluating the potential impact of enhancing HIV treatment and tuberculosis control programmes on the burden of tuberculosis
Chindelevitch L, Menzies NA, Pretorius C, Stover J, Salomon JA, Cohen T. Evaluating the potential impact of enhancing HIV treatment and tuberculosis control programmes on the burden of tuberculosis. Journal Of The Royal Society Interface 2015, 12: 20150146. PMID: 25878131, PMCID: PMC4424692, DOI: 10.1098/rsif.2015.0146.Peer-Reviewed Original ResearchConceptsAntiretroviral therapyTB incidenceTB burdenBurden of tuberculosisTuberculosis Control ProgrammePotential epidemiological impactART eligibilityMortality benefitTB programsHIV treatmentTB prevalenceTuberculosis incidenceEpidemiological impactART useProgram improvementHIVTreatment effectivenessIncidenceMortalityGreater reductionBurdenTBSaharan AfricaControl programsEligibility
2014
High Rates of Potentially Infectious Tuberculosis and Multidrug-Resistant Tuberculosis (MDR-TB) among Hospital Inpatients in KwaZulu Natal, South Africa Indicate Risk of Nosocomial Transmission
Bantubani N, Kabera G, Connolly C, Rustomjee R, Reddy T, Cohen T, Pym AS. High Rates of Potentially Infectious Tuberculosis and Multidrug-Resistant Tuberculosis (MDR-TB) among Hospital Inpatients in KwaZulu Natal, South Africa Indicate Risk of Nosocomial Transmission. PLOS ONE 2014, 9: e90868. PMID: 24625669, PMCID: PMC3953209, DOI: 10.1371/journal.pone.0090868.Peer-Reviewed Original ResearchConceptsMultidrug-resistant tuberculosisCurrent coughXDR-TBNosocomial transmissionInfectious tuberculosisInfectious TBHospital inpatientsClinical dataAnti-tuberculosis drug susceptibility testingMDR/XDR-TBPrevious TB treatmentDrug susceptibility testingTB treatmentHospital admissionMale sexTB inpatientsScotland hospitalsInpatient settingHigh burdenSputum samplesInfection controlInpatientsKwaZulu-NatalCoughDrug resistance
2012
Identifying multidrug resistant tuberculosis transmission hotspots using routinely collected data
Manjourides J, Lin HH, Shin S, Jeffery C, Contreras C, Santa Cruz J, Jave O, Yagui M, Asencios L, Pagano M, Cohen T. Identifying multidrug resistant tuberculosis transmission hotspots using routinely collected data. Tuberculosis 2012, 92: 273-279. PMID: 22401962, PMCID: PMC3323731, DOI: 10.1016/j.tube.2012.02.003.Peer-Reviewed Original ResearchConceptsDrug sensitivity testTransmission hotspotsRetreatment casesDrug-resistant tuberculosis epidemicRisk of MDRTime of diagnosisDrug-resistant diseaseTB casesResistant diseaseTuberculosis epidemicHigh riskUntreated casesProgrammatic dataMDRTBRiskMDRHigh levelsTargeted investigationGeographic areasCasesDiseaseDiagnosisSensitivity tests
2011
Dynamic Health Policies for Controlling the Spread of Emerging Infections: Influenza as an Example
Yaesoubi R, Cohen T. Dynamic Health Policies for Controlling the Spread of Emerging Infections: Influenza as an Example. PLOS ONE 2011, 6: e24043. PMID: 21915279, PMCID: PMC3167826, DOI: 10.1371/journal.pone.0024043.Peer-Reviewed Original ResearchConceptsHealth policyTransmission-reducing interventionsOverall population healthType of interventionAntiviral drugsNovel infectious pathogensOverall healthEmerging InfectionsInfectious pathogensMask useCurrent interventionsCourse of epidemicsPopulation healthInterventionEpidemicPublic healthVaccineInfluenzaHealthDisease spreadSocial distancingCurrent informationInfection
2009
Use of Cumulative Incidence of Novel Influenza A/H1N1 in Foreign Travelers to Estimate Lower Bounds on Cumulative Incidence in Mexico
Lipsitch M, Lajous M, O'Hagan JJ, Cohen T, Miller JC, Goldstein E, Danon L, Wallinga J, Riley S, Dowell SF, Reed C, McCarron M. Use of Cumulative Incidence of Novel Influenza A/H1N1 in Foreign Travelers to Estimate Lower Bounds on Cumulative Incidence in Mexico. PLOS ONE 2009, 4: e6895. PMID: 19742302, PMCID: PMC2731883, DOI: 10.1371/journal.pone.0006895.Peer-Reviewed Original ResearchConceptsInfluenza A/H1N1Influenza A/Cumulative incidenceNovel influenza A/Severity of illnessSeverity of diseaseSevere diseaseTotal numberSevere symptomsNumber of casesDisease severityCurrent epidemicInfectious diseasesCanadian travellersIncidenceDiseaseAffected individualsSeverityH1N1Mexican residentsObserved groupEpidemicNovel pathogensDisease spreadResidents
2008
Are Survey-Based Estimates of the Burden of Drug Resistant TB Too Low? Insight from a Simulation Study
Cohen T, Colijn C, Finklea B, Wright A, Zignol M, Pym A, Murray M. Are Survey-Based Estimates of the Burden of Drug Resistant TB Too Low? Insight from a Simulation Study. PLOS ONE 2008, 3: e2363. PMID: 18523659, PMCID: PMC2408555, DOI: 10.1371/journal.pone.0002363.Peer-Reviewed Original ResearchMeSH KeywordsData CollectionDisease OutbreaksHumansIncidencePopulation SurveillancePrevalenceTuberculosis, Multidrug-ResistantConceptsResistant tuberculosisIncident casesTotal burdenDrug-resistant TBDrug-resistant tuberculosisSecond-line antibioticsDrug treatment regimensDrug sensitivity testingDrug-resistant strainsBurden of resistanceEmergence of tuberculosisResistant TBTreatment regimensPrevalent casesWorldwide burdenIntroduction of interventionsRoutine surveillanceSurveillance strategiesDrug resistanceTuberculosisLaboratory capacityMycobacterium tuberculosisSensitivity testingTuberculosis modelBurden
2007
Emergent heterogeneity in declining tuberculosis epidemics
Colijn C, Cohen T, Murray M. Emergent heterogeneity in declining tuberculosis epidemics. Journal Of Theoretical Biology 2007, 247: 765-774. PMID: 17540410, PMCID: PMC2652758, DOI: 10.1016/j.jtbi.2007.04.015.Peer-Reviewed Original ResearchAntiviral Resistance and the Control of Pandemic Influenza
Lipsitch M, Cohen T, Murray M, Levin BR. Antiviral Resistance and the Control of Pandemic Influenza. PLOS Medicine 2007, 4: e15. PMID: 17253900, PMCID: PMC1779817, DOI: 10.1371/journal.pmed.0040015.Peer-Reviewed Original ResearchConceptsResistant strainsPandemic influenzaInfluenza pandemicAntiviral resistanceTransmission-reducing measuresNext influenza pandemicAntiviral drug useUse of antiviralsStrains of influenzaSuboptimal vaccinesAntiviral treatmentInfluenza infectionRisk of resistanceDeterministic compartmental modelAntiviral agentsAntiviral drugsPandemic planningDrug useVaccine developmentDrug resistanceControl measuresAntiviralsInfluenzaPandemic spreadPandemic
2006
Exogenous re-infection and the dynamics of tuberculosis epidemics: local effects in a network model of transmission
Cohen T, Colijn C, Finklea B, Murray M. Exogenous re-infection and the dynamics of tuberculosis epidemics: local effects in a network model of transmission. Journal Of The Royal Society Interface 2006, 4: 523-531. PMID: 17251134, PMCID: PMC2373405, DOI: 10.1098/rsif.2006.0193.Peer-Reviewed Original ResearchConceptsTB control strategiesPublic health policy makersType of TBMolecular epidemiologic toolsHealth policy makersTB diseasePrimary diseasePrimary progressionTB incidenceRecent infectionTB transmissionTuberculosis diseaseInfectious disease transmissionTuberculosis epidemicRecent transmissionEpidemiological dataForce of infectionInfectious casesLatent infectionEpidemiologic toolInfectionMycobacterium tuberculosisSpecific populationsDiseaseEpidemic trajectories
2004
Modeling epidemics of multidrug-resistant M. tuberculosis of heterogeneous fitness
Cohen T, Murray M. Modeling epidemics of multidrug-resistant M. tuberculosis of heterogeneous fitness. Nature Medicine 2004, 10: 1117-1121. PMID: 15378056, PMCID: PMC2652755, DOI: 10.1038/nm1110.Peer-Reviewed Original ResearchConceptsDrug-sensitive strainsMDR strainsMultidrug resistanceMultidrug-resistant M. tuberculosisM. tuberculosisMultidrug-resistant tuberculosisTuberculosis control effortsEmergence of resistanceTB controlFuture burdenMDR diseaseMDRTB strainsEpidemiological measuresTuberculosisMDRSmall subpopulationMDRTBControl programsBurdenSingle locus mutationsSequential acquisitionDisease
2003
Transmission Dynamics and Control of Severe Acute Respiratory Syndrome
Lipsitch M, Cohen T, Cooper B, Robins JM, Ma S, James L, Gopalakrishna G, Chew SK, Tan CC, Samore MH, Fisman D, Murray M. Transmission Dynamics and Control of Severe Acute Respiratory Syndrome. Science 2003, 300: 1966-1970. PMID: 12766207, PMCID: PMC2760158, DOI: 10.1126/science.1086616.Peer-Reviewed Original ResearchConceptsSevere acute respiratory syndromeAcute respiratory syndromeRespiratory syndromePublic health effortsDetailed epidemiologic dataSingle infectious caseEpidemiologic dataSecondary casesAbsence of interventionInfectious casesEpidemic curveTransmission dynamicsSyndromeReproductive numberControl measuresIllnessIllnesses of humansMonths