2021
A Cluster-based Method to Quantify Individual Heterogeneity in Tuberculosis Transmission
Smith JP, Gandhi NR, Silk BJ, Cohen T, Lopman B, Raz K, Winglee K, Kammerer S, Benkeser D, Kramer MR, Hill AN. A Cluster-based Method to Quantify Individual Heterogeneity in Tuberculosis Transmission. Epidemiology 2021, 33: 217-227. PMID: 34907974, PMCID: PMC8886690, DOI: 10.1097/ede.0000000000001452.Peer-Reviewed Original Research
2019
Cost-Effectiveness of Alternative Uses of Polyvalent Meningococcal Vaccines in Niger: An Agent-Based Transmission Modeling Study
Arifin SMN, Zimmer C, Trotter C, Colombini A, Sidikou F, LaForce FM, Cohen T, Yaesoubi R. Cost-Effectiveness of Alternative Uses of Polyvalent Meningococcal Vaccines in Niger: An Agent-Based Transmission Modeling Study. Medical Decision Making 2019, 39: 553-567. PMID: 31268405, PMCID: PMC6786941, DOI: 10.1177/0272989x19859899.Peer-Reviewed Original ResearchConceptsReactive campaignsSerogroup replacementConjugate vaccineOne-time catchPolyvalent meningococcal vaccineRoutine infant vaccinationMeningococcal conjugate vaccineMeningococcal polysaccharide vaccineRoutine infant immunizationCurrent vaccination practicesImportant health benefitsCost-effectiveness thresholdStandard cost-effectiveness thresholdsAgent-based transmission modelVaccination seriesImmunization seriesInfant vaccinationInfant immunizationPolysaccharide vaccineMeningococcal vaccineVaccination practicesPolyvalent vaccineLaboratory confirmationMenAfriVacSerogroups AEvaluating strategies for control of tuberculosis in prisons and prevention of spillover into communities: An observational and modeling study from Brazil
Mabud TS, de Lourdes Delgado Alves M, Ko AI, Basu S, Walter KS, Cohen T, Mathema B, Colijn C, Lemos E, Croda J, Andrews JR. Evaluating strategies for control of tuberculosis in prisons and prevention of spillover into communities: An observational and modeling study from Brazil. PLOS Medicine 2019, 16: e1002737. PMID: 30677013, PMCID: PMC6345418, DOI: 10.1371/journal.pmed.1002737.Peer-Reviewed Original ResearchConceptsIncidence of TBPrison-based interventionsTB incidenceGeneral populationTB casesCox proportional hazards modelNew TB casesControl of tuberculosisProportional hazards modelPaucity of dataTime of incarcerationTB burdenTB screeningTB riskTB transmissionTB ratesTB epidemicAdministrative databasesCommunity incidenceTuberculosis epidemicHazards modelTB databaseIncidenceEpidemiological contextIntervention
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
A Multistrain Mathematical Model To Investigate the Role of Pyrazinamide in the Emergence of Extensively Drug-Resistant Tuberculosis
Fofana MO, Shrestha S, Knight GM, Cohen T, White RG, Cobelens F, Dowdy DW. A Multistrain Mathematical Model To Investigate the Role of Pyrazinamide in the Emergence of Extensively Drug-Resistant Tuberculosis. Antimicrobial Agents And Chemotherapy 2017, 61: 10.1128/aac.00498-16. PMID: 27956422, PMCID: PMC5328532, DOI: 10.1128/aac.00498-16.Peer-Reviewed Original ResearchMeSH KeywordsAntitubercular AgentsBayes TheoremBiological AvailabilityComputer SimulationDrug Administration ScheduleDrug Resistance, Multiple, BacterialExtensively Drug-Resistant TuberculosisFluoroquinolonesHumansMicrobial Sensitivity TestsModels, StatisticalMycobacterium tuberculosisPyrazinamideRifampinTuberculosis, PulmonaryConceptsCompanion drugsExtensively Drug-Resistant TuberculosisSecond-line treatmentFirst-line treatmentSecond-line regimensDrug-resistant tuberculosisUse of pyrazinamideExtensive drug resistanceDrug resistance dataEmergence of strainsEmergence of mutationsXDR-TBSequential regimensHIV infectionAlternative drugsResistance amplificationPyrazinamide resistanceProlonged treatmentCombination antimicrobialsDrug resistanceInfectious diseasesPrevalenceProportion of simulationsAppropriate useRegimensA Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models
Zimmer C, Yaesoubi R, Cohen T. A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models. PLOS Computational Biology 2017, 13: e1005257. PMID: 28095403, PMCID: PMC5240920, DOI: 10.1371/journal.pcbi.1005257.Peer-Reviewed Original ResearchConceptsParameter estimationStochastic modelLinear noise approximationStochastic transmission-dynamic modelEnsemble Kalman filter methodReal-time parameter estimationKey epidemic parametersParticle filtering methodInfectious individualsStochastic systemsCompartmental epidemic modelLikelihood approximationMultiple shootingNoise approximationBenchmark methodsEpidemic modelPoisson observationsKalman filter methodUnobserved numberAccurate estimatesEpidemic parametersLikelihood approachFiltering methodDynamic modelApproximation
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
Bacillus Calmette-Guérin and Isoniazid Preventive Therapy Protect Contacts of Patients with Tuberculosis
Zelner JL, Murray MB, Becerra MC, Galea J, Lecca L, Calderon R, Yataco R, Contreras C, Zhang Z, Grenfell BT, Cohen T. Bacillus Calmette-Guérin and Isoniazid Preventive Therapy Protect Contacts of Patients with Tuberculosis. American Journal Of Respiratory And Critical Care Medicine 2014, 189: 853-859. PMID: 24592878, PMCID: PMC4225829, DOI: 10.1164/rccm.201310-1896oc.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAge FactorsAgedAged, 80 and overAntitubercular AgentsBCG VaccineChildChild, PreschoolContact TracingFemaleFollow-Up StudiesHumansInfantIsoniazidMaleMiddle AgedModels, StatisticalModels, TheoreticalMultivariate AnalysisOdds RatioPeruProspective StudiesTreatment OutcomeTuberculosis, PulmonaryYoung AdultConceptsIsoniazid preventive therapyAge-specific efficacyLatent TB infectionIncident tuberculosisHousehold contactsTB diseaseTB infectionPulmonary tuberculosisRisk ratioUse of IPTObservational prospective cohort studyBacillus Calmette-Guérin (BCG) vaccinationHigh TB burden settingsAdditional TB casesHIV-positive contactsIncident pulmonary tuberculosisHIV-negative childrenProspective cohort studyPublic Health CenterBacillus Calmette-GuérinYear-long followWorld Health OrganizationCohort studyPreventive therapyTB cases
2011
Test and treat in HIV: success could depend on rapid detection
Cohen T, Corbett EL. Test and treat in HIV: success could depend on rapid detection. The Lancet 2011, 378: 204-206. PMID: 21684592, DOI: 10.1016/s0140-6736(11)60896-9.Peer-Reviewed Original ResearchBayesian methods for fitting mixture models that characterize branching tree processes: An application to development of resistant TB strains
Izu A, Cohen T, Mitnick C, Murray M, De Gruttola V. Bayesian methods for fitting mixture models that characterize branching tree processes: An application to development of resistant TB strains. Statistics In Medicine 2011, 30: 2708-2720. PMID: 21717491, PMCID: PMC3219798, DOI: 10.1002/sim.4287.Peer-Reviewed Original ResearchConceptsCharacterization of uncertaintyBayesian approachBayesian methodsBranching tree modelStatistical methodsMixture modelBranching treeNatural wayPrior informationDrug resistance-conferring mutationsSuch cross-sectional dataDrug-resistant TBResistant TB strainsCombination of antibioticsDrug resistance mutationsMeasurement errorResistance-conferring mutationsTB strainsSingle patientTreatment policyPatientsMultiple drugsDiagnostic specimensCross-sectional dataGenetic mutations
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 Research
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