2024
Phylogeographic Analysis of Mycobacterium kansasii Isolates from Patients with M. kansasii Lung Disease in Industrialized City, Taiwan - Volume 30, Number 8—August 2024 - Emerging Infectious Diseases journal - CDC
Cudahy P, Liu P, Warren J, Sobkowiak B, Yang C, Ioerger T, Wu C, Lu P, Wang J, Chang H, Huang H, Cohen T, Lin H. Phylogeographic Analysis of Mycobacterium kansasii Isolates from Patients with M. kansasii Lung Disease in Industrialized City, Taiwan - Volume 30, Number 8—August 2024 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2024, 30: 1562-1570. PMID: 39043390, PMCID: PMC11286038, DOI: 10.3201/eid3008.240021.Peer-Reviewed Original ResearchConceptsM. kansasii lung diseaseM. kansasii pulmonary diseasePulmonary diseaseM. kansasii isolatesSputum mycobacterial cultureWhole-genome sequencingEvaluate risk factorsPhylogeographic analysisAge of participantsGenetic relatednessEnvironmental acquisitionLung diseaseMycobacterial cultureOdds ratioRisk factorsM. kansasiiPatientsDiseasePlantsEnvironmental transmissionIsolatesPark plantingsCDCRisk
2023
Global burden of disease due to rifampicin-resistant tuberculosis: a mathematical modeling analysis
Menzies N, Allwood B, Dean A, Dodd P, Houben R, James L, Knight G, Meghji J, Nguyen L, Rachow A, Schumacher S, Mirzayev F, Cohen T. Global burden of disease due to rifampicin-resistant tuberculosis: a mathematical modeling analysis. Nature Communications 2023, 14: 6182. PMID: 37794037, PMCID: PMC10550952, DOI: 10.1038/s41467-023-41937-9.Peer-Reviewed Original ResearchConceptsDisability-adjusted life yearsRifampicin-resistant tuberculosisRR-TBGlobal burdenSubstantial short-term morbidityRifampicin-susceptible tuberculosisShort-term morbidityOverall disease burdenLong-term health impactsPost-treatment careTB survivorsDisease burdenTreatment outcomesTuberculosis survivorsCase detectionLife yearsRifampicin resistanceTuberculosisHealth impactsBurdenHealth expenditureDiseaseSurvivorsMathematical modeling analysisFormer Soviet Union countriesChanges in Population Immunity Against Infection and Severe Disease From Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Variants in the United States Between December 2021 and November 2022
Klaassen F, Chitwood M, Cohen T, Pitzer V, Russi M, Swartwood N, Salomon J, Menzies N. Changes in Population Immunity Against Infection and Severe Disease From Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Variants in the United States Between December 2021 and November 2022. Clinical Infectious Diseases 2023, 77: 355-361. PMID: 37074868, PMCID: PMC10425195, DOI: 10.1093/cid/ciad210.Peer-Reviewed Original ResearchConceptsSevere diseasePopulation immunityOmicron infectionOmicron variantUS populationSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2SARS-CoV-2 infectionRespiratory syndrome coronavirus 2SARS-CoV-2 Omicron variantRestoration of immunitySyndrome coronavirus 2Bayesian evidence synthesis modelInfection-acquired immunityEvidence synthesis modelSARS-CoV-2Prior immunological exposureCoronavirus 2Additional infectionsImmunological exposureInfectionDiseaseImmunityVaccinationUnited States
2022
Population Immunity to Pre-Omicron and Omicron Severe Acute Respiratory Syndrome Coronavirus 2 Variants in US States and Counties Through 1 December 2021
Klaassen F, Chitwood MH, Cohen T, Pitzer VE, Russi M, Swartwood NA, Salomon JA, Menzies NA. Population Immunity to Pre-Omicron and Omicron Severe Acute Respiratory Syndrome Coronavirus 2 Variants in US States and Counties Through 1 December 2021. Clinical Infectious Diseases 2022, 76: e350-e359. PMID: 35717642, PMCID: PMC9214178, DOI: 10.1093/cid/ciac438.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionSARS-CoV-2Immunological exposureOmicron variantSevere diseaseAcute respiratory syndrome coronavirus 2 infectionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectionFuture SARS-CoV-2 infectionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variantsUS populationSyndrome coronavirus 2 infectionCoronavirus disease 2019 (COVID-19) vaccinationCoronavirus 2 infectionPopulation-level immunityPrior immunological exposurePopulation immunityImmune escapeVaccination dataInfectionInfection statusVaccinationUS statesEffective protectionDiseaseImmunity
2020
Transmission Modeling with Regression Adjustment for Analyzing Household-based Studies of Infectious Disease: Application to Tuberculosis.
Crawford FW, Marx FM, Zelner J, Cohen T. Transmission Modeling with Regression Adjustment for Analyzing Household-based Studies of Infectious Disease: Application to Tuberculosis. Epidemiology 2020, 31: 238-247. PMID: 31764276, PMCID: PMC7718772, DOI: 10.1097/ede.0000000000001143.Peer-Reviewed Original ResearchConceptsSusceptible household contactsHousehold contactsTB casesBacillus Calmette-Guérin (BCG) vaccinationInfected household contactsIsoniazid preventive therapyActive tuberculosis casesCulture-positive casesRisk of diseaseCohort studyMicrobiological confirmationPreventive therapyTuberculosis casesRisk factorsInfection resultsAdult contactsInfection riskInfectious diseasesLogistic regressionRate of transmissionTransmissible diseasesDiseaseIndividual-level characteristicsHigher hazardDisease susceptibilitySmoking and HIV associated with subclinical tuberculosis: analysis of a population-based prevalence survey
Gunasekera K, Cohen T, Gao W, Ayles H, Godfrey-Faussett P, Claassens M. Smoking and HIV associated with subclinical tuberculosis: analysis of a population-based prevalence survey. The International Journal Of Tuberculosis And Lung Disease 2020, 24: 340-346. PMID: 32228765, DOI: 10.5588/ijtld.19.0387.Peer-Reviewed Original ResearchConceptsActive TBPrevalence surveyPopulation-based prevalence surveyCurrent tobacco smokingTypical symptomsHIV-positive statusTuberculosis prevalence surveyPrevalence survey dataSubclinical tuberculosisPositive TBCrude prevalenceTobacco smokingEpidemiological burdenPrevalent casesReduction TrialSubclinical TBMedical variablesSecondary analysisEstimate associationsSouth African communitySymptomsHIVSmokingTuberculosisDisease
2018
Progression from latent infection to active disease in dynamic tuberculosis transmission models: a systematic review of the validity of modelling assumptions
Menzies NA, Wolf E, Connors D, Bellerose M, Sbarra AN, Cohen T, Hill AN, Yaesoubi R, Galer K, White PJ, Abubakar I, Salomon JA. Progression from latent infection to active disease in dynamic tuberculosis transmission models: a systematic review of the validity of modelling assumptions. The Lancet Infectious Diseases 2018, 18: e228-e238. PMID: 29653698, PMCID: PMC6070419, DOI: 10.1016/s1473-3099(18)30134-8.Peer-Reviewed Original ResearchConceptsTuberculosis transmission modelActive diseaseCumulative incidenceRisk factorsSystematic reviewNatural historyFeatures of epidemiologyDisease natural historyIndividual risk factorsTuberculosis natural historyEarliest available dateWeb of ScienceAnnual incidenceCochrane LibraryTuberculosis incidenceInclusion criteriaFuture tuberculosisLatent infectionInitial infectionIncidenceSubstantial proportionPopulation groupsAvailable dateInfectionDisease
2017
Population implications of the use of bedaquiline in people with extensively drug-resistant tuberculosis: are fears of resistance justified?
Kunkel A, Furin J, Cohen T. Population implications of the use of bedaquiline in people with extensively drug-resistant tuberculosis: are fears of resistance justified? The Lancet Infectious Diseases 2017, 17: e429-e433. PMID: 28533094, DOI: 10.1016/s1473-3099(17)30299-2.Peer-Reviewed Original ResearchConceptsUse of bedaquilineDrug-resistant tuberculosisXDR tuberculosisBedaquiline resistanceCohort study resultsMultidrug-resistant tuberculosisNew combination regimensHigh mortality rateFears of resistanceInfected contactsCombination regimensDrug combinationsPatientsEquivalent outcomesMortality rateAntituberculosis drugsBedaquilineTuberculosisNovel drugsDrug bedaquilineDrugsDiseasePopulation implicationsResistance concernsGreat need
2016
High burden of prevalent tuberculosis among previously treated people in Southern Africa suggests potential for targeted control interventions
Marx FM, Floyd S, Ayles H, Godfrey-Faussett P, Beyers N, Cohen T. High burden of prevalent tuberculosis among previously treated people in Southern Africa suggests potential for targeted control interventions. European Respiratory Journal 2016, 48: 1227-1230. PMID: 27390274, PMCID: PMC5512114, DOI: 10.1183/13993003.00716-2016.Peer-Reviewed Original ResearchConceptsHigh-burden settingsHigh TB prevalenceRecurrent tuberculosisExogenous reinfectionPrevalent tuberculosisTB prevalenceSuccessful treatmentHigh burdenImportant underlying mechanismHigh riskHigh incidenceControl interventionsTargeted interventionsTuberculosisUnderlying mechanismOne-thirdInterventionBurdenCape TownIndividualsReinfectionPrevalenceIncidenceDiseaseSettingAssessing Local Risk of Rifampicin-Resistant Tuberculosis in KwaZulu-Natal, South Africa Using Lot Quality Assurance Sampling
Heidebrecht CL, Podewils LJ, Pym A, Mthiyane T, Cohen T. Assessing Local Risk of Rifampicin-Resistant Tuberculosis in KwaZulu-Natal, South Africa Using Lot Quality Assurance Sampling. PLOS ONE 2016, 11: e0153143. PMID: 27050561, PMCID: PMC4822784, DOI: 10.1371/journal.pone.0153143.Peer-Reviewed Original ResearchConceptsIncident TB casesTB casesResistant TBDrug-resistant TB casesRifampicin-resistant tuberculosisMultidrug-resistant tuberculosisDrug susceptibility testingRIF-resistant TBLot Quality Assurance SamplingQuality assurance samplingResistant diseaseHigh burdenRIF resistanceKwaZulu-NatalSusceptibility testingHigh-risk areasTuberculosisRiskGreater proportionBurdenTBDiseaseGeographic heterogeneityCasesRifampicin
2015
How could preventive therapy affect the prevalence of drug resistance? Causes and consequences
Kunkel A, Colijn C, Lipsitch M, Cohen T. How could preventive therapy affect the prevalence of drug resistance? Causes and consequences. Philosophical Transactions Of The Royal Society B Biological Sciences 2015, 370: 20140306. PMID: 25918446, PMCID: PMC4424438, DOI: 10.1098/rstb.2014.0306.Peer-Reviewed Original ResearchConceptsPreventative therapyDrug resistanceDrug-sensitive pathogensProphylactic antimicrobial therapyLong-term prevalenceSmall pilot studyActive diseaseOverall prevalenceAntimicrobial therapyPrevalencePilot studyTherapyPopulation-level changesPotential population-level effectsDirect effectLevel of coveragePopulation-level effectsHIVTuberculosisMalariaDiseaseCare
2014
Incidence of multidrug-resistant tuberculosis disease in children: systematic review and global estimates
Jenkins HE, Tolman AW, Yuen CM, Parr JB, Keshavjee S, Pérez-Vélez CM, Pagano M, Becerra MC, Cohen T. Incidence of multidrug-resistant tuberculosis disease in children: systematic review and global estimates. The Lancet 2014, 383: 1572-1579. PMID: 24671080, PMCID: PMC4094366, DOI: 10.1016/s0140-6736(14)60195-1.Peer-Reviewed Original ResearchConceptsMultidrug-resistant tuberculosisMultidrug-resistant tuberculosis diseaseTreatment-naive adultsMultidrug-resistant diseaseTuberculosis diseaseTuberculosis incidenceGlobal incidenceSystematic reviewCases of tuberculosisHarvard Medical SchoolGlobal tuberculosis incidenceGlobal annual incidenceTuberculosis riskAnnual incidencePatient groupUS National InstitutesWomen's HospitalInclusion criteriaInternal medicineNew diagnostic instrumentDisease riskTuberculosisIncidenceDiseaseHealth equityStrengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID): an extension of the STROBE statement
Field N, Cohen T, Struelens MJ, Palm D, Cookson B, Glynn JR, Gallo V, Ramsay M, Sonnenberg P, MacCannell D, Charlett A, Egger M, Green J, Vineis P, Abubakar I. Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID): an extension of the STROBE statement. The Lancet Infectious Diseases 2014, 14: 341-352. PMID: 24631223, DOI: 10.1016/s1473-3099(13)70324-4.Peer-Reviewed Original ResearchConceptsEpidemiological studiesInfectious diseasesMolecular epidemiologyControl of infectionMultiple-strain infectionsMolecular epidemiological studiesHealth policy decisionsObservational studySTROBE checklistEpidemiological dataEvidence reviewCommunicable diseasesInfectious disease researchSTROBE statementDiseaseInfectious disease data
2013
Response to Comment on “Community-Wide Isoniazid Preventive Therapy Drives Drug-Resistant Tuberculosis: A Model-Based Analysis”
Mills HL, Cohen T, Colijn C. Response to Comment on “Community-Wide Isoniazid Preventive Therapy Drives Drug-Resistant Tuberculosis: A Model-Based Analysis”. Science Translational Medicine 2013, 5: 204lr4. PMID: 24068734, DOI: 10.1126/scitranslmed.3007442.Peer-Reviewed Original ResearchIsoniazid-resistant Tuberculosis in Children
Yuen CM, Tolman AW, Cohen T, Parr JB, Keshavjee S, Becerra MC. Isoniazid-resistant Tuberculosis in Children. The Pediatric Infectious Disease Journal 2013, 32: e217-e226. PMID: 23348808, PMCID: PMC3709006, DOI: 10.1097/inf.0b013e3182865409.Peer-Reviewed Original ResearchConceptsIsoniazid-resistant tuberculosisLatent tuberculosis infectionTuberculosis diseaseTuberculosis infectionIsoniazid resistancePediatric tuberculosis patientsTreatment of childrenIsoniazid-resistant strainsReports of childrenEffective regimensTuberculosis patientsTuberculosis treatmentAppropriate treatmentInclusion criteriaMedian proportionSystematic reviewRifampin resistanceDiseaseTuberculosisRegimensChildrenTreatmentInfectionIsoniazidHigher proportionDisease Mapping with Spatially Uncertain Data
Manjourides J, Cohen T, Jeffery C, Pagano M. Disease Mapping with Spatially Uncertain Data. Online Journal Of Public Health Informatics 2013, 5 PMCID: PMC3692831, DOI: 10.5210/ojphi.v5i1.4380.Peer-Reviewed Original ResearchNew TB casesDrug sensitivity testingTB casesProgrammatic dataHigh TB burdenDrug-resistant casesTB burdenIncident casesResistant casesUnderlying burdenHigh riskRoutine dataDisease acquisitionInverse probabilityTransmission hotspotsSensitivity testingNon-random sampleRiskLocation of casesReduced testingDiseaseRepresentative sampleUnadjusted dataDRTBUntested cases
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
2010
Assessing spatiotemporal patterns of multidrug-resistant and drug-sensitive tuberculosis in a South American setting
LIN H, SHIN S, BLAYA JA, ZHANG Z, CEGIELSKI P, CONTRERAS C, ASENCIOS L, BONILLA C, BAYONA J, PACIOREK CJ, COHEN T. Assessing spatiotemporal patterns of multidrug-resistant and drug-sensitive tuberculosis in a South American setting. Epidemiology And Infection 2010, 139: 1784-1793. PMID: 21205434, PMCID: PMC3153578, DOI: 10.1017/s0950268810002797.Peer-Reviewed Original ResearchConceptsTB casesMDR diseaseMultidrug-resistant tuberculosis (MDR-TB) casesDrug-sensitive tuberculosisDrug-resistant diseaseDrug susceptibility testingMDR-TBMDR casesTuberculosis casesIncident casesSubgroup analysisInfection controlK statisticInfectious durationAppearance of resistanceDistricts of LimaSusceptibility testingDiseasePatientsTBUrban settingsCasesTuberculosisSettingMDR
2009
What is the mechanism for persistent coexistence of drug-susceptible and drug-resistant strains of Streptococcus pneumoniae?
Colijn C, Cohen T, Fraser C, Hanage W, Goldstein E, Givon-Lavi N, Dagan R, Lipsitch M. What is the mechanism for persistent coexistence of drug-susceptible and drug-resistant strains of Streptococcus pneumoniae? Journal Of The Royal Society Interface 2009, 7: 905-919. PMID: 19940002, PMCID: PMC2871802, DOI: 10.1098/rsif.2009.0400.Peer-Reviewed Original ResearchConceptsDrug-resistant strainsStreptococcus pneumoniaeInfectious diseasesDrug-susceptible strainsHigher reproduction numberCent prevalenceSubstantial prevalencePersistent coexistenceDrug resistanceMultiple infectionsAntimicrobial useResistant strainsBacterial spreadAntimicrobial resistancePrevalenceDiseasePneumoniaeOutcomesReproduction numberTreatmentHost interactionsPathogensCoinfectionUse 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