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Biography
Dr. Jonathan Smith is a lecturer in Epidemiology of Microbial Diseases and Global Health at Yale University School of Public Health. His research focuses on characterizing tuberculosis (TB) transmission dynamics in high-burden populations, as well as improving pediatric TB diagnosis in infants and very young children. He is an affiliate of the Yale Global Health Leadership Institute and founding director of Visual Epidemiology, a project seeking to combine academic discourse with personal stories through filmmaking.
Last Updated on August 22, 2023.
Appointments
Health Policy & Management
LecturerPrimary
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Research
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Overview
Public Health Interests
Tuberculosis; HIV/AIDS; Infectious Diseases
ORCID
0000-0002-6396-9164
Research at a Glance
Yale Co-Authors
Frequent collaborators of Jonathan P Smith's published research.
Publications Timeline
A big-picture view of Jonathan P Smith's research output by year.
Ted Cohen, DPH, MD, MPH
Joshua Warren, PhD
31Publications
484Citations
Publications
2025
Phenotypic and genotypic characterization of Mycobacterium tuberculosis pyrazinamide resistance—India, 2018–2020
Tamilzhalagan S, Justin E, Selvaraj A, Venkateswaran K, Sivakumar A, Chittibabu S, McLaughlin H, Moonan P, Smith J, Suba S, Narayanan M, Ho C, Kumar N, Tripathy S, Shanmugam S, Hall-Eidson P, Ranganathan U. Phenotypic and genotypic characterization of Mycobacterium tuberculosis pyrazinamide resistance—India, 2018–2020. Frontiers In Microbiology 2025, 15: 1515627. PMID: 39845030, PMCID: PMC11750862, DOI: 10.3389/fmicb.2024.1515627.Peer-Reviewed Original ResearchCitationsAltmetricConceptsPZA resistancePyrazinamide resistanceMultidrug resistanceDuration of tuberculosis treatmentWhole-genome sequencingPrevalence of mutationsSecond-line drugsPZA-resistant isolatesResistance-conferring mutationsGenome sequenceTB burden countriesLineage 2Genotypic characterizationResistance markersNovel mutationsPhenotypic resistanceMutational diversityDiagnostic accuracyTuberculosis treatmentAntituberculosis drugsCo-resistanceBurden countriesPyrazinamideMutationsTB prevention
2024
Test and treat approach for tuberculosis infection amongst household contacts of drug-susceptible pulmonary tuberculosis, Mumbai, India
Shah D, Bhide S, Deshmukh R, Smith J, Kaiplyawar S, Puri V, Yeldandi V, Date A, Nyendak M, Ho C, Moonan P. Test and treat approach for tuberculosis infection amongst household contacts of drug-susceptible pulmonary tuberculosis, Mumbai, India. Frontiers In Tuberculosis 2024, 2: 1454277. PMID: 39421397, PMCID: PMC11485165, DOI: 10.3389/ftubr.2024.1454277.Peer-Reviewed Original ResearchCitationsAltmetricConceptsInterferon-gamma release assayTB preventive treatmentTB infectionHousehold contactsDrug-susceptible pulmonary tuberculosisTB diseaseTreat approachProgression to active TB diseaseDrug-susceptible pulmonary TBRate of TB infectionPrevalence of TB infectionActive TB diseaseAge 5 yearsSecondary TB casesCross-sectional studyAntituberculosis treatmentIGRA testPulmonary TBPulmonary tuberculosisTuberculosis infectionInterferon-gammaRelease assayClinical evaluationEarly diagnosisTreat strategyExhaled breath analysis: A promising triage test for tuberculosis in young children
Bijker E, Smith J, Mchembere W, McCarthy K, Oord H, Gerritsen J, Click E, Cain K, Song R. Exhaled breath analysis: A promising triage test for tuberculosis in young children. Tuberculosis 2024, 149: 102566. PMID: 39332067, PMCID: PMC11864270, DOI: 10.1016/j.tube.2024.102566.Peer-Reviewed Original ResearchCitationsAltmetricConceptsTriage testPaediatric pulmonary tuberculosisRespiratory tract infectionsSymptoms of tuberculosisDiagnose respiratory tract infectionsCross-sectional studyExpectorated sputumTract infectionsPulmonary tuberculosisPaediatric tuberculosisDiagnostic accuracyBreath testYoung childrenYoung infantsTuberculosisExhaled breath analysisBreathingBreath analysisChildrenTriageExhaled breathSputumInfantsFeasibility and utility of a combined nasogastric-tube-and-string-test device for bacteriologic confirmation of pulmonary tuberculosis in young children
Khambati N, Song R, Smith J, Bijker E, McCarthy K, Click E, Mchembere W, Okumu A, Musau S, Okeyo E, Perez-Velez C, Cain K. Feasibility and utility of a combined nasogastric-tube-and-string-test device for bacteriologic confirmation of pulmonary tuberculosis in young children. Diagnostic Microbiology And Infectious Disease 2024, 109: 116302. PMID: 38657352, PMCID: PMC11128341, DOI: 10.1016/j.diagmicrobio.2024.116302.Peer-Reviewed Original ResearchTuberculosis Preventive Treatment Update — U.S. President’s Emergency Plan for AIDS Relief, 36 Countries, 2016–2023
Ajiboye A, O’Connor S, Smith J, Ahmedov S, Coggin W, Charles M, Ghosh S, Pierre P, Shah N, Teran R, Moonan P, Date A. Tuberculosis Preventive Treatment Update — U.S. President’s Emergency Plan for AIDS Relief, 36 Countries, 2016–2023. MMWR Morbidity And Mortality Weekly Report 2024, 73: 233-238. PMID: 38512767, PMCID: PMC10967683, DOI: 10.15585/mmwr.mm7311a1.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsU.S. President's Emergency PlanPresident's Emergency Plan for AIDS ReliefTB preventive treatmentAIDS ReliefAntiretroviral treatmentU.S. President's Emergency Plan for AIDS ReliefElectronic medical record systemPresident's Emergency PlanPatient-centered approachFiscal yearNational HIV programTB-attributed deathsMedical record systemTB-related deathsOverall completion rateHIV programsCompletion ratesRecording systemTB diseaseStandard of careHIVHigh riskPersonsEmergency planningShorter regimensLong-term follow-up of persons diagnosed with multidrug-resistant TB in Chennai, India, 2013–2020
Surie D, Sathyanarayanan M, Lavanya J, Smith J, Shanmugam S, Tamilzhalagan S, Selvaraj A, Ramesh G, Tripathy S, Khaparde S, Ho C, Hall-Eidson P, Ranganathan U, Selvaraju S, Moonan P. Long-term follow-up of persons diagnosed with multidrug-resistant TB in Chennai, India, 2013–2020. The International Journal Of Tuberculosis And Lung Disease 2024, 28: 54-56. PMID: 38178300, PMCID: PMC10859871, DOI: 10.5588/ijtld.23.0272.Peer-Reviewed Original ResearchCitations
2023
Machine learning to predict bacteriologic confirmation of Mycobacterium tuberculosis in infants and very young children
Smith J, Milligan K, McCarthy K, Mchembere W, Okeyo E, Musau S, Okumu A, Song R, Click E, Cain K. Machine learning to predict bacteriologic confirmation of Mycobacterium tuberculosis in infants and very young children. PLOS Digital Health 2023, 2: e0000249. PMID: 37195976, PMCID: PMC10191346, DOI: 10.1371/journal.pdig.0000249.Peer-Reviewed Original ResearchCitationsAltmetricConceptsMicrobial confirmationTB diseaseYoung childrenNoninvasive procedureLarge prospective cohortCases of tuberculosisChest X-rayDiagnosis of tuberculosisClinical decision makingBacteriologic confirmationHousehold contactsTB infectionProspective cohortRadiologic factorsPaucibacillary natureClinical similaritiesDiagnostic cohortClinical diseaseChildhood diseasesInvasive proceduresNovel biomarkersTuberculosisClinical researchM. tuberculosisDiseaseRetaining Patients with Drug-Resistant Tuberculosis on Treatment During the COVID-19 Pandemic — Dharavi, Mumbai, India, 2020–2022
Gomare M, Bhide S, Deshmukh R, Kaipilyawar S, Puri V, Moonan P, Khetade D, Nyendak M, Yeldandi V, Smith J, Tobias J, Date A, Joshi R, Kumar R, Ho C. Retaining Patients with Drug-Resistant Tuberculosis on Treatment During the COVID-19 Pandemic — Dharavi, Mumbai, India, 2020–2022. MMWR Morbidity And Mortality Weekly Report 2023, 72: 304-308. PMID: 36952291, PMCID: PMC10042620, DOI: 10.15585/mmwr.mm7212a2.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsIsolation and Quarantine for Coronavirus Disease 2019 in the United States, 2020–2022
Oeltmann J, Vohra D, Matulewicz H, DeLuca N, Smith J, Couzens C, Lash R, Harvey B, Boyette M, Edwards A, Talboy P, Dubose O, Regan P, Loosier P, Caruso E, Katz D, Taylor M, Moonan P. Isolation and Quarantine for Coronavirus Disease 2019 in the United States, 2020–2022. Clinical Infectious Diseases 2023, 77: 212-219. PMID: 36947142, PMCID: PMC11094624, DOI: 10.1093/cid/ciad163.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsCoronavirus disease 2019Case patientsDisease 2019Positive severe acute respiratory syndrome coronavirus 2 test resultAdult case patientsCase investigationCOVID-19Public health programsPublic health workforceHealth programsHealth workforceContact tracingPatientsHealth officialsMost adultsAdultsDaysImpact of contactRepresentative sampleTotalMore adultsPanel SurveyQuarantineDevelopment of treatment-decision algorithms for children evaluated for pulmonary tuberculosis: an individual participant data meta-analysis
Gunasekera K, Marcy O, Muñoz J, Lopez-Varela E, Sekadde M, Franke M, Bonnet M, Ahmed S, Amanullah F, Anwar A, Augusto O, Aurilio R, Banu S, Batool I, Brands A, Cain K, Carratalá-Castro L, Caws M, Click E, Cranmer L, García-Basteiro A, Hesseling A, Huynh J, Kabir S, Lecca L, Mandalakas A, Mavhunga F, Myint A, Myo K, Nampijja D, Nicol M, Orikiriza P, Palmer M, Sant'Anna C, Siddiqui S, Smith J, Song R, Thuong Thuong N, Ung V, van der Zalm M, Verkuijl S, Viney K, Walters E, Warren J, Zar H, Marais B, Graham S, Debray T, Cohen T, Seddon J. Development of treatment-decision algorithms for children evaluated for pulmonary tuberculosis: an individual participant data meta-analysis. The Lancet Child & Adolescent Health 2023, 7: 336-346. PMID: 36924781, PMCID: PMC10127218, DOI: 10.1016/s2352-4642(23)00004-4.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsTreatment decision algorithmsPrimary health care settingsIndividual participant dataHigh tuberculosis incidencePulmonary tuberculosisManagement of tuberculosisHealth care centersComposite reference standardHealth care settingsClinical featuresTuberculosis incidenceClinical evaluationParticipant dataTreatment decisionsChest X-ray featuresPrimary health care centersFuture prospective evaluationTuberculosis-related mortalityEvidence-based algorithmChest X-rayVariable diagnostic performanceMultivariable prediction modelReference standardEvidence-based approachTuberculosis experts
Academic Achievements & Community Involvement
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Activities
activity Foundation for International Medical Relief of Children (FIMRC)
06/01/2009 - 05/23/2011Public ServiceFounder
Honors
honor Tuberculosis Survival Prize
11/01/2011International AwardLily MDR-TB FoundationDetailsUnited Stateshonor Lowell S. Levin Award for Excellence in Global Health
05/23/2011Yale School of Medicine AwardYale School of Public HealthDetailsUnited Stateshonor Outstanding Community Service Award (2005-2008)
01/01/2005Regional AwardClarke County Government (Georgia)DetailsUnited States
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