2022
Reconstructing the course of the COVID-19 epidemic over 2020 for US states and counties: Results of a Bayesian evidence synthesis model
Chitwood MH, Russi M, Gunasekera K, Havumaki J, Klaassen F, Pitzer VE, Salomon JA, Swartwood NA, Warren JL, Weinberger DM, Cohen T, Menzies NA. Reconstructing the course of the COVID-19 epidemic over 2020 for US states and counties: Results of a Bayesian evidence synthesis model. PLOS Computational Biology 2022, 18: e1010465. PMID: 36040963, PMCID: PMC9467347, DOI: 10.1371/journal.pcbi.1010465.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionCOVID-19 casesIncident SARS-CoV-2 infectionCOVID-19 disease burdenSymptomatic COVID-19 casesLocal epidemiological trendsSARS-CoV-2 transmissionBayesian evidence synthesis modelCOVID-19 outcomesEvidence synthesis modelMagnitude of infectionCOVID-19 deathsCumulative incidenceDisease burdenExcess mortalityCase ascertainmentEpidemiological trendsSeroprevalence estimatesUnderlying incidenceUS populationDisease trendsViral transmission dynamicsInfectionEpidemiological driversCOVID-19 epidemicPredicting resistance to fluoroquinolones among patients with rifampicin-resistant tuberculosis using machine learning methods
You S, Chitwood MH, Gunasekera KS, Crudu V, Codreanu A, Ciobanu N, Furin J, Cohen T, Warren JL, Yaesoubi R. Predicting resistance to fluoroquinolones among patients with rifampicin-resistant tuberculosis using machine learning methods. PLOS Digital Health 2022, 1: e0000059. PMID: 36177394, PMCID: PMC9518704, DOI: 10.1371/journal.pdig.0000059.Peer-Reviewed Original ResearchDrug susceptibility testXpert MTB/RIFMachine learning-based modelsLearning-based modelsMachine learning methodsRifampicin-resistant tuberculosisTime of diagnosisRifampin-resistant tuberculosisMTB/RIFNeural network modelLearning methodsNetwork modelMulti-drug resistant tuberculosisNational TB surveillanceDrug-resistant tuberculosisOptimism-corrected areaSelection of antibioticsAnti-TB agentsDistrict-level prevalenceLow-resource settingsPatient characteristicsResistant tuberculosisTB surveillanceAppropriate treatmentDST resultsPhylogeography and transmission of M. tuberculosis in Moldova: A prospective genomic analysis
Yang C, Sobkowiak B, Naidu V, Codreanu A, Ciobanu N, Gunasekera KS, Chitwood MH, Alexandru S, Bivol S, Russi M, Havumaki J, Cudahy P, Fosburgh H, Allender CJ, Centner H, Engelthaler DM, Menzies NA, Warren JL, Crudu V, Colijn C, Cohen T. Phylogeography and transmission of M. tuberculosis in Moldova: A prospective genomic analysis. PLOS Medicine 2022, 19: e1003933. PMID: 35192619, PMCID: PMC8903246, DOI: 10.1371/journal.pmed.1003933.Peer-Reviewed Original ResearchConceptsMultidrug-resistant tuberculosisDrug-resistant M. tuberculosisM. tuberculosis strainsPutative transmission clustersM. tuberculosisTransmission clustersMultidrug-resistant M. tuberculosis strainsTuberculosis strainsMultiple M. tuberculosis strainsCulture-positive TB casesLocal transmissionMDR-TB epidemicDrug-susceptible tuberculosisDrug resistance mutationsDrug resistance profilesUrgency of interventionTB casesDemographic dataNew casesTuberculosisInadequate treatmentNatural historyResistance mutationsBeijing lineageMycobacterium tuberculosis
2021
Development of a Treatment-decision Algorithm for Human Immunodeficiency Virus–uninfected Children Evaluated for Pulmonary Tuberculosis
Gunasekera KS, Walters E, van der Zalm MM, Palmer M, Warren JL, Hesseling AC, Cohen T, Seddon JA. Development of a Treatment-decision Algorithm for Human Immunodeficiency Virus–uninfected Children Evaluated for Pulmonary Tuberculosis. Clinical Infectious Diseases 2021, 73: e904-e912. PMID: 33449999, PMCID: PMC8366829, DOI: 10.1093/cid/ciab018.Peer-Reviewed Original ResearchConceptsPulmonary tuberculosisClinical evidenceXpert MTB/RIFBaseline clinical evaluationChest radiographic resultsRapid treatment initiationNational Tuberculosis ProgrammeTreatment decision algorithmsEvidence-based algorithmMTB/RIFDiagnosis of tuberculosisChest radiographicAntituberculosis treatmentProspective cohortRadiographic resultsTreatment initiationTuberculosis casesTuberculosis ProgrammeClinical evaluationCase definitionTreatment decisionsGlobal burdenChildhood mortalityChildren EvaluatedRapid clinical diagnosis
2020
Children as sentinels of tuberculosis transmission: disease mapping of programmatic data
Gunasekera KS, Zelner J, Becerra MC, Contreras C, Franke MF, Lecca L, Murray MB, Warren JL, Cohen T. Children as sentinels of tuberculosis transmission: disease mapping of programmatic data. BMC Medicine 2020, 18: 234. PMID: 32873309, PMCID: PMC7466499, DOI: 10.1186/s12916-020-01702-x.Peer-Reviewed Original ResearchConceptsNational Tuberculosis ProgrammeActive case-finding interventionsCase-finding interventionsTuberculosis transmissionNotification dataTuberculosis ProgrammeTuberculosis incidenceChild casesChildhood tuberculosis casesRecent transmission eventsProportion of casesCase notification dataMolecular epidemiological methodsMolecular epidemiologic methodsEndemic infectious diseasesTuberculosis casesProspective studyAdult casesDisease progressionNotification registerProgrammatic dataDistricts of LimaEpidemiological methodsInfectious diseasesTransmission hotspotsSmoking 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