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 plantingsCDCRiskMolecular Epidemiology of Isoniazid-resistant M tuberculosis in Port-au-Prince, Haiti
Walsh K, Lee M, Chaguza C, Pamphile W, Royal G, Escuyer V, Pape J, Fitzgerald D, Cohen T, Ocheretina O. Molecular Epidemiology of Isoniazid-resistant M tuberculosis in Port-au-Prince, Haiti. Open Forum Infectious Diseases 2024, 11: ofae421. PMID: 39119477, PMCID: PMC11306977, DOI: 10.1093/ofid/ofae421.Peer-Reviewed Original ResearchCulture-positive pulmonary tuberculosisIsoniazid-resistant isolatesHR-TBIsoniazid-resistant M. tuberculosisPulmonary tuberculosisIsoniazid resistanceMutations associated with INH resistanceTransmission clustersGenoType MTBDRplus assayINH-resistant isolatesIsoniazid-susceptible isolatesPhenotypic isoniazid resistanceRifampin-susceptible tuberculosisSingle nucleotide polymorphism distancesMolecular epidemiologyAssociated with poor treatment outcomesWhole-genome sequencingM. tuberculosisPutative transmission clustersPoor treatment outcomesMTBDRplus assayGenoType MTBDRplusCulture-based testsINH resistanceTuberculosis clinic
2022
Quantifying Mycobacterium tuberculosis Transmission Dynamics Across Global Settings: A Systematic Analysis
Smith J, Cohen T, Dowdy D, Shrestha S, Gandhi NR, Hill AN. Quantifying Mycobacterium tuberculosis Transmission Dynamics Across Global Settings: A Systematic Analysis. American Journal Of Epidemiology 2022, 192: 133-145. PMID: 36227246, PMCID: PMC10144641, DOI: 10.1093/aje/kwac181.Peer-Reviewed Original ResearchConceptsTB transmissionOngoing TB transmissionMinority of casesTuberculosis transmission dynamicsTB controlTuberculosis transmissionSecondary casesSources of heterogeneityInclusion criteriaSurveillance studyTransmission clustersInitial searchTransmission dynamicsWhole-genome sequencingPopulation levelSettingThe 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis
Walker T, Miotto P, Köser C, Fowler P, Knaggs J, Iqbal Z, Hunt M, Chindelevitch L, Farhat M, Cirillo D, Comas I, Posey J, Omar S, Peto T, Suresh A, Uplekar S, Laurent S, Colman R, Nathanson C, Zignol M, Walker A, Crook D, Ismail N, Rodwell T, Consortium T, Walker A, Steyn A, Lalvani A, Baulard A, Christoffels A, Mendoza-Ticona A, Trovato A, Skrahina A, Lachapelle A, Brankin A, Piatek A, Cruz A, Koch A, Cabibbe A, Spitaleri A, Brandao A, Chaiprasert A, Suresh A, Barbova A, Van Rie A, Ghodousi A, Bainomugisa A, Mandal A, Roohi A, Javid B, Zhu B, Letcher B, Rodrigues C, Nimmo C, NATHANSON C, Duncan C, Coulter C, Utpatel C, Liu C, Grazian C, Kong C, Köser C, Wilson D, Cirillo D, Matias D, Jorgensen D, Zimenkov D, Chetty D, Moore D, Clifton D, Crook D, van Soolingen D, Liu D, Kohlerschmidt D, Barreira D, Ngcamu D, Lazaro E, Kelly E, Borroni E, Roycroft E, Andre E, Böttger E, Robinson E, Menardo F, Mendes F, Jamieson F, Coll F, Gao G, Kasule G, Rossolini G, Rodger G, Smith E, Meintjes G, Thwaites G, Hoffmann H, Albert H, Cox H, Laurenson I, Comas I, Arandjelovic I, Barilar I, Robledo J, Millard J, Johnston J, Posey J, Andrews J, Knaggs J, Gardy J, Guthrie J, Taylor J, Werngren J, Metcalfe J, Coronel J, Shea J, Carter J, Pinhata J, Kus J, Todt K, Holt K, Nilgiriwala K, Ghisi K, Malone K, Faksri K, Musser K, Joseph L, Rigouts L, Chindelevitch L, Jarrett L, Grandjean L, Ferrazoli L, Rodrigues M, Farhat M, Schito M, Fitzgibbon M, Loembé M, Wijkander M, Ballif M, Rabodoarivelo M, Mihalic M, WILCOX M, Hunt M, ZIGNOL M, Merker M, Egger M, O'Donnell M, Caws M, Wu M, Whitfield M, Inouye M, Mansjö M, Thi M, Joloba M, Kamal S, Okozi N, ISMAIL N, Mistry N, Hoang N, Rakotosamimanana N, Paton N, Rancoita P, Miotto P, Lapierre P, Hall P, Tang P, Claxton P, Wintringer P, Keller P, Thai P, Fowler P, Supply P, Srilohasin P, Suriyaphol P, Rathod P, Kambli P, Groenheit R, Colman R, Ong R, Warren R, Wilkinson R, Diel R, Oliveira R, Khot R, Jou R, Tahseen S, Laurent S, Gharbia S, Kouchaki S, Shah S, Plesnik S, Earle S, Dunstan S, Hoosdally S, Mitarai S, Gagneux S, Omar S, Yao S, Lapierre S, Battaglia S, Niemann S, Pandey S, Uplekar S, Halse T, Cohen T, Cortes T, Prammananan T, Kohl T, Thuong N, Teo T, Peto T, Rodwell T, William T, Walker T, Rogers T, Surve U, Mathys V, Furió V, Cook V, Vijay S, Escuyer V, Dreyer V, Sintchenko V, Saphonn V, Solano W, Lin W, van Gemert W, He W, Yang Y, Zhao Y, Qin Y, Xiao Y, Hasan Z, Iqbal Z, Puyen Z. The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis. The Lancet Microbe 2022, 3: e265-e273. PMID: 35373160, PMCID: PMC7612554, DOI: 10.1016/s2666-5247(21)00301-3.Peer-Reviewed Original ResearchConceptsConsistent with susceptibilityAssociated with resistancePhenotypic resistanceDrug susceptibility testingSusceptibility testingPositive predictive valueAssociated with phenotypic resistanceWhole-genome sequencingPrevalence of phenotypic resistanceMolecular diagnosticsDrug susceptibility testing dataUniversal drug susceptibility testingMutations associated with drug resistanceOdds ratioSusceptibility testing dataDrug resistance predictionImplementation of molecular diagnosticsBinary phenotypesPredictive valueGene approachMTBC isolatesUnique mutationsFisher's exact testAnti-tuberculosis drugsGenotype analysis
2018
Internal migration and transmission dynamics of tuberculosis in Shanghai, China: an epidemiological, spatial, genomic analysis
Yang C, Lu L, Warren JL, Wu J, Jiang Q, Zuo T, Gan M, Liu M, Liu Q, DeRiemer K, Hong J, Shen X, Colijn C, Guo X, Gao Q, Cohen T. Internal migration and transmission dynamics of tuberculosis in Shanghai, China: an epidemiological, spatial, genomic analysis. The Lancet Infectious Diseases 2018, 18: 788-795. PMID: 29681517, PMCID: PMC6035060, DOI: 10.1016/s1473-3099(18)30218-4.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overChinaDisease Transmission, InfectiousFemaleGenotypeHumansMaleMiddle AgedMinisatellite RepeatsMolecular EpidemiologyMycobacterium tuberculosisPolymorphism, Single NucleotideRural PopulationSpatial AnalysisTransients and MigrantsTuberculosisUrban PopulationWhole Genome SequencingConceptsM tuberculosisEpidemiological dataSingle nucleotide polymorphismsCulture-positive Mycobacterium tuberculosis isolatesCulture-positive tuberculosisPopulation-based studyMycobacterium tuberculosis isolatesTransmission dynamicsTime of infectionDynamics of tuberculosisTuberculosis controlUS National InstitutesTuberculosis isolatesMore effective interventionsProximity of residenceRecent transmissionPatient's homeTuberculosisLocal transmission dynamicsEffective interventionsLocal transmissionLocal incidenceNational InstituteVNTR patternsWhole-genome sequencing
2017
Drivers of Tuberculosis Transmission
Mathema B, Andrews JR, Cohen T, Borgdorff MW, Behr M, Glynn JR, Rustomjee R, Silk BJ, Wood R. Drivers of Tuberculosis Transmission. The Journal Of Infectious Diseases 2017, 216: s644-s653. PMID: 29112745, PMCID: PMC5853844, DOI: 10.1093/infdis/jix354.Peer-Reviewed Original ResearchConceptsRecent transmissionTuberculosis transmissionTuberculosis casesCulture-positive tuberculosis casesInterferon-γ release assaysΓ release assaysTuberculin skin testMycobacterium tuberculosis infectionTuberculosis case notificationTransmission of tuberculosisPublic health systemPrevalent tuberculosisTuberculosis infectionSkin testIncident diseaseCase notificationClinical diseaseHealth systemCapacity of healthcareOngoing transmissionTuberculosisYoung childrenHighlight knowledge gapsInfection eventsWhole-genome sequencing