Agonafir M, Lemma E, Wolde-Meskel D, Goshu S, Santhanam A, Girmachew F, et al. Phenotypic and genotypic analysis of multidrug-resistant tuberculosis in Ethiopia. Int J Tuberc Lung Dis 2010;14:1259–65.
Alaridah N, Hallbäck ET, Tångrot J, Winqvist N, Sturegård E, Florén-Johansson K, et al. Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden. Sci Rep 2019;9:1–9.
Allix-Beguec C, Harmsen D, Weniger T, Supply P, Niemann S, Allix-Béguec C, et al. Evaluation and strategy for use of MIRU-VNTRplus, a multifunctional database for online analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates. J Clin Microbiol 2008;46:2692–9.
De Almeida IN, Vasconcellos SEG, de Assis Figueredo LJ, Dantas NGT, Augusto CJ, Hadaad JPA, et al. Frequency of the Mycobacterium tuberculosis RDRio genotype and its association with multidrug-resistant tuberculosis. BMC Infect Dis 2019;19:1–9.
Alyamani EJ, Marcus SA, Ramirez-Busby SM, Hansen C, Rashid J, El-kholy A, et al. Genomic analysis of the emergence of drug-resistant strains of Mycobacterium tuberculosis in the Middle East. Sci Rep 2019;9:1–12.
Andersson DI. The biological cost of mutational antibiotic resistance: any practical conclusions? Curr Opin Microbiol 2006;9:461–5.
Asare P, Otchere ID, Bedeley E, Brites D, Loiseau C, Baddoo NA, et al. Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana. Front Med 2020;7:161.
Bakuła Z, Javed H, Pleń M, Jamil N, Tahir Z, Jagielski T. Genetic diversity of multidrug- resistant Mycobacterium tuberculosis isolates in Punjab, Pakistan. Infect Genet Evol 2019;72:16–24.
Bakuła Z, Napiórkowska A, Bielecki J, Augustynowicz-Kopeć E, Zwolska Z, Jagielski T. Mutations in the embB Gene and Their Association with Ethambutol Resistance in Multidrug- Resistant Mycobacterium tuberculosis Clinical Isolates from Poland. Biomed Res Int 2013; 2013:167954.
Balasubramanian V, Wiegeshaus EH, Taylor BT, Smith DW. Pathogenesis of tuberculosis: pathway to apical localization. Tuber Lung Dis 1994;75:168–78.
Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, et al. Community- Driven Data Analysis Training for Biology. Cell Syst 2018;6:752--758.e1.
Bhembe NL, Green E. Molecular epidemiological study of multidrug-resistant tuberculosis isolated from sputum samples in Eastern Cape, South Africa. Infect Genet Evol 2020;80:104182.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30:2114–20.
Boshoff HIM, Barry CE. Tuberculosis — metabolism and respiration in the absence of growth. Nat Rev Microbiol 2005 31 2005;3:70–80.
Brandis G, Wrande M, Liljas L, Hughes D. Fitness-compensatory mutations in rifampicin- resistant RNA polymerase. Mol Microbiol 2012;85:142–51.
Brynildsrud OB, Pepperell CS, Suffys P, Grandjean L, Monteserin J, Debech N, et al. Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation. Sci Adv 2018;4:1–12.
Bwalya P, Yamaguchi T, Solo ES, Chizimu JY, Mbulo G, Nakajima C, et al. Characterization of Mutations Associated with Streptomycin Resistance in Multidrug- Resistant Mycobacterium tuberculosis in Zambia. Antibiotics (Basel) 2021;10:1169.
Casper C, Singh SP, Rave S, Daley CL, Schecter GS, Riley LW, et al. The transcontinental transmission of tuberculosis: A molecular epidemiological assessment. Am J Public Health 1996;86:551–3.
CDC. TB Risk Factors | Basic TB Facts | TB | CDC 2016.
Chihota VN, Müller B, Mlambo CK, Pillay M, Tait M, Streicher EM, et al. Population structure of multi- and extensively drug-resistant Mycobacterium tuberculosis strains in South Africa. J Clin Microbiol 2012;50:995–1002.
Chihota VN, Niehaus A, Streicher EM, Wang X, Sampson SL, Mason P, et al. Geospatial distribution of Mycobacterium tuberculosis genotypes in Africa. PLoS One 2018;13:e0200632.
Chizimu JY, Solo ES, Bwalya P, Kapalamula TF, Akapelwa ML, Lungu P, et al. Genetic Diversity and Transmission of Multidrug Resistant Mycobacterium tuberculosis strains in Lusaka, Zambia. Int J Infect Dis 2021;114: 142–150,.
CLC Genomics Workbench. CLC Genomics Workbench 20.0 (QIAGEN). Workbench 2013:1–70.
Coll F, McNerney R, Preston MD, Guerra-Assunção JA, Warry A, Hill-Cawthorne G, et al. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med 2015;7:51.
Coll I Cerezo F. Bioinformatic analysis of Mycobacterium tuberculosis whole genome data. PhD thesis. London School of Hygiene & Tropical Medicine, London, UK, 2015.
Comas I, Borrell S, Roetzer A, Rose G, Malla B, Kato-Maeda M, et al. Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nat Genet 2011;44:106–10.
Commissioner UNH, Grandi RF. UNHCR chief applauds Zambia’s openness to refugees 2019.
Coscolla M. Biological and Epidemiological Consequences of MTBC Diversity. Adv Exp Med Biol 2017;1019:95–116.
Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD, et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res 2014;43:e15.
Daffé M, Draper P. The Envelope Layers of Mycobacteria with Reference to their Pathogenicity. Adv Microb Physiol 1997;39:131–203.
David S, Duarte EL, Leite CQF, Ribeiro J-NN, Maio J-NN, Paixão E, et al. Implication of the RDRio Mycobacterium tuberculosis sublineage in multidrug resistant tuberculosis in Portugal. Infect Genet Evol 2012;12:1362–7.
Demay C, Liens B, Burguière T, Hill V, Couvin D, Millet J, et al. SITVITWEB – A publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology. Infect Genet Evol 2012;12:755–66.
Disease Profiling Project. DNA Sequencing: Illumina Workflow Part-2 (DNA Tagmentation, Amplification, and Cleanup) 2018.
Easterbrook PJ, Gibson A, Murad S, Lamprecht D, Ives N, Ferguson A, et al. High rates of clustering of strains causing tuberculosis in Harare, Zimbabwe: A molecular epidemiological study. J Clin Microbiol 2004;42:4536–44.
Ernst JD. The immunological life cycle of tuberculosis. Nat Rev Immunol 2012;12:581–91.
Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 2016;32:3047–8.
Feliciano CS, Namburete EI, Rodrigues Plaça J, Peronni K, Dippenaar A, Warren RM, et al. Accuracy of whole genome sequencing versus phenotypic (MGIT) and commercial molecular tests for detection of drug-resistant Mycobacterium tuberculosis isolated from patients in Brazil and Mozambique. Tuberculosis 2018;110:59–67.
Feuerriegel S, Schleusener V, Beckert P, Kohl TA, Miotto P, Cirillo DM, et al. PhyResSE: a Web Tool Delineating Mycobacterium tuberculosis Antibiotic Resistance and Lineage from Whole-Genome Sequencing Data. J Clin Microbiol 2015;53:1908–14.
Gagneux S. Strain Variation in the Mycobacterium tuberculosis Complex : Its Role in Biology, Epidemiology and Control 2017; 1019:319.
Gagneux S. Host-pathogen coevolution in human tuberculosis. Philos Trans R Soc London Ser B, Biol Sci 2012;367:850–9.
Gagneux S, DeRiemer K, Van T, Kato-Maeda M, de Jong BC, Narayanan S, et al. Variable host-pathogen compatibility in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2006;103:2869–73.
Gillespie S. Tuberculosis: evolution in millennia and minutes. Biochem Soc Trans 2007;35:1317–20.
Gutierrez MC, Brisse S, Brosch R, Fabre M, Omaïs B, Marmiesse M, et al. Ancient Origin and Gene Mosaicism of the Progenitor of Mycobacterium tuberculosis. PLOS Pathog 2005;1:e5.
Hamblion EL, Le Menach A, Anderson LF, Lalor MK, Brown T, Abubakar I, et al. Recent TB transmission, clustering and predictors of large clusters in London, 2010-2012: Results from first 3-years of universal MIRU-VNTR strain typing. Thorax 2016;71:749–56.
Hazbón MH, Valle MB del, Guerrero MI, Varma-Basil M, Filliol I, Cavatore M, et al. Role of embB Codon 306 Mutations in Mycobacterium tuberculosis Revisited: a Novel Association with Broad Drug Resistance and IS6110 Clustering Rather than Ethambutol Resistance. Antimicrob Agents Chemother 2005;49:3794.
Heusden P van, Gladman S, Lose T. M. tuberculosis Variant Analysis (Galaxy Training Materials) 2021.
Hunter PR. Reproducibility and indices of discriminatory power of microbial typing methods. J Clin Microbiol 1990;28:1903–5.
Hunter PR, Gaston MA, Hunter PR, Gaston MA, Hunter PR, Gaston MA. Numerical index of the discriminatory ability of typing systems: An application of Simpson’s index of diversity. J Clin Microbiol 1988;26:2465–6.
Kaiser G. The Prokaryotic cell- Bacteria. Microbiology. Community College of Baltimore County (Cantonsville): LibreTexts libraries 2019;782.
Kalscheuer R, Palacios A, Anso I, Cifuente J, Anguita J, Jacobs Jr WR, et al. The Mycobacterium tuberculosis capsule: a cell structure with key implications in pathogenesis. Biochem J 2019;476:1995–2016.
Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S, et al. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol 1997;35:907–14.
Kapata N, Chanda-Kapata P, Bates M, Mwaba P, Cobelens F, Grobusch MP, et al. Multidrug-resistant TB in Zambia: Review of national data from 2000 to 2011. Trop Med Int Heal 2013;18:1386–91.
Katale BZ, Mbelele PM, Lema NA, Campino S, Mshana SE, Rweyemamu MM, et al. Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania. BMC Genomics 2020;21:174.
Kochi A, Vareldzis B, Styblo K. Multidrug-resistant tuberculosis and its control. Res Microbiol 1993;144:104–10.
Kurbatova E V., Kaminski DA, Erokhin V V., Volchenkov G V., Andreevskaya SN, Chernousova LN, et al. Performance of Cepheid® Xpert MTB/RIF® and TB-Biochip® MDR in two regions of Russia with a high prevalence of drug-resistant tuberculosis. Eur J Clin Microbiol Infect Dis 2013;6:735–43.
Lacoma A, García-Sierra N, Prat C, Maldonado J, Ruiz-Manzano J, Haba L, et al. GenoType MTBDRsl for molecular detection of second-line-drug and ethambutol resistance in Mycobacterium tuberculosis strains and clinical samples. J Clin Microbiol 2012;50:30–6.
Lalor M, Casali N, Walker T, Anderson L, Davidson J, Ratna N, et al. The use of whole- genome sequencing in cluster investigation of an MDR-TB outbreak. Eur Respir J 2018;51:1702313.
Lazzarini LCO, Huard RC, Boechat NL, Gomes HM, Oelemann MC, Kurepina N, et al. Discovery of a novel Mycobacterium tuberculosis lineage that is a major cause of tuberculosis in Rio de Janeiro, Brazil. J Clin Microbiol 2007;45:3891–902.
Lee ASG, Othman SNK, Ho YM, Wong SY. Novel mutations within the embB gene in ethambutol-susceptible clinical isolates of Mycobacterium tuberculosis. Antimicrob Agents Chemother 2004;48:4447–9.
Leung ECC, Leung CC, Kam KM, Yew WW, Chang KC, Leung WM, et al. Transmission of multidrug-resistant and extensively drug-resistant tuberculosis in a metropolitan city. Eur Respir J 2013;41:901–8.
Li M, Chen R, Lin S, Lu Y, Liu H, Li G, et al. Detecting Ethambutol Resistance in Mycobacterium tuberculosis Isolates in China: A Comparison Between Phenotypic Drug Susceptibility Testing Methods and DNA Sequencing of embAB. Front Microbiol 2020;11:781.
Li Q jing, Jiao W wei, Yin Q qin, Li Y jia, Li J qiong, Xu F, et al. Positive epistasis of major low-cost drug resistance mutations rpoB531-TTG and katG315-ACC depends on the phylogenetic background of Mycobacterium tuberculosis strains. Int J Antimicrob Agents 2017;49:757–62.
Luo D, Chen Q, Xiong G, Peng Y, Liu T, Chen X, et al. Prevalence and molecular characterization of multidrug-resistant M. tuberculosis in Jiangxi province, China. Sci Rep 2019;9:7315.
Luo T, Yang C, Peng Y, Lu L, Sun G, Wu J, et al. Whole-genome sequencing to detect
recent transmission of Mycobacterium tuberculosis in settings with a high burden of tuberculosis. Tuberculosis (Edinb) 2014;94:434–40.
Malama S, Muma J, Munyeme M, Mbulo G, Muwonge A, Shamputa IC, et al. Isolation and Molecular Characterization of Mycobacterium tuberculosis from Humans and Cattle in Namwala District, Zambia. EcoHealth 2014;11:564-70.
Maruri F, Sterling TR, Kaiga AW, Blackman A, van der Heijden YF, Mayer C, et al. A systematic review of gyrase mutations associated with fluoroquinolone-resistant Mycobacterium tuberculosis and a proposed gyrase numbering system. J Antimicrob Chemother 2012;67:819–31.
Mbugi E V., Katale BZ, Siame KK, Keyyu JD, Kendall SL, Dockrell HM, et al. Genetic diversity of Mycobacterium tuberculosis isolated from tuberculosis patients in the Serengeti ecosystem in Tanzania. Tuberculosis 2015;95:170–8.
Mbugi E V, Katale BZ, Streicher EM, Keyyu JD, Kendall SL, Dockrell HM, et al. Mapping of Mycobacterium tuberculosis Complex Genetic Diversity Profiles in Tanzania and Other African Countries. PLoS One 2016;11:e0154571.
Meier A, Sander P, Schaper KJ, Scholz M, Böttger EC. Correlation of molecular resistance mechanisms and phenotypic resistance levels in streptomycin-resistant Mycobacterium tuberculosis. Antimicrob Agents Chemother 1996;40:2452-54.
Metcalfe JZ, Kim EY, Lin S-YG, Cattamanchi A, Oh P, Flood J, et al. Determinants of Multidrug-Resistant Tuberculosis Clusters, California, USA, 2004–2007. Emerg Infect Dis 2010;16:1403-9.
Ministry of Health. Zambia National TB Strategic Plan 2017-2021 2017.
Mokrousov I, Vyazovaya A, Iwamoto T, Skiba Y, Pole I, Zhdanova S, et al. Latin- American-Mediterranean lineage of Mycobacterium tuberculosis: Human traces across pathogen’s phylogeography. Mol Phylogenet Evol 2016;99:133–43.
Moström P, Gordon M, Sola C, Ridell M, Rastogi N. Methods used in the molecular epidemiology of tuberculosis. Clin Microbiol Infect 2002;8:694–704.
Mulenga C, Shamputa IC, Mwakazanga D, Kapata N, Portaels F, Rigouts L. Diversity of Mycobacterium tuberculosis genotypes circulating in Ndola, Zambia. BMC Infect Dis 2010;10:177.
Namburete EI, Dippenaar A, Conceição EC, Feliciano C, Nascimento MMP do, Peronni KC, et al. Phylogenomic assessment of drug-resistant Mycobacterium tuberculosis strains from Beira, Mozambique. Tuberculosis 2020;121:101905.
Napier G, Campino S, Merid Y, Abebe M, Woldeamanuel Y, Aseffa A, et al. Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies. Genome Med 2020 121 2020;12:1–10.
O’Neill MB, Shockey A, Zarley A, Aylward W, Eldholm V, Kitchen A, et al. Lineage specific histories of Mycobacterium tuberculosis dispersal in Africa and Eurasia. Mol Ecol 2019;28:3241–56.
Oudghiri A, Chaoui I, Elmzibri M. Molecular Epidemiology of Tuberculosis: A Review of Tools and Applications. J Infect Dis Ther 2018;6:1–7.
Oudghiri A, Momen G, Aainouss A, Laglaoui A, El Messaoudi MD, El Mzibri M, et al. Genotypic diversity of multi- and pre-extremely drug-resistant Mycobacterium tuberculosis isolates from Morocco. PLoS One 2021;16:e0253826.
Palomino JC, Martin A. Drug resistance mechanisms in Mycobacterium tuberculosis. Antibiotics 2014;3:317–40.
Paradis E, Claude J SK. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 2004;20:289–90.
Parsons LM, Salfinger M, Clobridge A, Dormandy J, Mirabello L, Polletta VL, et al. Phenotypic and Molecular Characterization of Mycobacterium tuberculosis Isolates Resistant to both Isoniazid and Ethambutol. Antimicrob Agents Chemother 2005;49:2218.
Perdigão J, Clemente S, Ramos J, Masakidi P, Machado D, Silva C, et al. Genetic diversity, transmission dynamics and drug resistance of Mycobacterium tuberculosis in Angola. Sci Rep 2017;7:42814.
Perdigão J, Silva C, Diniz J, Pereira C, Machado D, Ramos J, et al. Clonal expansion across the seas as seen through CPLP-TB database: A joint effort in cataloguing Mycobacterium tuberculosis genetic diversity in Portuguese-speaking countries. Infect Genet Evol 2019;72:44–58.
Phelan JE, O’Sullivan DM, Machado D, Ramos J, Oppong YEA, Campino S, et al. Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. Genome Med 2019;11:41.
Qing S, Tong-yang X, Hai-can L, Xiu-qin Z, Zhi-guang L, Ya-nan L, et al. Mutations within embCAB Are Associated with Variable Level of Ethambutol Resistance in Mycobacterium tuberculosis Isolates from China. Antimicrob Agents Chemother 2021;62:e01279–317.
Ramaswamy S, Musser JM. Molecular genetic basis of antimicrobial agent resistance in Mycobacterium tuberculosis: 1998 update. Tuber Lung Dis 1998;79:3–29.
Roetzer A, Diel R, Kohl TA, Rückert C, Nübel U, Blom J, et al. Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study. PLoS Med 2013;10:e1001387.
Safi H, Sayers B, Hazbón MH, Alland D. Transfer of embB Codon 306 Mutations into Clinical Mycobacterium tuberculosis Strains Alters Susceptibility to Ethambutol, Isoniazid, and Rifampin. Antimicrob Agents Chemother 2008;52:2027-34.
Sagonda T, Mupfumi L, Manzou R, Makamure B, Tshabalala M, Gwanzura L, et al. Prevalence of Extensively Drug Resistant Tuberculosis among Archived Multidrug Resistant Tuberculosis Isolates in Zimbabwe. Tuberc Res Treat 2014;2014:1–8.
Said HM, Kock MM, Ismail NA, Mphahlele M, Baba K, Omar S V, et al. Molecular characterization and second-line antituberculosis drug resistance patterns of multidrug- resistant Mycobacterium tuberculosis isolates from the northern region of South Africa. J Clin Microbiol 2012;50:2857–62.
Scorpio A, Lindholm-Levy P, Heifets L, Gilman R, Siddiqi S, Cynamon M, et al. Characterization of pncA mutations in pyrazinamide-resistant Mycobacterium tuberculosis. Antimicrob Agents Chemother 1997;41:540–3.
Seemann. T. snippy: Rapid haploid variant calling and core genome alignment 2020.
Shah Y, Maharjan B, Thapa J, Poudel A, Diab HM, Pandey BD, et al. High diversity of multidrug-resistant Mycobacterium tuberculosis Central Asian Strain isolates in Nepal. Int J Infect Dis 2017;63:13–20.
Shen X, Shen G, Wu J, Gui X, Li X, Mei J, et al. Association between embB Codon 306 Mutations and Drug Resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2007;51:2618–20.
Shuaib YA, Khalil EAG, Wieler LH, Schaible UE, Bakheit MA, Mohamed-Noor SE, et al. Mycobacterium tuberculosis Complex Lineage 3 as Causative Agent of Pulmonary Tuberculosis, Eastern Sudan. Emerg Infect Dis 2020;26:427–36.
Silva C, Perdigão J, Jordão L, Portugal I. Mycobacterial interspersed repetitive unit typing and mutational profile for multidrug-resistant and extensively drug-resistant tuberculosis surveillance in Portugal: a 3-year period overview. Int J Antimicrob Agents 2014;44:546–51.
Smith I. Mycobacterium tuberculosis Pathogenesis and Molecular Determinants of Virulence. Clin Microbiol Rev 2003;16:463–96.
Solo ES, Nakajima C, Kaile T, Bwalya P, Fukushima Y, Chila S, et al. Mutations of rpoB, katG and inhA genes in multidrug-resistant Mycobacterium tuberculosis isolates from Zambia. J Glob Antimicrob Resist 2020;22:302-7.
Solo ES, Suzuki Y, Kaile T, Bwalya P, Lungu P, Chizimu JY, et al. Characterization of Mycobacterium tuberculosis genotypes and their correlation to multidrug resistance in Lusaka, Zambia. Int J Infect Dis 2021;102:489–96.
Sreevatsan S, Pan X, Stockbauer KE, Connell ND, Kreiswirth BN, Whittam TS, et al. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc Natl Acad Sci U S A 1997;94:9869–74.
Sun H, Zhang C, Xiang L, Pi R, Guo Z, Zheng C, et al. Characterization of mutations in streptomycin-resistant Mycobacterium tuberculosis isolates in Sichuan, China and the association between Beijing-lineage and dual-mutation in gidB. Tuberculosis 2016;96:102–6.
Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rüsch-Gerdes S, Willery E, et al. Proposal for Standardization of Optimized Mycobacterial Interspersed Repetitive Unit – Variable-Number Tandem Repeat Typing of Mycobacterium tuberculosis. J Clin Microbiol 2006;44:4498–510.
Suzuki Y, Katsukawa C, Tamaru A, Abe C, Makino M, Mizuguchi Y, et al. Detection of kanamycin-resistant Mycobacterium tuberculosis by identifying mutations in the 16S rRNA gene. J Clin Microbiol 1998;36:1220–5.
Team Rs. RStudio: Integrated Development for R. RStudio, PBC, Boston, MA 2020.
Telenti A, Philipp WJ, Sreevatsan S, Bernasconi C, Stockbauer KE, Wieles B, et al. The emb operon, a gene cluster of Mycobacterium tuberculosis involved in resistance to ethambutol. Nat Med 1997;3:567–70.
UNAIDS. Tuberculosis and Hiv Tb Is the Leading Cause of Death. vol. 54, p. 20. UAIDS: Geneva, Switzerland: 2018.
Viegas SO, MacHado A, Groenheit R, Ghebremichael S, Pennhag A, Gudo PS, et al. Molecular diversity of Mycobacterium tuberculosis isolates from patients with pulmonary tuberculosis in Mozambique. BMC Microbiol 2010;10:195.
Walker TM, Ip CLC, Harrell RH, Evans JT, Kapatai G, Dedicoat MJ, et al. Whole- genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis 2013;13:137–46.
Walker TM, Merker M, Knoblauch AM, Helbling P, Schoch OD, van der Werf MJ, et al. A cluster of multidrug-resistant Mycobacterium tuberculosis among patients arriving in Europe from the Horn of Africa: a molecular epidemiological study. Lancet Infect Dis 2018;18:431–40.
Weniger T, Krawczyk J, Supply P, Niemann S, Harmsen D. MIRU-VNTRplus: A web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria. vol. 38. 2010.
WHO. Global Tuberculosis Report 2021 2021a. WHO. Global Tuberculosis Programme 2021b. WHO. TB country, regional and global profiles 2021c. WHO. TB profile 2021d.
WHO. WHO consolidated guidelines on tuberculosis Module 4: Treatment Drug-resistant tuberculosis treatment 2020.
WHO. ANNEX 2 Country profiles for 30 high-TB burden countries 2019a.
WHO. Global Tuberculosis Report 2019. 2019b.
WHO. ANNEX 2 Country profiles for 30 high-TB burden countries 2018.
WHO. Annex 2: Country profiles for 30 high-TB burden countries. Glob Tuberc Rep 2017 2017:1–61.
WHO. ANNEX 2 Country profiles for 30 high-TB burden countries 2016.
WHO 2019. Executive summary. 2019.
Wong SY, Lee JS, Kwak HK, Via LE, Boshoff HIM, Barry CE. Mutations in gidB Confer Low-Level Streptomycin Resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2011;55:2515-22.
Xu G, Mao X, Wang J, Pan H. Clustering and recent transmission of Mycobacterium tuberculosis in a Chinese population. Infect Drug Resist 2018;11:323–30.
Xu Y, Cancino-Muñoz I, Torres-Puente M, Villamayor LM, Borrá R, Borrá s-Má ñez M, et al. High-resolution mapping of tuberculosis transmission: Whole genome sequencing and phylogenetic modelling of a cohort from Valencia Region, Spain. PLoS Med. 2019;16:e1002961.
Yu G. Using ggtree to Visualize Data on Tree-Like Structures. Curr Protoc Bioinforma 2020;69:e96.
Yu G, Lam TT-Y, Zhu H, Guan Y. Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree. Mol Biol Evol 2018;35:3041–3.
Yu G, Smith DK, Zhu H, Guan Y, Lam TT-Y. ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol 2017;8:28–36.
論文の公開元へ
