{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T03:54:52Z","timestamp":1790913292842,"version":"4.1.0"},"reference-count":54,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2018,12,1]],"date-time":"2018-12-01T00:00:00Z","timestamp":1543622400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Infect Dis"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1186\/s12879-018-3626-3","type":"journal-article","created":{"date-parts":[[2018,12,29]],"date-time":"2018-12-29T11:11:06Z","timestamp":1546081866000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["First insights on the genetic diversity of MDR Mycobacterium tuberculosis in Lebanon"],"prefix":"10.1186","volume":"18","author":[{"given":"Balig","family":"Panossian","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tamara","family":"Salloum","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George F.","family":"Araj","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Georges","family":"Khazen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3653-8940","authenticated-orcid":false,"given":"Sima","family":"Tokajian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2018,12,29]]},"reference":[{"key":"3626_CR1","unstructured":"WHO, World Health Organization. Global Tuberculosis Report 2017. WHO. :2017 http:\/\/www.who.int\/tb\/publications\/global_report\/gtbr2017_main_text.pdf . Accessed 1 June 2018."},{"key":"3626_CR2","unstructured":"WHO, World Health Organization. Guidelines on the management of latent tuberculosis infection. WHO. 2015; http:\/\/www.who.int\/tb\/publications\/ltbi_document_page\/en\/ . Accessed 1 June 2018."},{"key":"3626_CR3","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1016\/j.smim.2014.09.012","volume":"26","author":"M Coscolla","year":"2014","unstructured":"Coscolla M, Gagneux S. Consequences of genomic diversity in Mycobacterium tuberculosis. Semin Immunol. 2014;26:431\u201344.","journal-title":"Semin Immunol"},{"key":"3626_CR4","doi-asserted-by":"publisher","first-page":"e744","DOI":"10.1371\/journal.pntd.0000744","volume":"9","author":"BC Jong De","year":"2010","unstructured":"De Jong BC, Antonio M, Gagneux S. Mycobacterium africanum\u2014review of an important cause of human tuberculosis in West Africa. PLoS Negl Trop Dis. 2010;9:e744.","journal-title":"PLoS Negl Trop Dis"},{"key":"3626_CR5","first-page":"1","volume":"64","author":"GF Araj","year":"2016","unstructured":"Araj GF, Saade A, Itani LY, Avedissian AZ. Tuberculosis burden in Lebanon: evolution and current status. J Med Liban. 2016;64:1\u20137.","journal-title":"J Med Liban"},{"key":"3626_CR6","doi-asserted-by":"publisher","first-page":"860","DOI":"10.5588\/ijtld.12.0180","volume":"16","author":"F Drobniewski","year":"2012","unstructured":"Drobniewski F, Nikolayevskyy V, Balabanova Y, Bang D, Papaventsis D. Diagnosis of tuberculosis and drug resistance: what can new tools bring us? Int J Tuberc Lung Dis. 2012;16:860\u201370.","journal-title":"Int J Tuberc Lung Dis"},{"key":"3626_CR7","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/S2213-2600(15)00466-X","volume":"4","author":"LJ Pankhurst","year":"2016","unstructured":"Pankhurst LJ, del Ojo EC, Votintseva AA, Walker TM, Cole K, Davies J, et al. Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study. Lancet Respir Med. 2016;4:49\u201358.","journal-title":"Lancet Respir Med"},{"key":"3626_CR8","doi-asserted-by":"publisher","first-page":"1701354","DOI":"10.1183\/13993003.01354-2017","volume":"50","author":"P Miotto","year":"2017","unstructured":"Miotto P, Tessema B, Tagliani E, Chindelevitch L, Starks AM, Emerson C, et al. A standardized method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis. Eur Respir J. 2017;50:1701354.","journal-title":"Eur Respir J"},{"key":"3626_CR9","doi-asserted-by":"publisher","first-page":"621630","DOI":"10.1164\/rccm.201510-2091OC","volume":"194","author":"MR Farhat","year":"2016","unstructured":"Farhat MR, Sultana R, Iartchouk O, Bozeman S, Galagan J, Sisk P, et al. Genetic determinants of drug resistance in Mycobacterium tuberculosis and their diagnostic value. Am J Respir Crit Care Med. 2016;194:621630.","journal-title":"Am J Respir Crit Care Med"},{"key":"3626_CR10","first-page":"786792","volume":"1","author":"J Parkhill","year":"2013","unstructured":"Parkhill J, Dawson R, Diacon AH, van Helden P, Pym A, Mahayiddin A, et al. Whole genome sequencing to establish relapse or reinfection with Mycobacterium tuberculosis: a retrospective observational study. Lancet Respir Med. 2013;1:786792.","journal-title":"Lancet Respir Med"},{"key":"3626_CR11","doi-asserted-by":"publisher","first-page":"11541163","DOI":"10.1093\/infdis\/jiu574","volume":"211","author":"JA Guerra Assun\u00e7\u00e3o","year":"2015","unstructured":"Guerra Assun\u00e7\u00e3o JA, Houben RMGJ, Crampin AC, Mzembe T, Mallard K, Coll F, et al. Recurrence due to relapse or reinfection with Mycobacterium tuberculosis: a whole genome sequencing approach in a large, population based cohort with a high hiv infection prevalence and active follow up. J Infect Dis. 2015;211:11541163.","journal-title":"J Infect Dis"},{"key":"3626_CR12","first-page":"18","volume":"3099","author":"C Yang","year":"2018","unstructured":"Yang C, Lu L, Warren JL, Wu J, Jiang Q, Zuo T, et al. Internal migration and transmission dynamics of tuberculosis in Shanghai, China: an epidemiological, spatial, genomic analysis. Lancet Infect Dis. 2018;3099:18.","journal-title":"Lancet Infect Dis"},{"key":"3626_CR13","doi-asserted-by":"publisher","first-page":"e05166","DOI":"10.7554\/eLife.05166","volume":"4","author":"J Guerra Assun\u00e7\u00e3o","year":"2015","unstructured":"Guerra Assun\u00e7\u00e3o J, Crampin A, Houben R, Mzembe T, Mallard K, Coll F, et al. Largescale whole genome sequencing of M tuberculosis provides insights into transmission in a high prevalencemarea. eLife. 2015;4:e05166.","journal-title":"eLife"},{"key":"3626_CR14","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1186\/1471-2334-13-110","volume":"13","author":"JM Bryant","year":"2013","unstructured":"Bryant JM, Sch\u00fcrch AC, van Deutekom H, Harris SR, de Beer JL, de Jager V, et al. Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data. BMC Infect Dis. 2013;13:110.","journal-title":"BMC Infect Dis"},{"key":"3626_CR15","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1056\/NEJMc1215305","volume":"369","author":"CU K\u00f6ser","year":"2013","unstructured":"K\u00f6ser CU, Bryant JM, Becq J, T\u00f6r\u00f6k ME, Ellington MJ, Marti-Renom MA, et al. Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis. N Engl J Med. 2013;369:290\u20132.","journal-title":"N Engl J Med"},{"key":"3626_CR16","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1186\/s13073-015-0164-0","volume":"7","author":"F Coll","year":"2015","unstructured":"Coll F, McNerney R, Preston MD, GuerraAssun\u00e7\u00e3o JA, Warry A, HillCawthorne G, et al. Rapid determination of antituberculosis drug resistance from whole genome sequences. Genome Med. 2015;7:51.","journal-title":"Genome Med"},{"key":"3626_CR17","doi-asserted-by":"publisher","first-page":"19081914","DOI":"10.1128\/JCM.00025-15","volume":"53","author":"S Feuerriegel","year":"2015","unstructured":"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 ed. K.C. Carroll. J Clin Microbiol. 2015;53:19081914.","journal-title":"J Clin Microbiol"},{"key":"3626_CR18","doi-asserted-by":"publisher","first-page":"10063","DOI":"10.1038\/ncomms10063","volume":"6","author":"P Bradley","year":"2015","unstructured":"Bradley P, Gordon NC, Walker TM, Dunn L, Heys S, Huang B, et al. Rapid antibiotic resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat Commun. 2015;6:10063.","journal-title":"Nat Commun"},{"key":"3626_CR19","doi-asserted-by":"publisher","first-page":"1285","DOI":"10.1128\/JCM.02483-16","volume":"55","author":"AA Votintseva","year":"2017","unstructured":"Votintseva AA, Bradley P, Pankhurst L, del Ojo EC, Loose M, Nilgiriwala K, et al. Same-day diagnostic and surveillance data for tuberculosis via whole-genome sequencing of direct respiratory samples. J Clin Microbiol. 2017;55:1285\u201398.","journal-title":"J Clin Microbiol"},{"key":"3626_CR20","first-page":"877","volume":"4","author":"GF Araj","year":"2000","unstructured":"Araj GF, Talhouk RS, Itani LY, Jaber W, Jamaleddine GW. Comparative performance of PCR-based assay versus microscopy and culture for the direct detection of Mycobacterium tuberculosis in clinical respiratory specimens in Lebanon. Int J Tuberc Lung Dis. 2000;4:877\u201381.","journal-title":"Int J Tuberc Lung Dis."},{"key":"3626_CR21","doi-asserted-by":"publisher","first-page":"e0142951","DOI":"10.1371\/journal.pone.0142951","volume":"10","author":"T Sekizuka","year":"2015","unstructured":"Sekizuka T, Yamashita A, Murase Y, Iwamoto T, Mitarai S, Kato S, Kuroda M. TGS-TB: total genotyping solution for Mycobacterium tuberculosis using short-read whole-genome sequencing. PLoS One. 2015;10:e0142951.","journal-title":"PLoS One"},{"key":"3626_CR22","doi-asserted-by":"publisher","first-page":"881","DOI":"10.1186\/1471-2164-15-881","volume":"15","author":"A Steiner","year":"2014","unstructured":"Steiner A, Stucki D, Coscolla M, Borrell S, Gagneux S. KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes. BMC Genomics. 2014;15:881.","journal-title":"BMC Genomics"},{"key":"3626_CR23","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1186\/1471-2105-15-182","volume":"15","author":"H Jiang","year":"2014","unstructured":"Jiang H, Lei R, Ding SW, Zhu S. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC bioinformatics. 2014;15:182.","journal-title":"BMC bioinformatics"},{"key":"3626_CR24","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1038\/31159","volume":"393","author":"S Cole","year":"1998","unstructured":"Cole S, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998;393:537.","journal-title":"Nature"},{"key":"3626_CR25","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","volume":"26","author":"H Li","year":"2010","unstructured":"Li H, Durbin R. Fast and accurate long-read alignment with burrows\u2013wheeler transform. Bioinformatics. 2010;26:589\u201395.","journal-title":"Bioinformatics"},{"issue":"16","key":"3626_CR26","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment\/map format and SAMtools. Bioinformatics. 2009;25(16):2078\u20139.","journal-title":"Bioinformatics"},{"key":"3626_CR27","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","volume":"30","author":"A Stamatakis","year":"2014","unstructured":"Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312\u20133.","journal-title":"Bioinformatics"},{"key":"3626_CR28","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1093\/nar\/gkw290","volume":"44","author":"I Letunic","year":"2016","unstructured":"Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44:242\u20135.","journal-title":"Nucleic Acids Res"},{"key":"3626_CR29","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1128\/JCM.35.4.907-914.1997","volume":"35","author":"J Kamerbeek","year":"1997","unstructured":"Kamerbeek J, Schouls LE, 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\u201314.","journal-title":"J Clin Microbiol"},{"issue":"1","key":"3626_CR30","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/s13073-016-0270-7","volume":"8","author":"E Xia","year":"2016","unstructured":"Xia E, Teo YY, Ong RT. SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Genome med. 2016;8(1):19.","journal-title":"Genome med"},{"key":"3626_CR31","doi-asserted-by":"publisher","first-page":"e5090","DOI":"10.7717\/peerj.5090","volume":"6","author":"R Rajwani","year":"2018","unstructured":"Rajwani R, Shehzad S, Siu GK. MIRU-profiler: a rapid tool for determination of 24-loci MIRU-VNTR profiles from assembled genomes of Mycobacterium tuberculosis. PeerJ. 2018;6:e5090.","journal-title":"PeerJ"},{"key":"3626_CR32","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1016\/S1473-3099(12)70277-3","volume":"13","author":"TM Walker","year":"2013","unstructured":"Walker TM, Ip CL, 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\u201346.","journal-title":"Lancet Infect Dis"},{"key":"3626_CR33","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1016\/j.tube.2016.02.009","volume":"98","author":"V Nikolayevskyy","year":"2016","unstructured":"Nikolayevskyy V, Kranzer K, Niemann S, Drobniewski F. Whole genome sequencing of Mycobacterium tuberculosis for detection of recent transmission and tracing outbreaks: a systematic review. Tuberculosis. 2016;98:77\u201385.","journal-title":"Tuberculosis"},{"key":"3626_CR34","doi-asserted-by":"publisher","first-page":"12567","DOI":"10.1038\/srep12567","volume":"5","author":"T Roychowdhury","year":"2015","unstructured":"Roychowdhury T, Mandal S, Bhattacharya A. Analysis of IS6110 insertion sites provide a glimpse into genome evolution of Mycobacterium tuberculosis. Sci Rep. 2015;5:12567.","journal-title":"Sci Rep"},{"key":"3626_CR35","doi-asserted-by":"publisher","first-page":"e47113","DOI":"10.1371\/journal.pone.0047113","volume":"7","author":"O Lahlou","year":"2012","unstructured":"Lahlou O, Millet J, Chaoui I, Sabouni R, Filali-Maltouf A, Akrim M, et al. The genotypic population structure of Mycobacterium tuberculosis complex from Moroccan patients reveals a predominance of euro-American lineages. PLoS One. 2012;7:e47113.","journal-title":"PLoS One"},{"key":"3626_CR36","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1038\/ng.2878","volume":"46","author":"N Casali","year":"2014","unstructured":"Casali N, Nikolayevskyy V, Balabanova Y, Harris SR, Ignatyeva O, Kontsevaya I, et al. Evolution and transmission of drug-resistant tuberculosis in a Russian population. Nat Genet. 2014;46:279.","journal-title":"Nat Genet"},{"key":"3626_CR37","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1128\/CMR.00087-12","volume":"26","author":"I Mokrousov","year":"2013","unstructured":"Mokrousov I. Insights into the origin, emergence, and current spread of a successful Russian clone of Mycobacterium tuberculosis. Clin Microbiol Rev. 2013;26:342\u201360.","journal-title":"Clin Microbiol Rev"},{"key":"3626_CR38","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1086\/376837","volume":"188","author":"SS Munsiff","year":"2003","unstructured":"Munsiff SS, Nivin B, Sacajiu G, Mathema B, Bifani P, Kreiswirth BN. Persistence of a highly resistant strain of tuberculosis in new York City during 1990\u20131999. J Infect Dis. 2003;188:356\u201363.","journal-title":"J Infect Dis"},{"key":"3626_CR39","doi-asserted-by":"publisher","first-page":"1252","DOI":"10.1086\/592575","volume":"47","author":"D Cowley","year":"2008","unstructured":"Cowley D, Govender D, February B, Wolfe M, Steyn L, Evans J, et al. Recent and rapid emergence of W-Beijing strains of Mycobacterium tuberculosis in Cape Town. South Africa Clin Infect Dis. 2008;47:1252\u20139.","journal-title":"South Africa Clin Infect Dis"},{"key":"3626_CR40","doi-asserted-by":"publisher","first-page":"784","DOI":"10.1038\/ng.2656","volume":"45","author":"CB Ford","year":"2013","unstructured":"Ford CB, Shah RR, Maeda MK, Gagneux S, Murray MB, Cohen T, et al. Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis. Nat Genet. 2013;45:784.","journal-title":"Nat Genet"},{"key":"3626_CR41","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1016\/j.tube.2011.07.005","volume":"91","author":"M Hanekom","year":"2011","unstructured":"Hanekom M, Van Pittius NG, McEvoy C, Victor TC, Van Helden PD, Warren RM. Mycobacterium tuberculosis Beijing genotype: a template for success. Tuberculosis. 2011;91:510\u201323.","journal-title":"Tuberculosis"},{"key":"3626_CR42","doi-asserted-by":"publisher","first-page":"341","DOI":"10.4103\/0971-5916.182625","volume":"143","author":"P Singhal","year":"2016","unstructured":"Singhal P, Dixit P, Singh P, Jaiswal I, Singh M, Jain A. A study on pre-XDR & XDR tuberculosis & their prevalent genotypes in clinical isolates of Mycobacterium tuberculosis in North India. Indian J Med Res. 2016;143:341.","journal-title":"Indian J Med Res"},{"key":"3626_CR43","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1054\/tube.2002.0332","volume":"82","author":"NV Bhanu","year":"2002","unstructured":"Bhanu NV, Van Soolingen D, Van Embden JD, Dar L, Pandey RM, Seth P. Predominace of a novel Mycobacterium tuberculosis genotype in the Delhi region of India. Tuberculosis. 2002;82:105\u201312.","journal-title":"Tuberculosis"},{"key":"3626_CR44","doi-asserted-by":"publisher","first-page":"e02133","DOI":"10.1128\/mBio.02133-16","volume":"8","author":"MA DeJesus","year":"2017","unstructured":"DeJesus MA, Gerrick ER, Xu W, Park SW, Long JE, Boutte CC, et al. Comprehensive essentiality analysis of the Mycobacterium tuberculosis genome via saturating transposon mutagenesis. MBio. 2017;8:e02133\u201316.","journal-title":"MBio"},{"key":"3626_CR45","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1007\/s11033-016-4084-x","volume":"44","author":"S Thabet","year":"2017","unstructured":"Thabet S, Souissi N. Transposition mechanism, molecular characterization and evolution of IS6110, the specific evolutionary marker of Mycobacterium tuberculosis complex. Mol Biol Rep. 2017;44:25\u201334.","journal-title":"Mol Biol Rep"},{"key":"3626_CR46","doi-asserted-by":"publisher","first-page":"11491","DOI":"10.1073\/pnas.1406693111","volume":"111","author":"J Gonzalo-Asensio","year":"2014","unstructured":"Gonzalo-Asensio J, Malaga W, Pawlik A, Astarie-Dequeker C, Passemar C, Moreau F, et al. Evolutionary history of tuberculosis shaped by conserved mutations in the PhoPR virulence regulator. Proc Natl Acad Sci U S A. 2014;111:11491\u20136.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"3626_CR47","doi-asserted-by":"publisher","first-page":"119","DOI":"10.26719\/2013.19.2.119","volume":"19","author":"N Bedrossian","year":"2013","unstructured":"Bedrossian N, Hamze M, Rahmo AK, Jurjus A, Saliba J, Dabboussi F, et al. Mycobacterium tuberculosis spoligotypes circulating in the Lebanese population: a retrospective study\/Spoligotypes de Mycobacterium tuberculosis circulant dans la population libanaise: Une \u00e9tude r\u00e9trospective. East Mediterr Health J. 2013;19:119.","journal-title":"East Mediterr Health J"},{"key":"3626_CR48","unstructured":"Ministry of Health, Lebanon. National Guidelines for Tuberculosis Prevention, Care and Elimination in LEBANON National TB Programme \u2013 2017. MOPH. 2017. https:\/\/www.moph.gov.lb\/DynamicPages\/download_file\/1721 . Accessed 1 June 2018."},{"key":"3626_CR49","doi-asserted-by":"publisher","first-page":"899","DOI":"10.3201\/eid1906.120543","volume":"19","author":"B M\u00fcller","year":"2013","unstructured":"M\u00fcller B, D\u00fcrr S, Alonso S, Hattendorf J, Laisse CJ, Parsons SD, et al. Zoonotic Mycobacterium bovis\u2013induced tuberculosis in humans. Emerg Infect Dis. 2013;19:899.","journal-title":"Emerg Infect Dis"},{"key":"3626_CR50","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1016\/j.vetmic.2005.11.035","volume":"112","author":"AL Michel","year":"2006","unstructured":"Michel AL, Bengis RG, Keet DF, Hofmeyr M, De Klerk LM, Cross PC, et al. Wildlife tuberculosis in south African conservation areas: implications and challenges. Vet Microbiol. 2006;112:91\u2013100.","journal-title":"Vet Microbiol"},{"key":"3626_CR51","doi-asserted-by":"publisher","first-page":"e21","DOI":"10.1016\/S1473-3099(16)30139-6","volume":"17","author":"F Olea-Popelka","year":"2017","unstructured":"Olea-Popelka F, Muwonge A, Perera A, Dean AS, Mumford E, Erlacher-Vindel E, et al. Zoonotic tuberculosis in human beings caused by Mycobacterium bovis\u2014a call for action. Lancet Infect Dis. 2017;17:e21\u20135.","journal-title":"Lancet Infect Dis"},{"key":"3626_CR52","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1186\/s12916-017-0834-4","volume":"15","author":"AA Witney","year":"2017","unstructured":"Witney AA, Bateson AL, Jindani A, Phillips PP, Coleman D, Stoker NG, et al. Use of whole-genome sequencing to distinguish relapse from reinfection in a completed tuberculosis clinical trial. BMC Med. 2017;15:71.","journal-title":"BMC Med"},{"key":"3626_CR53","doi-asserted-by":"publisher","first-page":"7119","DOI":"10.1038\/ncomms8119","volume":"6","author":"V Eldholm","year":"2015","unstructured":"Eldholm V, Monteserin J, Rieux A, Lopez B, Sobkowiak B, Ritacco V, et al. Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain. Nat Commun. 2015;6:7119.","journal-title":"Nat Commun"},{"key":"3626_CR54","doi-asserted-by":"publisher","first-page":"e1007014","DOI":"10.1371\/journal.ppat.1007014","volume":"14","author":"MB Ismail","year":"2018","unstructured":"Ismail MB, Rafei R, Dabboussi F, Hamze M. Tuberculosis, war, and refugees: spotlight on the Syrian humanitarian crisis. PLoS Pathog. 2018;14:e1007014.","journal-title":"PLoS Pathog"}],"container-title":["BMC Infectious Diseases"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12879-018-3626-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12879-018-3626-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12879-018-3626-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,21]],"date-time":"2020-11-21T00:22:17Z","timestamp":1605918137000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcinfectdis.biomedcentral.com\/articles\/10.1186\/s12879-018-3626-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,12]]},"references-count":54,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["3626"],"URL":"https:\/\/doi.org\/10.1186\/s12879-018-3626-3","relation":{},"ISSN":["1471-2334"],"issn-type":[{"value":"1471-2334","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,12]]},"assertion":[{"value":"9 August 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 December 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 December 2018","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Ethical approval was not required as the clinical isolates were collected and stored as part of routine clinical care. Clinical isolates and patients\u2019 record\/information were anonymized and de-identified prior to analysis and accordingly an informed consent was not needed.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"710"}}