{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T08:20:34Z","timestamp":1777969234006,"version":"3.51.4"},"reference-count":91,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/1471-2164-15-991","type":"journal-article","created":{"date-parts":[[2014,11,18]],"date-time":"2014-11-18T22:02:11Z","timestamp":1416348131000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":56,"title":["Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting"],"prefix":"10.1186","volume":"15","author":[{"given":"Jo\u00e3o","family":"Perdig\u00e3o","sequence":"first","affiliation":[]},{"given":"Hugo","family":"Silva","sequence":"additional","affiliation":[]},{"given":"Diana","family":"Machado","sequence":"additional","affiliation":[]},{"given":"Rita","family":"Macedo","sequence":"additional","affiliation":[]},{"given":"Fernando","family":"Maltez","sequence":"additional","affiliation":[]},{"given":"Carla","family":"Silva","sequence":"additional","affiliation":[]},{"given":"Luisa","family":"Jordao","sequence":"additional","affiliation":[]},{"given":"Isabel","family":"Couto","sequence":"additional","affiliation":[]},{"given":"Kim","family":"Mallard","sequence":"additional","affiliation":[]},{"given":"Francesc","family":"Coll","sequence":"additional","affiliation":[]},{"given":"Grant A","family":"Hill-Cawthorne","sequence":"additional","affiliation":[]},{"given":"Ruth","family":"McNerney","sequence":"additional","affiliation":[]},{"given":"Arnab","family":"Pain","sequence":"additional","affiliation":[]},{"given":"Taane G","family":"Clark","sequence":"additional","affiliation":[]},{"given":"Miguel","family":"Viveiros","sequence":"additional","affiliation":[]},{"given":"Isabel","family":"Portugal","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,11,18]]},"reference":[{"key":"6861_CR1","volume-title":"Tuberculosis surveillance and monitoring in Europe 2012","author":"European Centre for Disease Prevention and Control\/WHO Regional Office for Europe","year":"2012","unstructured":"European Centre for Disease Prevention and Control\/WHO Regional Office for Europe: Tuberculosis surveillance and monitoring in Europe 2012. 2012, Stockholm: European Centre for Disease Prevention and Control"},{"key":"6861_CR2","volume-title":"Global Tuberculosis Control 2012","author":"World Health Organization","year":"2012","unstructured":"World Health Organization: Global Tuberculosis Control 2012. 2012, Geneva: World Health Organization"},{"issue":"6","key":"6861_CR3","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1016\/S1473-3099(13)70030-6","volume":"13","author":"I Abubakar","year":"2013","unstructured":"Abubakar I, Zignol M, Falzon D, Raviglione MC, Ditiu L, Masham S, Adetifa I, Ford N, Cox H, Lawn SD, Marais BJ, McHugh TD, Mwaba P, Bates M, Lipman M, Zijenah L, Logan S, McNerney R, Zumla A, Sarda K, Nahid P, Hoelscher M, Pletschette M, Memish ZA, Kim P, Hafner R, Cole S, Migliori GB, Maeurer M, Schito M, et al: Drug-resistant tuberculosis: time for a visionary political leadership. Lancet Infect Dis. 2013, 13 (6): 529-530. 10.1016\/S1473-3099(13)70030-6.","journal-title":"Lancet Infect Dis"},{"issue":"2","key":"6861_CR4","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1089\/mdr.2008.0798","volume":"14","author":"J Perdigao","year":"2008","unstructured":"Perdigao J, Macedo R, Joao I, Fernandes E, Brum L, Portugal I: Multidrug-resistant tuberculosis in Lisbon, Portugal: a molecular epidemiological perspective. Microb Drug Resist. 2008, 14 (2): 133-143. 10.1089\/mdr.2008.0798.","journal-title":"Microb Drug Resist"},{"issue":"2","key":"6861_CR5","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1093\/jac\/dkp452","volume":"65","author":"J Perdigao","year":"2010","unstructured":"Perdigao J, Macedo R, Malaquias A, Ferreira A, Brum L, Portugal I: Genetic analysis of extensively drug-resistant Mycobacterium tuberculosis strains in Lisbon, Portugal. J Antimicrob Chemother. 2010, 65 (2): 224-227. 10.1093\/jac\/dkp452.","journal-title":"J Antimicrob Chemother"},{"issue":"1","key":"6861_CR6","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/jac\/dks371","volume":"68","author":"J Perdigao","year":"2013","unstructured":"Perdigao J, Macedo R, Silva C, Machado D, Couto I, Viveiros M, Jordao L, Portugal I: From multidrug-resistant to extensively drug-resistant tuberculosis in Lisbon, Portugal: the stepwise mode of resistance acquisition. J Antimicrob Chemother. 2013, 68 (1): 27-33. 10.1093\/jac\/dks371.","journal-title":"J Antimicrob Chemother"},{"issue":"3","key":"6861_CR7","first-page":"207","volume":"3","author":"I Portugal","year":"1999","unstructured":"Portugal I, Covas MJ, Brum L, Viveiros M, Ferrinho P, Moniz-Pereira J, David H: Outbreak of multiple drug-resistant tuberculosis in Lisbon: detection by restriction fragment length polymorphism analysis. Int J Tuberc Lung Dis. 1999, 3 (3): 207-213.","journal-title":"Int J Tuberc Lung Dis"},{"issue":"9","key":"6861_CR8","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1128\/JCM.37.9.3022-3024.1999","volume":"37","author":"I Portugal","year":"1999","unstructured":"Portugal I, Maia S, Moniz-Pereira J: Discrimination of multidrug-resistant Mycobacterium tuberculosis IS6110 fingerprint subclusters by rpoB gene mutation analysis. J Clin Microbiol. 1999, 37 (9): 3022-3024.","journal-title":"J Clin Microbiol"},{"issue":"9","key":"6861_CR9","doi-asserted-by":"publisher","first-page":"1397","DOI":"10.1111\/j.1469-0691.2010.03351.x","volume":"17","author":"J Perdigao","year":"2011","unstructured":"Perdigao J, Macedo R, Silva C, Pinto C, Furtado C, Brum L, Portugal I: Tuberculosis drug-resistance in Lisbon, Portugal: a 6-year overview. Clin Microbiol Infect. 2011, 17 (9): 1397-1402.","journal-title":"Clin Microbiol Infect"},{"issue":"5","key":"6861_CR10","doi-asserted-by":"publisher","first-page":"O278","DOI":"10.1111\/1469-0691.12392","volume":"20","author":"J Perdigao","year":"2014","unstructured":"Perdigao J, Macedo R, Machado D, Silva C, Jordao L, Couto I, Viveiros M, Portugal I: GidB mutation as a phylogenetic marker for Q1 cluster Mycobacterium tuberculosis isolates and intermediate-level streptomycin resistance determinant in Lisbon. Portugal Clin Microbiol Infect. 2014, 20 (5): O278-O284. 10.1111\/1469-0691.12392.","journal-title":"Portugal Clin Microbiol Infect"},{"issue":"5","key":"6861_CR11","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1016\/S1473-3099(07)70108-1","volume":"7","author":"S Gagneux","year":"2007","unstructured":"Gagneux S, Small PM: Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infect Dis. 2007, 7 (5): 328-337. 10.1016\/S1473-3099(07)70108-1.","journal-title":"Lancet Infect Dis"},{"issue":"12","key":"6861_CR12","doi-asserted-by":"publisher","first-page":"e311","DOI":"10.1371\/journal.pbio.0060311","volume":"6","author":"R Hershberg","year":"2008","unstructured":"Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, Homolka S, Roach JC, Kremer K, Petrov DA, Feldman MW, Gagneux S: High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol. 2008, 6 (12): e311-10.1371\/journal.pbio.0060311.","journal-title":"PLoS Biol"},{"issue":"10","key":"6861_CR13","doi-asserted-by":"publisher","first-page":"e7407","DOI":"10.1371\/journal.pone.0007407","volume":"4","author":"S Niemann","year":"2009","unstructured":"Niemann S, Koser CU, Gagneux S, Plinke C, Homolka S, Bignell H, Carter RJ, Cheetham RK, Cox A, Gormley NA, Kokko-Gonzales P, Murray LJ, Rigatti R, Smith VP, Arends FP, Cox HS, Smith G, Archer JA: Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints. PLoS One. 2009, 4 (10): e7407-10.1371\/journal.pone.0007407.","journal-title":"PLoS One"},{"issue":"18","key":"6861_CR14","doi-asserted-by":"publisher","first-page":"9869","DOI":"10.1073\/pnas.94.18.9869","volume":"94","author":"S Sreevatsan","year":"1997","unstructured":"Sreevatsan S, Pan X, Stockbauer KE, Connell ND, Kreiswirth BN, Whittam TS, Musser JM: Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc Natl Acad Sci U S A. 1997, 94 (18): 9869-9874. 10.1073\/pnas.94.18.9869.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"14","key":"6861_CR15","doi-asserted-by":"publisher","first-page":"3645","DOI":"10.1128\/JB.00166-10","volume":"192","author":"TR Ioerger","year":"2010","unstructured":"Ioerger TR, Feng Y, Ganesula K, Chen X, Dobos KM, Fortune S, Jacobs WR, Mizrahi V, Parish T, Rubin E, Sassetti C, Sacchettini JC: Variation among genome sequences of H37Rv strains of Mycobacterium tuberculosis from multiple laboratories. J Bacteriol. 2010, 192 (14): 3645-3653. 10.1128\/JB.00166-10.","journal-title":"J Bacteriol"},{"issue":"3","key":"6861_CR16","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1016\/j.tube.2011.11.003","volume":"92","author":"C Ford","year":"2012","unstructured":"Ford C, Yusim K, Ioerger T, Feng S, Chase M, Greene M, Korber B, Fortune S: Mycobacterium tuberculosis--heterogeneity revealed through whole genome sequencing. Tuberculosis (Edinburgh, Scotland). 2012, 92 (3): 194-201. 10.1016\/j.tube.2011.11.003.","journal-title":"Tuberculosis (Edinburgh, Scotland)"},{"issue":"1","key":"6861_CR17","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1016\/j.meegid.2009.10.002","volume":"10","author":"AC Schurch","year":"2009","unstructured":"Schurch AC, Kremer K, Kiers A, Daviena O, Boeree MJ, Siezen RJ, Smith NH, van Soolingen D: The tempo and mode of molecular evolution of Mycobacterium tuberculosis at patient-to-patient scale. Infect Genet Evol. 2009, 10 (1): 108-114.","journal-title":"Infect Genet Evol"},{"issue":"4","key":"6861_CR18","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1101\/gr.128678.111","volume":"22","author":"N Casali","year":"2012","unstructured":"Casali N, Nikolayevskyy V, Balabanova Y, Ignatyeva O, Kontsevaya I, Harris SR, Bentley SD, Parkhill J, Nejentsev S, Hoffner SE, Horstmann RD, Brown T, Drobniewski F: Microevolution of extensively drug-resistant tuberculosis in Russia. Genome Res. 2012, 22 (4): 735-745. 10.1101\/gr.128678.111.","journal-title":"Genome Res"},{"issue":"11","key":"6861_CR19","doi-asserted-by":"publisher","first-page":"e7778","DOI":"10.1371\/journal.pone.0007778","volume":"4","author":"TR Ioerger","year":"2009","unstructured":"Ioerger TR, Koo S, No EG, Chen X, Larsen MH, Jacobs WR, Pillay M, Sturm AW, Sacchettini JC: Genome analysis of multi- and extensively-drug-resistant tuberculosis from KwaZulu-Natal. South Africa PLoS One. 2009, 4 (11): e7778-10.1371\/journal.pone.0007778.","journal-title":"South Africa PLoS One"},{"issue":"2","key":"6861_CR20","doi-asserted-by":"publisher","first-page":"759","DOI":"10.1128\/JB.188.2.759-772.2006","volume":"188","author":"I Filliol","year":"2006","unstructured":"Filliol I, Motiwala AS, Cavatore M, Qi W, Hazbon MH, Bobadilla del Valle M, Fyfe J, Garcia-Garcia L, Rastogi N, Sola C, Zozio T, Guerrero MI, Leon CI, Crabtree J, Angiuoli S, Eisenach KD, Durmaz R, Joloba ML, Rendon A, Sifuentes-Osornio J, Ponce De Leon A, Cave MD, Fleischmann R, Whittam TS, Alland D: Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set. J Bacteriol. 2006, 188 (2): 759-772. 10.1128\/JB.188.2.759-772.2006.","journal-title":"J Bacteriol"},{"issue":"12","key":"6861_CR21","doi-asserted-by":"publisher","first-page":"3891","DOI":"10.1128\/JCM.01394-07","volume":"45","author":"LC Lazzarini","year":"2007","unstructured":"Lazzarini LC, Huard RC, Boechat NL, Gomes HM, Oelemann MC, Kurepina N, Shashkina E, Mello FC, Gibson AL, Virginio MJ, Marsico AG, Butler WR, Kreiswirth BN, Suffys PN, Lapa ESJR, Ho JL: Discovery of a novel Mycobacterium tuberculosis lineage that is a major cause of tuberculosis in Rio de Janeiro, Brazil. J Clin Microbiol. 2007, 45 (12): 3891-3902. 10.1128\/JCM.01394-07.","journal-title":"J Clin Microbiol"},{"issue":"14","key":"6861_CR22","doi-asserted-by":"publisher","first-page":"4865","DOI":"10.1073\/pnas.0305634101","volume":"101","author":"AG Tsolaki","year":"2004","unstructured":"Tsolaki AG, Hirsh AE, DeRiemer K, Enciso JA, Wong MZ, Hannan M, Goguet de la Salmoniere YO, Aman K, Kato-Maeda M, Small PM: Functional and evolutionary genomics of Mycobacterium tuberculosis: insights from genomic deletions in 100 strains. Proc Natl Acad Sci U S A. 2004, 101 (14): 4865-4870. 10.1073\/pnas.0305634101.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"8","key":"6861_CR23","doi-asserted-by":"publisher","first-page":"2869","DOI":"10.1073\/pnas.0511240103","volume":"103","author":"S Gagneux","year":"2006","unstructured":"Gagneux S, DeRiemer K, Van T, Kato-Maeda M, de Jong BC, Narayanan S, Nicol M, Niemann S, Kremer K, Gutierrez MC, Hilty M, Hopewell PC, Small PM: Variable host-pathogen compatibility in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2006, 103 (8): 2869-2873. 10.1073\/pnas.0511240103.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"4","key":"6861_CR24","doi-asserted-by":"publisher","first-page":"1259","DOI":"10.1128\/JCM.02231-07","volume":"46","author":"AL Gibson","year":"2008","unstructured":"Gibson AL, Huard RC, Gey van Pittius NC, Lazzarini LC, Driscoll J, Kurepina N, Zozio T, Sola C, Spindola SM, Kritski AL, Fitzgerald D, Kremer K, Mardassi H, Chitale P, Brinkworth J, Garcia de Viedma D, Gicquel B, Pape JW, van Soolingen D, Kreiswirth BN, Warren RM, Van Helden PD, Rastogi N, Suffys PN, Lapa e Silva J, Ho JL: Application of sensitive and specific molecular methods to uncover global dissemination of the major RDRio Sublineage of the Latin American-Mediterranean Mycobacterium tuberculosis spoligotype family. J Clin Microbiol. 2008, 46 (4): 1259-1267. 10.1128\/JCM.02231-07.","journal-title":"J Clin Microbiol"},{"issue":"16","key":"6861_CR25","doi-asserted-by":"publisher","first-page":"4430","DOI":"10.1128\/JB.00453-12","volume":"194","author":"GK Madhavilatha","year":"2012","unstructured":"Madhavilatha GK, Joseph BV, Paul LK, Kumar RA, Hariharan R, Mundayoor S: Whole-genome sequences of two clinical isolates of Mycobacterium tuberculosis from Kerala, South India. J Bacteriol. 2012, 194 (16): 4430-10.1128\/JB.00453-12.","journal-title":"J Bacteriol"},{"issue":"5","key":"6861_CR26","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1007\/s00284-006-0135-1","volume":"53","author":"S Srivastava","year":"2006","unstructured":"Srivastava S, Garg A, Ayyagari A, Nyati KK, Dhole TN, Dwivedi SK: Nucleotide polymorphism associated with ethambutol resistance in clinical isolates of Mycobacterium tuberculosis. Curr Microbiol. 2006, 53 (5): 401-405. 10.1007\/s00284-006-0135-1.","journal-title":"Curr Microbiol"},{"issue":"8","key":"6861_CR27","doi-asserted-by":"publisher","first-page":"1728","DOI":"10.1093\/jac\/dkt090","volume":"68","author":"D Machado","year":"2013","unstructured":"Machado D, Perdigao J, Ramos J, Couto I, Portugal I, Ritter C, Boettger EC, Viveiros M: High-level resistance to isoniazid and ethionamide in multidrug-resistant Mycobacterium tuberculosis of the Lisboa family is associated with inhA double mutations. J Antimicrob Chemother. 2013, 68 (8): 1728-1732. 10.1093\/jac\/dkt090.","journal-title":"J Antimicrob Chemother"},{"issue":"5782","key":"6861_CR28","doi-asserted-by":"publisher","first-page":"1944","DOI":"10.1126\/science.1124410","volume":"312","author":"S Gagneux","year":"2006","unstructured":"Gagneux S, Long CD, Small PM, Van T, Schoolnik GK, Bohannan BJ: The competitive cost of antibiotic resistance in Mycobacterium tuberculosis. Science (New York, NY). 2006, 312 (5782): 1944-1946. 10.1126\/science.1124410.","journal-title":"Science (New York, NY)"},{"issue":"1","key":"6861_CR29","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1038\/ng.1038","volume":"44","author":"I Comas","year":"2012","unstructured":"Comas I, Borrell S, Roetzer A, Rose G, Malla B, Kato-Maeda M, Galagan J, Niemann S, Gagneux S: Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nat Genet. 2012, 44 (1): 106-110.","journal-title":"Nat Genet"},{"issue":"2","key":"6861_CR30","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1128\/AAC.01541-12","volume":"57","author":"M de Vos","year":"2012","unstructured":"de Vos M, Muller B, Borrell S, Black P, van Helden P, Warren R, Gagneux S, Victor T: Putative compensatory mutations in the rpoC gene of rifampicin-resistant Mycobacterium tuberculosis are associated with ongoing transmission. Antimicrob Agents Chemother. 2012, 57 (2): 827-832.","journal-title":"Antimicrob Agents Chemother"},{"issue":"7","key":"6861_CR31","doi-asserted-by":"publisher","first-page":"1073","DOI":"10.1038\/nprot.2009.86","volume":"4","author":"P Kumar","year":"2009","unstructured":"Kumar P, Henikoff S, Ng PC: Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009, 4 (7): 1073-1081.","journal-title":"Nat Protoc"},{"issue":"6","key":"6861_CR32","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1016\/j.tube.2008.03.006","volume":"88","author":"Y Casart","year":"2008","unstructured":"Casart Y, Turcios L, Florez I, Jaspe R, Guerrero E, de Waard J, Aguilar D, Hernandez-Pando R, Salazar L: IS6110 in oriC affects the morphology and growth of Mycobacterium tuberculosis and attenuates virulence in mice. Tuberculosis (Edinburgh, Scotland). 2008, 88 (6): 545-552. 10.1016\/j.tube.2008.03.006.","journal-title":"Tuberculosis (Edinburgh, Scotland)"},{"issue":"1","key":"6861_CR33","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1128\/JCM.42.1.212-219.2004","volume":"42","author":"CY Soto","year":"2004","unstructured":"Soto CY, Menendez MC, Perez E, Samper S, Gomez AB, Garcia MJ, Martin C: IS6110 mediates increased transcription of the phoP virulence gene in a multidrug-resistant clinical isolate responsible for tuberculosis outbreaks. J Clin Microbiol. 2004, 42 (1): 212-219. 10.1128\/JCM.42.1.212-219.2004.","journal-title":"J Clin Microbiol"},{"issue":"5","key":"6861_CR34","doi-asserted-by":"publisher","first-page":"2148","DOI":"10.1128\/JCM.43.5.2148-2154.2005","volume":"43","author":"N Kurepina","year":"2005","unstructured":"Kurepina N, Likhoshvay E, Shashkina E, Mathema B, Kremer K, van Soolingen D, Bifani P, Kreiswirth BN: Targeted hybridization of IS6110 fingerprints identifies the W-Beijing Mycobacterium tuberculosis strains among clinical isolates. J Clin Microbiol. 2005, 43 (5): 2148-2154. 10.1128\/JCM.43.5.2148-2154.2005.","journal-title":"J Clin Microbiol"},{"issue":"6","key":"6861_CR35","doi-asserted-by":"crossref","first-page":"1542","DOI":"10.1128\/jcm.32.6.1542-1546.1994","volume":"32","author":"BB Plikaytis","year":"1994","unstructured":"Plikaytis BB, Marden JL, Crawford JT, Woodley CL, Butler WR, Shinnick TM: Multiplex PCR assay specific for the multidrug-resistant strain W of Mycobacterium tuberculosis. J Clin Microbiol. 1994, 32 (6): 1542-1546.","journal-title":"J Clin Microbiol"},{"issue":"4","key":"6861_CR36","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1101\/gr.129544.111","volume":"22","author":"A Namouchi","year":"2012","unstructured":"Namouchi A, Didelot X, Schock U, Gicquel B, Rocha EP: After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection. Genome Res. 2012, 22 (4): 721-734. 10.1101\/gr.129544.111.","journal-title":"Genome Res"},{"issue":"1","key":"6861_CR37","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1128\/JCM.02483-05","volume":"45","author":"D Alland","year":"2007","unstructured":"Alland D, Lacher DW, Hazbon MH, Motiwala AS, Qi W, Fleischmann RD, Whittam TS: Role of large sequence polymorphisms (LSPs) in generating genomic diversity among clinical isolates of Mycobacterium tuberculosis and the utility of LSPs in phylogenetic analysis. J Clin Microbiol. 2007, 45 (1): 39-46. 10.1128\/JCM.02483-05.","journal-title":"J Clin Microbiol"},{"issue":"5","key":"6861_CR38","first-page":"568","volume":"8","author":"J Lin","year":"2004","unstructured":"Lin J, Sattar AN, Puckree T: An alarming rate of drug-resistant tuberculosis at Ngwelezane Hospital in northern KwaZulu Natal, South Africa. Int J Tuberc Lung Dis. 2004, 8 (5): 568-573.","journal-title":"Int J Tuberc Lung Dis"},{"issue":"11","key":"6861_CR39","doi-asserted-by":"publisher","first-page":"1409","DOI":"10.1086\/522987","volume":"45","author":"M Pillay","year":"2007","unstructured":"Pillay M, Sturm AW: Evolution of the extensively drug-resistant F15\/LAM4\/KZN strain of Mycobacterium tuberculosis in KwaZulu-Natal, South Africa. Clin Infect Dis. 2007, 45 (11): 1409-1414. 10.1086\/522987.","journal-title":"Clin Infect Dis"},{"issue":"4","key":"6861_CR40","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1016\/j.meegid.2012.02.004","volume":"12","author":"C Demay","year":"2012","unstructured":"Demay C, Liens B, Burguiere T, Hill V, Couvin D, Millet J, Mokrousov I, Sola C, Zozio T, Rastogi N: SITVITWEB\u2013a publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology. Infect Genet Evol. 2012, 12 (4): 755-766. 10.1016\/j.meegid.2012.02.004.","journal-title":"Infect Genet Evol"},{"issue":"7","key":"6861_CR41","doi-asserted-by":"publisher","first-page":"2175","DOI":"10.1128\/JCM.00065-08","volume":"46","author":"LC Lazzarini","year":"2008","unstructured":"Lazzarini LC, Spindola SM, Bang H, Gibson AL, Weisenberg S, da Silva CW, Augusto CJ, Huard RC, Kritski AL, Ho JL: RDRio Mycobacterium tuberculosis infection is associated with a higher frequency of cavitary pulmonary disease. J Clin Microbiol. 2008, 46 (7): 2175-2183. 10.1128\/JCM.00065-08.","journal-title":"J Clin Microbiol"},{"issue":"1","key":"6861_CR42","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1016\/j.biochi.2011.09.026","volume":"94","author":"Y Akhter","year":"2012","unstructured":"Akhter Y, Ehebauer MT, Mukhopadhyay S, Hasnain SE: The PE\/PPE multigene family codes for virulence factors and is a possible source of mycobacterial antigenic variation: perhaps more?. Biochimie. 2012, 94 (1): 110-116. 10.1016\/j.biochi.2011.09.026.","journal-title":"Biochimie"},{"issue":"5","key":"6861_CR43","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1016\/j.tube.2011.04.004","volume":"91","author":"S Mukhopadhyay","year":"2011","unstructured":"Mukhopadhyay S, Balaji KN: The PE and PPE proteins of Mycobacterium tuberculosis. Tuberculosis (Edinburgh, Scotland). 2011, 91 (5): 441-447. 10.1016\/j.tube.2011.04.004.","journal-title":"Tuberculosis (Edinburgh, Scotland)"},{"issue":"9151","key":"6861_CR44","doi-asserted-by":"publisher","first-page":"444","DOI":"10.1016\/S0140-6736(98)03406-0","volume":"353","author":"MA Behr","year":"1999","unstructured":"Behr MA, Warren SA, Salamon H, Hopewell PC, Ponce de Leon A, Daley CL, Small PM: Transmission of Mycobacterium tuberculosis from patients smear-negative for acid-fast bacilli. Lancet. 1999, 353 (9151): 444-449. 10.1016\/S0140-6736(98)03406-0.","journal-title":"Lancet"},{"issue":"4","key":"6861_CR45","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1136\/thx.2003.011759","volume":"59","author":"E Hernandez-Garduno","year":"2004","unstructured":"Hernandez-Garduno E, Cook V, Kunimoto D, Elwood RK, Black WA, FitzGerald JM: Transmission of tuberculosis from smear negative patients: a molecular epidemiology study. Thorax. 2004, 59 (4): 286-290. 10.1136\/thx.2003.011759.","journal-title":"Thorax"},{"issue":"9","key":"6861_CR46","doi-asserted-by":"publisher","first-page":"1135","DOI":"10.1086\/591974","volume":"47","author":"A Tostmann","year":"2008","unstructured":"Tostmann A, Kik SV, Kalisvaart NA, Sebek MM, Verver S, Boeree MJ, van Soolingen D: Tuberculosis transmission by patients with smear-negative pulmonary tuberculosis in a large cohort in the Netherlands. Clin Infect Dis. 2008, 47 (9): 1135-1142. 10.1086\/591974.","journal-title":"Clin Infect Dis"},{"issue":"11","key":"6861_CR47","doi-asserted-by":"publisher","first-page":"6338","DOI":"10.1128\/IAI.71.11.6338-6343.2003","volume":"71","author":"RK Choudhary","year":"2003","unstructured":"Choudhary RK, Mukhopadhyay S, Chakhaiyar P, Sharma N, Murthy KJ, Katoch VM, Hasnain SE: PPE antigen Rv2430c of Mycobacterium tuberculosis induces a strong B-cell response. Infect Immun. 2003, 71 (11): 6338-6343. 10.1128\/IAI.71.11.6338-6343.2003.","journal-title":"Infect Immun"},{"issue":"10","key":"6861_CR48","doi-asserted-by":"publisher","first-page":"e3586","DOI":"10.1371\/journal.pone.0003586","volume":"3","author":"S Tundup","year":"2008","unstructured":"Tundup S, Pathak N, Ramanadham M, Mukhopadhyay S, Murthy KJ, Ehtesham NZ, Hasnain SE: The co-operonic PE25\/PPE41 protein complex of Mycobacterium tuberculosis elicits increased humoral and cell mediated immune response. PLoS One. 2008, 3 (10): e3586-10.1371\/journal.pone.0003586.","journal-title":"PLoS One"},{"issue":"6","key":"6861_CR49","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1128\/AAC.06460-11","volume":"56","author":"L Fenner","year":"2012","unstructured":"Fenner L, Egger M, Bodmer T, Altpeter E, Zwahlen M, Jaton K, Pfyffer GE, Borrell S, Dubuis O, Bruderer T, Siegrist HH, Furrer H, Calmy A, Fehr J, Stalder JM, Ninet B, Bottger EC, Gagneux S: Effect of mutation and genetic background on drug resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2012, 56 (6): 3047-3053. 10.1128\/AAC.06460-11.","journal-title":"Antimicrob Agents Chemother"},{"issue":"11","key":"6861_CR50","doi-asserted-by":"publisher","first-page":"4157","DOI":"10.1128\/AAC.00619-07","volume":"51","author":"M Brimacombe","year":"2007","unstructured":"Brimacombe M, Hazbon M, Motiwala AS, Alland D: Antibiotic resistance and single-nucleotide polymorphism cluster grouping type in a multinational sample of resistant Mycobacterium tuberculosis isolates. Antimicrob Agents Chemother. 2007, 51 (11): 4157-4159. 10.1128\/AAC.00619-07.","journal-title":"Antimicrob Agents Chemother"},{"issue":"8","key":"6861_CR51","doi-asserted-by":"publisher","first-page":"3192","DOI":"10.1128\/AAC.49.8.3192-3197.2005","volume":"49","author":"CE Maus","year":"2005","unstructured":"Maus CE, Plikaytis BB, Shinnick TM: Molecular analysis of cross-resistance to capreomycin, kanamycin, amikacin, and viomycin in Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2005, 49 (8): 3192-3197. 10.1128\/AAC.49.8.3192-3197.2005.","journal-title":"Antimicrob Agents Chemother"},{"issue":"11","key":"6861_CR52","first-page":"1347","volume":"13","author":"ET Richardson","year":"2009","unstructured":"Richardson ET, Lin SY, Pinsky BA, Desmond E, Banaei N: First documentation of isoniazid reversion in Mycobacterium tuberculosis. Int J Tuberc Lung Dis. 2009, 13 (11): 1347-1354.","journal-title":"Int J Tuberc Lung Dis"},{"issue":"1","key":"6861_CR53","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1111\/j.1365-2958.2012.08099.x","volume":"85","author":"G Brandis","year":"2012","unstructured":"Brandis G, Wrande M, Liljas L, Hughes D: Fitness-compensatory mutations in rifampicin-resistant RNA polymerase. Mol Microbiol. 2012, 85 (1): 142-151. 10.1111\/j.1365-2958.2012.08099.x.","journal-title":"Mol Microbiol"},{"issue":"10","key":"6861_CR54","doi-asserted-by":"publisher","first-page":"1183","DOI":"10.1038\/ng.2747","volume":"45","author":"MR Farhat","year":"2013","unstructured":"Farhat MR, Shapiro BJ, Kieser KJ, Sultana R, Jacobson KR, Victor TC, Warren RM, Streicher EM, Calver A, Sloutsky A, Kaur D, Posey JE, Plikaytis B, Oggioni MR, Gardy JL, Johnston JC, Rodrigues M, Tang PK, Kato-Maeda M, Borowsky ML, Muddukrishna B, Kreiswirth BN, Kurepina N, Galagan J, Gagneux S, Birren B, Rubin EJ, Lander ES, Sabeti PC, Murray M: Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat Genet. 2013, 45 (10): 1183-1189. 10.1038\/ng.2747.","journal-title":"Nat Genet"},{"issue":"9","key":"6861_CR55","doi-asserted-by":"publisher","first-page":"e1000483","DOI":"10.1371\/journal.pbio.1000483","volume":"8","author":"N Opalka","year":"2010","unstructured":"Opalka N, Brown J, Lane WJ, Twist KA, Landick R, Asturias FJ, Darst SA: Complete structural model of Escherichia coli RNA polymerase from a hybrid approach. PLoS Biol. 2010, 8 (9): e1000483-10.1371\/journal.pbio.1000483.","journal-title":"PLoS Biol"},{"issue":"1","key":"6861_CR56","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1128\/JCM.39.1.107-110.2001","volume":"39","author":"M Heep","year":"2001","unstructured":"Heep M, Brandstatter B, Rieger U, Lehn N, Richter E, Rusch-Gerdes S, Niemann S: Frequency of rpoB mutations inside and outside the cluster I region in rifampin-resistant clinical Mycobacterium tuberculosis isolates. J Clin Microbiol. 2001, 39 (1): 107-110. 10.1128\/JCM.39.1.107-110.2001.","journal-title":"J Clin Microbiol"},{"issue":"4","key":"6861_CR57","doi-asserted-by":"publisher","first-page":"730","DOI":"10.1093\/jac\/dkq519","volume":"66","author":"GK Siu","year":"2011","unstructured":"Siu GK, Zhang Y, Lau TC, Lau RW, Ho PL, Yew WW, Tsui SK, Cheng VC, Yuen KY, Yam WC: Mutations outside the rifampicin resistance-determining region associated with rifampicin resistance in Mycobacterium tuberculosis. J Antimicrob Chemother. 2011, 66 (4): 730-733. 10.1093\/jac\/dkq519.","journal-title":"J Antimicrob Chemother"},{"issue":"5268","key":"6861_CR58","doi-asserted-by":"publisher","first-page":"1641","DOI":"10.1126\/science.272.5268.1641","volume":"272","author":"DR Sherman","year":"1996","unstructured":"Sherman DR, Mdluli K, Hickey MJ, Arain TM, Morris SL, Barry CE, Stover CK: Compensatory ahpC gene expression in isoniazid-resistant Mycobacterium tuberculosis. Science (New York, NY). 1996, 272 (5268): 1641-1643. 10.1126\/science.272.5268.1641.","journal-title":"Science (New York, NY)"},{"issue":"4","key":"6861_CR59","doi-asserted-by":"publisher","first-page":"830","DOI":"10.1111\/j.1365-2958.2010.07218.x","volume":"7","author":"D Shcherbakov","year":"2010","unstructured":"Shcherbakov D, Akbergenov R, Matt T, Sander P, Andersson DI, Bottger EC: Directed mutagenesis of Mycobacterium smegmatis 16S rRNA to reconstruct the in-vivo evolution of aminoglycoside resistance in Mycobacterium tuberculosis. Mol Microbiol. 2010, 7 (4): 830-840.","journal-title":"Mol Microbiol"},{"issue":"6","key":"6861_CR60","doi-asserted-by":"publisher","first-page":"e61","DOI":"10.1371\/journal.ppat.0020061","volume":"2","author":"S Gagneux","year":"2006","unstructured":"Gagneux S, Burgos MV, DeRiemer K, Encisco A, Munoz S, Hopewell PC, Small PM, Pym AS: Impact of bacterial genetics on the transmission of isoniazid-resistant Mycobacterium tuberculosis. PLoS Pathog. 2006, 2 (6): e61-10.1371\/journal.ppat.0020061.","journal-title":"PLoS Pathog"},{"issue":"10","key":"6861_CR61","doi-asserted-by":"publisher","first-page":"1190","DOI":"10.1038\/ng.2743","volume":"45","author":"H Safi","year":"2013","unstructured":"Safi H, Lingaraju S, Amin A, Kim S, Jones M, Holmes M, McNeil M, Peterson SN, Chatterjee D, Fleischmann R, Alland D: Evolution of high-level ethambutol-resistant tuberculosis through interacting mutations in decaprenylphosphoryl-beta-D-arabinose biosynthetic and utilization pathway genes. Nat Genet. 2013, 45 (10): 1190-1197. 10.1038\/ng.2743.","journal-title":"Nat Genet"},{"issue":"10","key":"6861_CR62","doi-asserted-by":"publisher","first-page":"1255","DOI":"10.1038\/ng.2735","volume":"45","author":"H Zhang","year":"2013","unstructured":"Zhang H, Li D, Zhao L, Fleming J, Lin N, Wang T, Liu Z, Li C, Galwey N, Deng J, Zhou Y, Zhu Y, Gao Y, Wang S, Huang Y, Wang M, Zhong Q, Zhou L, Chen T, Zhou J, Yang R, Zhu G, Hang H, Zhang J, Li F, Wan K, Wang J, Zhang XE, Bi L: Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance. Nat Genet. 2013, 45 (10): 1255-1260. 10.1038\/ng.2735.","journal-title":"Nat Genet"},{"issue":"4","key":"6861_CR63","doi-asserted-by":"publisher","first-page":"1238","DOI":"10.1086\/314979","volume":"180","author":"AS de Boer","year":"1999","unstructured":"de Boer AS, Borgdorff MW, de Haas PE, Nagelkerke NJ, van Embden JD, van Soolingen D: Analysis of rate of change of IS6110 RFLP patterns of Mycobacterium tuberculosis based on serial patient isolates. J Infect Dis. 1999, 180 (4): 1238-1244. 10.1086\/314979.","journal-title":"J Infect Dis"},{"issue":"4","key":"6861_CR64","doi-asserted-by":"publisher","first-page":"1107","DOI":"10.1086\/517406","volume":"177","author":"RW Yeh","year":"1998","unstructured":"Yeh RW, Ponce de Leon A, Agasino CB, Hahn JA, Daley CL, Hopewell PC, Small PM: Stability of Mycobacterium tuberculosis DNA genotypes. J Infect Dis. 1998, 177 (4): 1107-1111. 10.1086\/517406.","journal-title":"J Infect Dis"},{"issue":"9","key":"6861_CR65","doi-asserted-by":"publisher","first-page":"3423","DOI":"10.1128\/JCM.39.9.3423-3424.2001","volume":"39","author":"S Sampson","year":"2001","unstructured":"Sampson S, Warren R, Richardson M, van der Spuy G, van Helden P: IS6110 insertions in Mycobacterium tuberculosis: predominantly into coding regions. J Clin Microbiol. 2001, 39 (9): 3423-3424. 10.1128\/JCM.39.9.3423-3424.2001.","journal-title":"J Clin Microbiol"},{"issue":"6685","key":"6861_CR66","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1038\/31159","volume":"393","author":"ST Cole","year":"1998","unstructured":"Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Krogh A, McLean J, Moule S, Murphy L, Oliver K, Osborne J, et al: Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998, 393 (6685): 537-544. 10.1038\/31159.","journal-title":"Nature"},{"issue":"12","key":"6861_CR67","doi-asserted-by":"publisher","first-page":"2195","DOI":"10.1093\/molbev\/msh234","volume":"21","author":"MM Tanaka","year":"2004","unstructured":"Tanaka MM, Rosenberg NA, Small PM: The control of copy number of IS6110 in Mycobacterium tuberculosis. Mol Biol Evol. 2004, 21 (12): 2195-2201. 10.1093\/molbev\/msh234.","journal-title":"Mol Biol Evol"},{"issue":"4","key":"6861_CR68","doi-asserted-by":"publisher","first-page":"999","DOI":"10.1111\/j.1365-2958.2004.04037.x","volume":"52","author":"H Safi","year":"2004","unstructured":"Safi H, Barnes PF, Lakey DL, Shams H, Samten B, Vankayalapati R, Howard ST: IS6110 functions as a mobile, monocyte-activated promoter in Mycobacterium tuberculosis. Mol Microbiol. 2004, 52 (4): 999-1012. 10.1111\/j.1365-2958.2004.04037.x.","journal-title":"Mol Microbiol"},{"issue":"1","key":"6861_CR69","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1016\/j.meegid.2010.09.011","volume":"11","author":"N Thorne","year":"2011","unstructured":"Thorne N, Borrell S, Evans J, Magee J, Garcia de Viedma D, Bishop C, Gonzalez-Martin J, Gharbia S, Arnold C: IS6110-based global phylogeny of Mycobacterium tuberculosis. Infect Genet Evol. 2011, 11 (1): 132-138. 10.1016\/j.meegid.2010.09.011.","journal-title":"Infect Genet Evol"},{"issue":"5","key":"6861_CR70","doi-asserted-by":"publisher","first-page":"R89","DOI":"10.1186\/gb-2007-8-5-r89","volume":"8","author":"DJ Beste","year":"2007","unstructured":"Beste DJ, Hooper T, Stewart G, Bonde B, Avignone-Rossa C, Bushell ME, Wheeler P, Klamt S, Kierzek AM, McFadden J: GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism. Genome Biol. 2007, 8 (5): R89-10.1186\/gb-2007-8-5-r89.","journal-title":"Genome Biol"},{"key":"6861_CR71","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1186\/1752-0509-4-160","volume":"4","author":"X Fang","year":"2010","unstructured":"Fang X, Wallqvist A, Reifman J: Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis. BMC Syst Biol. 2010, 4: 160-10.1186\/1752-0509-4-160.","journal-title":"BMC Syst Biol"},{"key":"6861_CR72","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1186\/1752-0509-1-26","volume":"1","author":"N Jamshidi","year":"2007","unstructured":"Jamshidi N, Palsson BO: Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. BMC Syst Biol. 2007, 1: 26-10.1186\/1752-0509-1-26.","journal-title":"BMC Syst Biol"},{"issue":"14","key":"6861_CR73","doi-asserted-by":"publisher","first-page":"4871","DOI":"10.1073\/pnas.0305627101","volume":"101","author":"AE Hirsh","year":"2004","unstructured":"Hirsh AE, Tsolaki AG, DeRiemer K, Feldman MW, Small PM: Stable association between strains of Mycobacterium tuberculosis and their human host populations. Proc Natl Acad Sci U S A. 2004, 101 (14): 4871-4876. 10.1073\/pnas.0305627101.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"7","key":"6861_CR74","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1016\/j.tim.2008.04.005","volume":"16","author":"J Jang","year":"2008","unstructured":"Jang J, Becq J, Gicquel B, Deschavanne P, Neyrolles O: Horizontally acquired genomic islands in the tubercle bacilli. Trends Microbiol. 2008, 16 (7): 303-308. 10.1016\/j.tim.2008.04.005.","journal-title":"Trends Microbiol"},{"issue":"2","key":"6861_CR75","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, Eyre DW, Wilson DJ, Hawkey PM, Crook DW, Parkhill J, Harris D, Walker AS, Bowden R, Monk P, Smith EG, Peto TE: Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis. 2013, 13 (2): 137-146. 10.1016\/S1473-3099(12)70277-3.","journal-title":"Lancet Infect Dis"},{"issue":"2","key":"6861_CR76","doi-asserted-by":"publisher","first-page":"e32158","DOI":"10.1371\/journal.pone.0032158","volume":"7","author":"Y Liu","year":"2012","unstructured":"Liu Y, Painter JA, Posey DL, Cain KP, Weinberg MS, Maloney SA, Ortega LS, Cetron MS: Estimating the impact of newly arrived foreign-born persons on tuberculosis in the United States. PLoS One. 2012, 7 (2): e32158-10.1371\/journal.pone.0032158.","journal-title":"PLoS One"},{"issue":"12","key":"6861_CR77","doi-asserted-by":"publisher","first-page":"1613","DOI":"10.5588\/ijtld.12.0296","volume":"16","author":"Z Mor","year":"2012","unstructured":"Mor Z, Pinsker G, Cedar N, Lidji M, Grotto I: Adult tuberculosis in Israel and migration: trends and challenges between 1999 and 2010. Int J Tuberc Lung Dis. 2012, 16 (12): 1613-1618. 10.5588\/ijtld.12.0296.","journal-title":"Int J Tuberc Lung Dis"},{"key":"6861_CR78","doi-asserted-by":"publisher","first-page":"330","DOI":"10.1186\/1471-2334-10-330","volume":"10","author":"V Field","year":"2010","unstructured":"Field V, Gautret P, Schlagenhauf P, Burchard GD, Caumes E, Jensenius M, Castelli F, Gkrania-Klotsas E, Weld L, Lopez-Velez R, de Vries P, von Sonnenburg F, Loutan L, Parola P: Travel and migration associated infectious diseases morbidity in Europe, 2008. BMC Infect Dis. 2010, 10: 330-10.1186\/1471-2334-10-330.","journal-title":"BMC Infect Dis"},{"key":"6861_CR79","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1016\/j.meegid.2014.06.011","volume":"26C","author":"I Mokrousov","year":"2014","unstructured":"Mokrousov I, Jiao WW, Wan K, Shen A: Stranger in a strange land: Ibero-American strain of Mycobacterium tuberculosis in Tibet, China. Infect Genet Evol. 2014, 26C: 323-326.","journal-title":"Infect Genet Evol"},{"key":"6861_CR80","volume-title":"Bilthoven, The Netherlands: National Intitute of Public Health and The Environment","author":"D van Soolingen","year":"2002","unstructured":"van Soolingen D, de Haas PEW, Kremer K: Restriction fragment length polymorphism (RFLP) typing of mycobacteria. Bilthoven, The Netherlands: National Intitute of Public Health and The Environment. 2002, 52:"},{"issue":"12","key":"6861_CR81","doi-asserted-by":"publisher","first-page":"4498","DOI":"10.1128\/JCM.01392-06","volume":"44","author":"P Supply","year":"2006","unstructured":"Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rusch-Gerdes S, Willery E, Savine E, de Haas P, van Deutekom H, Roring S, Bifani P, Kurepina N, Kreiswirth B, Sola C, Rastogi N, Vatin V, Gutierrez MC, Fauville M, Niemann S, Skuce R, Kremer K, Locht C, van Soolingen D: Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol. 2006, 44 (12): 4498-4510. 10.1128\/JCM.01392-06.","journal-title":"J Clin Microbiol"},{"issue":"14","key":"6861_CR82","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25 (14): 1754-1760. 10.1093\/bioinformatics\/btp324.","journal-title":"Bioinformatics"},{"issue":"16","key":"6861_CR83","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, Marth G, Abecasis G, Durbin R: The Sequence Alignment\/Map format and SAMtools. Bioinformatics. 2009, 25 (16): 2078-2079. 10.1093\/bioinformatics\/btp352.","journal-title":"Bioinformatics"},{"issue":"21","key":"6861_CR84","doi-asserted-by":"publisher","first-page":"2865","DOI":"10.1093\/bioinformatics\/btp394","volume":"25","author":"K Ye","year":"2009","unstructured":"Ye K, Schulz MH, Long Q, Apweiler R, Ning Z: Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009, 25 (21): 2865-2871. 10.1093\/bioinformatics\/btp394.","journal-title":"Bioinformatics"},{"issue":"9","key":"6861_CR85","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1038\/nmeth.1363","volume":"6","author":"K Chen","year":"2009","unstructured":"Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER: BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 2009, 6 (9): 677-681. 10.1038\/nmeth.1363.","journal-title":"Nat Methods"},{"issue":"12","key":"6861_CR86","doi-asserted-by":"publisher","first-page":"R128","DOI":"10.1186\/gb-2010-11-12-r128","volume":"11","author":"K Wong","year":"2010","unstructured":"Wong K, Keane TM, Stalker J, Adams DJ: Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly. Genome Biol. 2010, 11 (12): R128-10.1186\/gb-2010-11-12-r128.","journal-title":"Genome Biol"},{"issue":"5","key":"6861_CR87","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1101\/gr.074492.107","volume":"18","author":"DR Zerbino","year":"2008","unstructured":"Zerbino DR, Birney E: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008, 18 (5): 821-829. 10.1101\/gr.074492.107.","journal-title":"Genome Res"},{"issue":"6","key":"6861_CR88","doi-asserted-by":"publisher","first-page":"3684","DOI":"10.1073\/pnas.052548299","volume":"99","author":"R Brosch","year":"2002","unstructured":"Brosch R, Gordon SV, Marmiesse M, Brodin P, Buchrieser C, Eiglmeier K, Garnier T, Gutierrez C, Hewinson G, Kremer K, Parsons LM, Pym AS, Samper S, van Soolingen D, Cole ST: A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc Natl Acad Sci U S A. 2002, 99 (6): 3684-3689. 10.1073\/pnas.052548299.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5","key":"6861_CR89","first-page":"914","volume":"12","author":"MD Shriver","year":"1995","unstructured":"Shriver MD, Jin L, Boerwinkle E, Deka R, Ferrell RE, Chakraborty R: A novel measure of genetic distance for highly polymorphic tandem repeat loci. Mol Biol Evol. 1995, 12 (5): 914-920.","journal-title":"Mol Biol Evol"},{"issue":"22","key":"6861_CR90","doi-asserted-by":"publisher","first-page":"2991","DOI":"10.1093\/bioinformatics\/bts544","volume":"28","author":"F Coll","year":"2012","unstructured":"Coll F, Mallard K, Preston MD, Bentley S, Parkhill J, McNerney R, Martin N, Clark TG: SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences. Bioinformatics. 2012, 28 (22): 2991-2993. 10.1093\/bioinformatics\/bts544.","journal-title":"Bioinformatics"},{"issue":"2","key":"6861_CR91","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1093\/molbev\/msp259","volume":"27","author":"M Gouy","year":"2010","unstructured":"Gouy M, Guindon S, Gascuel O: SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol. 2010, 27 (2): 221-224. 10.1093\/molbev\/msp259.","journal-title":"Mol Biol Evol"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2164-15-991.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T07:18:03Z","timestamp":1630567083000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/1471-2164-15-991"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,11,18]]},"references-count":91,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["6861"],"URL":"https:\/\/doi.org\/10.1186\/1471-2164-15-991","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,11,18]]},"assertion":[{"value":"25 September 2013","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 November 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 November 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"991"}}