The discovery, function and development of the variable number tandem repeats in different Mycobacterium species

References

• Ablordey A, Hilty M, Stragier P, et al. (2005a). Comparative nucleotide sequence analysis of polymorphic variable-number tandem-repeat Loci in Mycobacterium ulcerans. J Clin Microbiol 43:5281–54
   PubMed Web of Science ®Google Scholar
• Ablordey A, Swings J, Hubans C, et al. (2005b). Multilocus variable-number tandem repeat typing of Mycobacterium ulcerans. J Clin Microbiol 43:1546–51
   PubMed Web of Science ®Google Scholar
• Alland D, Kalkut GE, Moss AR, et al. (1994). Transmission of tuberculosis in New York City. An analysis by DNA fingerprinting and conventional epidemiologic methods. N Engl J Med 330:1710–16
   PubMed Web of Science ®Google Scholar
• Allix C, Walravens K, Saegerman C, et al. (2006). Evaluation of the epidemiological relevance of variable-number tandem-repeat genotyping of Mycobacterium bovis and comparison of the method with IS6110 restriction fragment length polymorphism analysis and spoligotyping. J Clin Microbiol 44:1951–62
   PubMed Web of Science ®Google Scholar
• Allix-Béguec C, Fauville-Dufaux M, Supply P. (2008). Three-year population-based evaluation of standardized mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing of Mycobacterium tuberculosis. J Clin Microbiol 46:1398–406
   PubMed Web of Science ®Google Scholar
• Allix-Béguec C, Wahl C, Hanekom M, et al. (2014). Proposal of a consensus set of hypervariable mycobacterial interspersed repetitive-unit-variable-number tandem-repeat loci for subtyping of Mycobacterium tuberculosis Beijing isolates. J Clin Microbiol 52:164–72
   PubMed Web of Science ®Google Scholar
• Ameni G, Aseffa A, Sirak A, et al. (2007). Effect of skin testing and segregation on the prevalence of bovine tuberculosis, and molecular typing of Mycobacterium bovis, in Ethiopia. Vet Rec 161:782–6
   PubMed Web of Science ®Google Scholar
• Arnvig KB, Comas I, Thomson NR, et al. (2011). Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis. PLoS Pathog 7:e1002342
   PubMed Web of Science ®Google Scholar
• Benedetti A, Menzies D, Behr MA, et al. (2010). How close is close enough? Exploring matching criteria in the estimation of recent transmission of tuberculosis. Am J Epidemiol 172:318–26
   PubMed Web of Science ®Google Scholar
• Benson G. (1999). Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–80
   PubMed Web of Science ®Google Scholar
• Bidovec-Stojkovic U, Zolnir-Dovc M, Supply P. (2011). One year nationwide evaluation of 24-locus MIRU-VNTR genotyping on Slovenian Mycobacterium tuberculosis isolates. Respir Med 105:S67–73
   PubMed Web of Science ®Google Scholar
• Biet F, Sevilla IA, Cochard T, et al. (2012). Inter- and intra-subtype genotypic differences that differentiate Mycobacterium avium subspecies paratuberculosis strains. BMC Microbiol 12:264
   PubMed Web of Science ®Google Scholar
• Boniotti MB, Goria M, Loda D, et al. (2009). Molecular typing of Mycobacterium bovis strains isolated in Italy from 2000 to 2006 and evaluation of variable-number tandem repeats for geographically optimized genotyping. J Clin Microbiol 47:636–44
   PubMed Web of Science ®Google Scholar
• Britten RJ, Kohne D. (1968). Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms. Science 161:529
   Google Scholar
• Brosch R, Gordon SV, Marmiesse M, et al. (2002). A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc Natl Acad Sci USA 99:3684–9
   PubMed Web of Science ®Google Scholar
• Brosch R, Pym AS, Gordon SV, Cole ST. (2001). The evolution of mycobacterial pathogenicity: clues from comparative genomics. Trends Microbiol 9:452–8
   PubMed Web of Science ®Google Scholar
• Brown TJ, Nikolayevskyy VN, Drobniewski FA. (2009). Typing Mycobacterium tuberculosis using variable number tandem repeat analysis. Methods Mol Biol 465:371–94
   PubMedGoogle Scholar
• Canetti G, Fox W, Khomenko A, et al. (1969). Advances in techniques of testing mycobacterial drug sensitivity, and the use of sensitivity tests in tuberculosis control programmes. Bull World Health Organ 41:21–43
   PubMed Web of Science ®Google Scholar
• Castets M, Boisvert H, Grumbach F, et al. (1968). Tuberculosis bacilli of the African type: preliminary note. Rev Tuberc Pneumol (Paris) 32:179–84
   PubMedGoogle Scholar
• Choi GE, Chang CL, Whang J, et al. (2011). Efficient differentiation of Mycobacterium abscessus complex isolates to the species level by a novel PCR-based variable number tandem-repeat assay. J Clin Microbiol 49:1107–9
   PubMed Web of Science ®Google Scholar
• Coil DA, Vandersmissen L, Ginevra C, et al. (2008). Intragenic tandem repeat variation between Legionella pneumophila strains. BMC Microbiol 8:218
   PubMedGoogle Scholar
• Cole ST, Brosch R, Parkhill J, et al. (1998). Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature, 393:537–44
   PubMed Web of Science ®Google Scholar
• Collins DM. (2011). Advances in molecular diagnostics for Mycobacterium bovis. Vet Microbiol 151:2–7
   PubMed Web of Science ®Google Scholar
• Converse PJ, Nuermberger EL, Almeida DV, Grosset JH. (2011). Treating Mycobacterium ulcerans disease (Buruli ulcer): from surgery to antibiotics, is the pill mightier than the knife? Future Microbiol 6:1185–98
   PubMed Web of Science ®Google Scholar
• Cook VJ, Shah L, Gardy J, Bourgeois AC. (2012). Recommendations on modern contact investigation methods for enhancing tuberculosis control. Int J Tuberc Lung Dis 16:297–305
   PubMed Web of Science ®Google Scholar
• Coulibaly-N'Golo GM, Ekaza E, Coulibaly B, et al. (2011). Multilocus VNTR analysis of Mycobacterium ulcerans strains isolated in Côte d'Ivoire. J Infect Dev Ctries 5:59–63
   PubMed Web of Science ®Google Scholar
• Cttskey CT, Pizzuti A, Fu YH, et al. (1992). Triplet repeat mutalions in human disease. Science 256:784–9
   PubMed Web of Science ®Google Scholar
• Dauchy FA, Dégrange S, Charron A, et al. (2010). Variable-number tandem-repeat markers for typing Mycobacterium intracellular restrains isolated in humans. BMC Microbiol 10:93
   PubMedGoogle Scholar
• de Beer JL, van Ingen J, de Vries G, et al. (2013). Comparative study of IS6110 restriction fragment length polymorphism and variable-number tandem-repeat typing of Mycobacterium tuberculosis isolates in the Netherlands, based on a 5-year nationwide survey. J Clin Microbiol 51:1193–8
   PubMed Web of Science ®Google Scholar
• Debrauwere H, Gendrel CG, Lechat S, Dutreix M. (1997). Differences and similarities between various tandem repeat sequences: minisatellites and microsatellites. Biochimie 79:577–86
   PubMed Web of Science ®Google Scholar
• Delihas N. (2011). Impact of small repeat sequences on bacterial genome evolution. Genome Biol Evol 3:959–73
   PubMed Web of Science ®Google Scholar
• Dirac MA, Weigel KM, Yakrus MA, et al. (2013). Shared Mycobacterium avium genotypes observed among unlinked clinical and environmental isolates. Appl Environ Microbiol 79:5601–7
   PubMed Web of Science ®Google Scholar
• Douarre PE, Cashman W, Buckley J, et al. (2011). Molecular characterization of Mycobacterium avium subsp. paratuberculosis using multi-locus short sequence repeat (MLSSR) and mycobacterial interspersed repetitive units-variable number tandem repeat (MIRU-VNTR) typing methods. Vet Microbiol 149:482–7
   PubMed Web of Science ®Google Scholar
• Duarte EL, Domingos M, Amado A, et al. (2010). MIRU-VNTR typing adds discriminatory value to groups of Mycobacterium bovis and Mycobacterium caprae strains defined by spoligotyping. Vet Microbiol 143:299–306
   PubMed Web of Science ®Google Scholar
• Ehrlich SD, Bierne H, d'Alençon E, et al. (1993). Mechanisms of illegitimate recombination. Gene 135:161–6
   PubMed Web of Science ®Google Scholar
• Fabre M, Koeck JL, Le Flèche P, et al. (2004). High genetic diversity revealed by variable-number tandem repeat genotyping and analysis of hsp65 gene polymorphism in a large collection of “Mycobacterium canettii” strains indicates that the M. tuberculosis complex is a recently emerged clone of “M. canettii". J Clin Microbiol 42:3248–55
   PubMed Web of Science ®Google Scholar
• Fontes AN, Sakamuri RM, Baptista IM, et al. (2009). Genetic diversity of mycobacterium leprae isolates from Brazilian leprosy patients. Lepr Rev 80:302–15
   PubMed Web of Science ®Google Scholar
• Frothingham R. (1995). Differentiation of strains in Mycobacterium tuberculosis complex by DNA sequence polymorphisms, including rapid identification of M. bovis BCG. J Clin Microbiol 33:840–4
   PubMed Web of Science ®Google Scholar
• Frothingham R, Meeker-O'Connell W. (1998). Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats. Microbiology 144:1189–96
   PubMed Web of Science ®Google Scholar
• Furphy C, Costello E, Murphy D, et al. (2012). DNA Typing of Mycobacterium bovis isolates from badgers (Meles meles) culled from areas in Ireland with different levels of tuberculosis prevalence. Vet Med Int 2012:742478
   PubMedGoogle Scholar
• Gagneux S, DeRiemer K, Van T, et al. (2006). Variable host-pathogen compatibility in Mycobacterium tuberculosis. Proc Natl Acad Sci USA 103:2869–73
   PubMed Web of Science ®Google Scholar
• Garnier T, Eiglmeier K, Camus JC, et al. (2003). The complete genome sequence of Mycobacterium bovis. Proc Natl Acad Sci USA 100:7877–82
   PubMed Web of Science ®Google Scholar
• Gerritsmann H, Stalder GL, Spergser J, et al. (2014). Multiple strain infections and high genotypic diversity among Mycobacterium avium subsp. paratuberculosis field isolates from diseased wild and domestic ruminant species in the eastern Alpine region of Austria. Infect Genet Evol 21:244–51
   PubMed Web of Science ®Google Scholar
• Gillis T, Vissa V, Matsuoka M, et al; Ideal Consortium Partners. (2009). Characterisation of short tandem repeats for genotyping Mycobacterium leprae. Lepr Rev 80:250–60
   PubMed Web of Science ®Google Scholar
• Gormley E, Corner LA, Costello E, Rodriguez-Campos S. (2014). Bacteriological diagnosis and molecular strain typing of Mycobacterium bovis and Mycobacterium caprae. Res Vet Sci 97:S30–43
   PubMed Web of Science ®Google Scholar
• Goyal M, Young D, Zhang Y, et al. (1994). PCR amplification of variable sequence upstream of katG gene to subdivide strains of Mycobacterium tuberculosis complex. J Clin Microbiol 32:3070–1
   PubMed Web of Science ®Google Scholar
• Guo X, Mrázek J. (2008). Long simple sequence repeats in host-adapted pathogens localize near genes encoding antigens, housekeeping genes, and pseudogenes. J Mol Evol 67:497–509
   PubMed Web of Science ®Google Scholar
• Gutierrez MC, Ahmed N, Willery E, et al. (2006). Predominance of ancestral lineages of Mycobacterium tuberculosis in India. Emerg Infect Dis 12:1367–74
   PubMed Web of Science ®Google Scholar
• Harris KA, Kenna DT, Blauwendraat C, et al. (2012). Molecular fingerprinting of Mycobacterium abscessus strains in a cohort of pediatric cystic fibrosis patients. J Clin Microbiol 50:1758–61
   PubMed Web of Science ®Google Scholar
• Hermans PW, van Soolingen D, van Embden JD. (1992). Characterization of a major polymorphic tandem repeat in Mycobacterium tuberculosis and its potential use in the epidemiology of Mycobacterium kansasii and Mycobacterium gordonae. J Bacteriol 174:4157–65
   PubMed Web of Science ®Google Scholar
• Hill V, Zozio T, Sadikalay S, et al. (2012). MLVA based classification of Mycobacterium tuberculosis complex lineages for a robust phylogeographic snapshot of its worldwide molecular diversity. PLoS One 7:e41991
   PubMedGoogle Scholar
• Hilty M, Diguimbaye C, Schelling E, et al. (2005). Evaluation of the discriminatory power of variable number tandem repeat (VNTR) typing of Mycobacterium bovis strains. Vet Microbiol 109:217–22
   PubMed Web of Science ®Google Scholar
• Hilty M, Käser M, Zinsstag J, et al. (2007). Analysis of the Mycobacterium ulcerans genome sequence reveals new loci for variable number tandem repeats (VNTR) typing. Microbiology 153:1483–7
   PubMed Web of Science ®Google Scholar
• Huey B, Hall J. (1989). Hypervariable DNA fingerprinting in Escherichia coli: minisatellite probe from bacteriophage M13. J Bacteriol 171:2528–32
   PubMed Web of Science ®Google Scholar
• Iakhiaeva E, McNulty S, Brown Elliott BA, et al. (2013). Mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) genotyping of mycobacterium intracellulare for strain comparison with establishment of a PCR-based database. J Clin Microbiol 51:4009–16
   Google Scholar
• Ichikawa K, Yagi T, Inagaki T, et al. (2010). Molecular typing of Mycobacterium intracellulare using multilocus variable-number of tandem-repeat analysis: identification of loci and analysis of clinical isolates. Microbiology 156:496–504
   PubMed Web of Science ®Google Scholar
• Inagaki T, Nishimori K, Yagi T, et al. (2009). Comparison of a variable-number tandem-repeat (VNTR) method for typing Mycobacterium avium with mycobacterial interspersed repetitive-unit-VNTR and IS1245 restriction fragment length polymorphism typing. J Clin Microbiol 47:2156–64
   PubMed Web of Science ®Google Scholar
• Iwamoto T, Nakajima C, Nishiuchi Y, et al. (2012). Genetic diversity of Mycobacterium avium subsp. hominissuis strains isolated from humans, pigs, and human living environment. Infect Genet Evol 12:846–52
   PubMed Web of Science ®Google Scholar
• Jeffreys AJ, Wilson V, Kelly R, et al. (1987). Mouse DNA ‘fingerprints': analysis of chromosome localization and germ-line stability of hypervariable loci in recombinant inbred strains. Nucleic Acids Res 15:2823–36
   PubMed Web of Science ®Google Scholar
• Jeon B, Je S, Park J, et al. (2008). Variable number tandem repeat analysis of Mycobacterium bovis isolates from Gyeonggi-do, Korea. J Vet Sci 9:145–53
   PubMed Web of Science ®Google Scholar
• Jiang Y, Liu HC, Zheng H, et al. (2013). 19-VNTR loci used in genotyping Chinese clinical Mycobacterium tuberculosis complex strains and in association with spoligotyping. J Basic Microbiol 53:562–80
   PubMed Web of Science ®Google Scholar
• Jiang Y, Liu HC, Zheng HJ, et al. (2012). Evaluation of four candidate VNTR Loci for genotyping 225 Chinese clinical Mycobacterium tuberculosis complex strains. Biomed Environ Sci 25:82–90
   PubMed Web of Science ®Google Scholar
• Johnston HH. (2011). The prefatory of the Nile quest: a record of the exploration of the Nile and its basin. Cambridge University Press
   Google Scholar
• Junop MS, Obmolova G, Rausch K, et al. (2001). Composite active site of an ABC ATPase: MutS uses ATP to verify mismatch recognition and authorize DNA repair. Molecular Cell 7:1–12
   PubMed Web of Science ®Google Scholar
• Kikuchi T, Watanabe A, Gomi K, et al. (2009). Association between mycobacterial genotypes and disease progression in Mycobacterium avium pulmonary infection. Thorax 64:901–7
   PubMed Web of Science ®Google Scholar
• Kim SY, Lee ST, Jeong BH, et al. (2012). Clinical significance of mycobacterial genotyping in Mycobacterium avium lung disease in Korea. Int J Tuberc Lung Dis 16:1393–9
   PubMed Web of Science ®Google Scholar
• Kim SY, Lee ST, Jeong BH, et al. (2013). Genotyping of Mycobacterium intracellulare isolates and clinical characteristics of lung disease. Int J Tuberc Lung Dis 17:669–75
   PubMed Web of Science ®Google Scholar
• Kimura M, Sakamuri RM, Groathouse NA, et al. (2009). Rapid variable-number tandem-repeat genotyping for Mycobacterium leprae clinical specimens. J Clin Microbiol 47:1757–66
   PubMed Web of Science ®Google Scholar
• Kondo J, Adachi W, Umeda S, et al. (2004). Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats. Nucleic Acids Res 32:2541–9
   PubMed Web of Science ®Google Scholar
• Kremer K, van Soolingen D, Frothingham R, et al. (1999). Comparison of methods based on different molecular epidemiological markers for typing of Mycobacterium tuberculosis complex strains: interlaboratory study of discriminatory power and reproducibility. J Clin Microbiol 37:2607–18
   PubMed Web of Science ®Google Scholar
• Kuruwa S, Vissa V, Mistry N. (2012). Distribution of Mycobacterium leprae strains among cases in a rural and urban population of Maharashtra, India. J Clin Microbiol 50:1406–11
   PubMed Web of Science ®Google Scholar
• Laniado-Laborín R, Muñiz-Salazar R, García-Ortiz RA, et al. (2014). Molecular characterization of Mycobacterium bovis isolates from patients with tuberculosis in Baja California, Mexico. Infect Genet Evol 27:1–5
   PubMed Web of Science ®Google Scholar
• Lari N, Bimbi N, Rindi L, et al. (2011). Genetic diversity of human isolates of Mycobacterium bovis assessed by spoligotyping and Variable Number Tandem Repeat genotyping. Infect Genet Evol 11:175–80
   PubMed Web of Science ®Google Scholar
• Lari N, Rindi L, Bonanni D, et al. (2006). Molecular analysis of clinical isolates of Mycobacterium bovis recovered from humans in Italy. J Clin Microbiol 44:4218–21
   PubMed Web of Science ®Google Scholar
• Lavender CJ, Stinear TP, Johnson PD, et al. (2008). Evaluation of VNTR typing for the identification of Mycobacterium ulcerans in environmental samples from Victoria, Australia. FEMS Microbiol Lett 287:250–5
   PubMed Web of Science ®Google Scholar
• Le Fleche P, Fabre M, Denoeud F, et al. (2002). High resolution, on-line identification of strains from the Mycobacterium tuberculosis complex based on tandem repeat typing. BMC Microbiol 2:37
   PubMed Web of Science ®Google Scholar
• Le Fleche P, Hauck Y, Onteniente L, et al. (2001). A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis. BMC Microbiol 1:2
   PubMedGoogle Scholar
• Leão C, Canto A, Machado D, et al. (2014). Relatedness of Mycobacterium avium subspecies hominissuis clinical isolates of human and porcine origins assessed by MLVA. Vet Microbiol 173:92–100
   PubMed Web of Science ®Google Scholar
• Lee J, Kang H, Kim S, et al. (2014). Optimal combination of VNTR typing for discrimination of isolated Mycobacterium tuberculosis in Korea. Tuberc Respir Dis (Seoul) 6:59–65
   Google Scholar
• Lieb M. (1987). Bacterial genes mutL, mutS, and dcm participate in repair of mismatches at 5-methylcytosine sites. J Bacteriol 169:5241–6
   PubMed Web of Science ®Google Scholar
• Liu J, Wang Z, Wen Y, et al. (2007). Study on genotyping of Mycobacterium leprae and families with multi-cases. Zhonghua Liu Xing Bing Xue Za Zhi 28:649–55 [ Article in Chinese]
   PubMedGoogle Scholar
• Loeffler SH, de Lisle GW, Neill MA, et al. (2014). The seal tuberculosis agent, Mycobacterium pinnipedii, infects domestic cattle in New Zealand: epidemiologic factors and DNA strain typing. J Wildl Dis 50:180–7
   PubMed Web of Science ®Google Scholar
• Luo T, Yang C, Pang Y, et al. (2014). Development of a hierarchical variable-number tandem repeat typing scheme for Mycobacterium tuberculosis in China. PLoS One 9:e89726
   PubMed Web of Science ®Google Scholar
• Malama S, Johansen TB, Muma JB, et al. (2014). Characterization of Mycobacterium bovis from humans and cattle in Namwala District, Zambia. Vet Med Int 2014:187842
   PubMedGoogle Scholar
• Man L, Lee DJ, Toekman MS, et al. (1994). Microsatellite alterations as clonal markers for the detection of huntan cancer. Proc Natl Acad Sci USA 91:9871–5
   PubMed Web of Science ®Google Scholar
• Mandal S, Bradshaw L, Anderson LF, et al. (2011). Investigating transmission of Mycobacterium bovis in the United Kingdom in 2005 to 2008. J Clin Microbiol 49:1943–50
   PubMed Web of Science ®Google Scholar
• Martinez LR, Harris B, Black 4th WC, et al. (2008). Genotyping North American animal Mycobacterium bovis isolates using multilocus variable number tandem repeat analysis. J Vet Diagn Invest 20:707–15
   PubMed Web of Science ®Google Scholar
• Matsuoka M, Maeda S, Kai M, et al. (2000). Mycobacterium leprae typing by genomic diversity and global distribution of genotypes. Int J Lepr 68:121–8
   Google Scholar
• Mazars E, Lesjean S, Banuls AL, et al. (2001). High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology. Proc Natl Acad Sci USA 98:1901–6
   PubMed Web of Science ®Google Scholar
• McLernon J, Costello E, Flynn O, et al. (2010). Evaluation of mycobacterial interspersed repetitive-unit-variable-number tandem-repeat analysis and spoligotyping for genotyping of Mycobacterium bovis isolates and a comparison with restriction fragment length polymorphism typing. J Clin Microbiol 48:4541–5
   PubMed Web of Science ®Google Scholar
• McVean G. (2010). What drives recombination hotspots to repeat DNA in humans? Philos Trans R Soc Lond B Biol Sci 365:1213–18
   PubMed Web of Science ®Google Scholar
• Michel AL, Hlokwe TM, Coetzee ML, et al. (2008). High Mycobacterium bovis genetic diversity in a low prevalence setting. Vet Microbiol 126:151–9
   PubMed Web of Science ®Google Scholar
• Michel B. (2000). Replication fork arrest and DNA recombination. Trends Biochem Sci 25:173–8
   PubMed Web of Science ®Google Scholar
• Miltgen J, Morillon M, Koeck JL, et al. (2002). Two cases of pulmonary tuberculosis caused by Mycobacterium tuberculosis subsp canetti. Emerg Infect Dis 8:1350–2
   PubMed Web of Science ®Google Scholar
• Mishra AK. (2009). Biochemical and molecular characterisation of cell wall glycosyltransferases in Mycobacterium tuberculosis [PhD dissertation]. University of Birmingham
   Google Scholar
• Modrich P, Lahue R. (1996). Mismatch repair in replication fidelity, genetic recombination and cancer biology. Annu Rev Biochem 65:101–33
   PubMed Web of Science ®Google Scholar
• Monot M, Honore N, Baliere C, et al. (2008). Are variable-number tandem repeats appropriate for genotyping Mycobacterium leprae? J Clin Microbiol 46:2291–7
   PubMed Web of Science ®Google Scholar
• Monot M, Honoré N, Garnier T, et al. (2009). Comparative genomic and phylogeographic analysis of Mycobacterium leprae. Nat Genet 41:1282–9
   PubMed Web of Science ®Google Scholar
• Moser I, Prodinger WM, Hotzel H, et al. (2008). Mycobacterium pinnipedii: transmission from South American sea lion (Otaria byronia) to Bactrian camel (Camelus bactrianus actrianus) and Malayan tapirs (Tapirus indicus). Vet Microbiol 127:399–406
   PubMed Web of Science ®Google Scholar
• Mostowy S, Onipede A, Gagneux S, et al. (2004). Genomic analysis distinguishes Mycobacterium africanum. J Clin Microbiol 42:3594–9
   PubMed Web of Science ®Google Scholar
• Motiwala AS, Strother M, Amonsin A, et al. (2003). Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis: evidence for limited strain diversity, strain sharing, and identification of unique targets for diagnosis. J Clin Microbiol 41:2015–26
   PubMed Web of Science ®Google Scholar
• Müller B, Steiner B, Bonfoh B, et al. (2008). Molecular characterisation of Mycobacterium bovis isolated from cattle slaughtered at the Bamako abattoir in Mali. BMC Vet Res 4:26
   PubMed Web of Science ®Google Scholar
• Murase Y, Mitarai S, Sugawara I, et al. (2008). Promising loci of variable numbers of tandem repeats for typing Beijing family Mycobacterium tuberculosis. J Med Microbiol 57:873–80
   PubMed Web of Science ®Google Scholar
• Musser JM, Amin A, Ramaswamy S. (2000). Negligible genetic diversity of Mycobacterium tuberculosis host immune system protein targets: evidence of limited selective pressure. Genetics 155:7–16
   PubMed Web of Science ®Google Scholar
• Muwonge A, Oloya J, Kankya C, et al. (2014). Molecular characterization of Mycobacterium avium subspecies hominissuis isolated from humans, cattle and pigs in the Uganda cattle corridor using VNTR analysis. Infect Genet Evol 21:184–91
   PubMed Web of Science ®Google Scholar
• Namwat W, Luangsuk P, Palittapongarnpim P. (1998). The genetic diversity of Mycobacterium tuberculosis strains in Thailand studied by amplification of DNA segments containing direct repetitive sequences. Int J Tuberculosis Lung Dis 2:153–9
   PubMed Web of Science ®Google Scholar
• Ojo O, Sheehan S, Corcoran GD, et al. (2008). Mycobacterium bovis strains causing smear-positive human tuberculosis, Southwest Ireland. Emerg Infect Dis 14:1931–4
   PubMed Web of Science ®Google Scholar
• Overduin P, Schouls L, Roholl P, et al. (2004). Use of multilocus variable-number tandem-repeat analysis for typing Mycobacterium avium subsp. Paratuberculosis. J Clin Microbiol 42:5022–8
   PubMed Web of Science ®Google Scholar
• Parreiras PM, Andrade GI, Nascimento Tde F, et al. (2012). Spoligotyping and variable number tandem repeat analysis of Mycobacterium bovis isolates from cattle in Brazil. Mem Inst Oswaldo Cruz 107:64–73
   PubMed Web of Science ®Google Scholar
• Pate M, Kušar D, Zolnir-Dovč M, Ocepek M. (2011). MIRU-VNTR typing of Mycobacterium avium in animals and humans: heterogeneity of Mycobacterium avium subsp. hominissuis versus homogeneity of Mycobacterium avium subsp. avium strains. Res Vet Sci 91:376–81
   PubMed Web of Science ®Google Scholar
• Pillon MC, Dubinsky M, Johnston RN, et al. (2013). Characterization of the defects in the ATP lid of E. coli MutL that cause transient hypermutability. DNA Repair (Amst) 12:864–9
   PubMed Web of Science ®Google Scholar
• Price-Carter M, Rooker S, Collins DM. (2011). Comparison of 45 variable number tandem repeat (VNTR) and two direct repeat (DR) assays to restriction endonuclease analysis for typing isolates of Mycobacterium bovis. Vet Microbiol 150:107–14
   PubMed Web of Science ®Google Scholar
• Prunier AL, Leclercq R. (2005). Role of mutS and mutL genes in hypermutability and recombination in Staphylococcus aureus. J Bacteriol 187:3455–64
   PubMed Web of Science ®Google Scholar
• Puopolo KM, Madoff LC. (2003). Upstream short sequence repeats regulate expression of the alpha C protein of group B Streptococcus. Mol Microbiol 50:977–91
   PubMed Web of Science ®Google Scholar
• Renders N, Licciardello L, IJsseldijk C, et al. (1999). Variable numbers of tandem repeat loci in genetically homogeneous Haemophilus influenzae strains alter during persistent colonisation of cystic fibrosis patients. FEMS Microbiol Lett 173:95–102
   PubMed Web of Science ®Google Scholar
• Richter E, Weizenegger M, Rüsch-Gerdes S, Niemann S. (2003). Evaluation of genotype MTBC assay for differentiation of clinical Mycobacterium tuberculosis complex isolates. J Clin Microbiol 41:2672–5
   PubMed Web of Science ®Google Scholar
• Rindi L, Buzzigoli A, Medici C, Garzelli C. (2013). High phylogenetic proximity of isolates of Mycobacterium avium subsp. Hominissuis over a two decades-period. Infect Genet Evol 16:99–102
   PubMed Web of Science ®Google Scholar
• Rodriguez-Campos S, Aranaz A, de Juan L, et al. (2011). Limitations of spoligotyping and variable-number tandem-repeat typing for molecular tracing of Mycobacterium bovis in a high-diversity setting. J Clin Microbiol 49:3361–4
   PubMed Web of Science ®Google Scholar
• Rodriguez-Campos S, Navarro Y, Romero B, et al. (2013). Splitting of a prevalent Mycobacterium bovis spoligotype by variable-number tandem-repeat typing reveals high heterogeneity in an evolving clonal group. J Clin Microbiol 51:3658–65
   PubMed Web of Science ®Google Scholar
• Roring S, Scott A, Brittain D, et al. (2002). Development of variable-number tandem repeat typing of Mycobacterium bovis: comparison of results with those obtained by using existing exact tandem repeats and spoligotyping. J Clin Microbiol 40:2126–33
   PubMed Web of Science ®Google Scholar
• Roring S, Scott AN, Glyn Hewinson R, et al. (2004). Evaluation of variable number tandem repeat (VNTR) loci in molecular typing of Mycobacterium bovis isolates from Ireland. Vet Microbiol 101:65–73
   PubMed Web of Science ®Google Scholar
• Sahraoui N, Muller B, Djamel Y, et al. (2010). Evaluation of variable number of tandem repeats (VNTR) isolates of Mycobacterium bovis in Algeria. Ann Biol Clin (Paris) 68:449–53
   PubMed Web of Science ®Google Scholar
• Sakamuri RM, Harrison J, Gelber R, et al. (2009). A continuation: study and characterisation of Mycobacterium leprae short tandem repeat genotypes and transmission of leprosy in Cebu, Philippines. Lepr Rev 80:272–9
   PubMed Web of Science ®Google Scholar
• Sakamuri RM, Kimura M, Li W, et al. (2009). Population-based molecular epidemiology of leprosy in Cebu, Philippines. J Clin Microbiol 47:2844–54
   PubMed Web of Science ®Google Scholar
• Salipante SJ, Hall BG. (2011). Towards the molecular epidemiology of Mycobacterium leprae: strategies, successes, and shortcomings. Infect Genet Evol 11:1505–13
   PubMed Web of Science ®Google Scholar
• Sampson SL, Lukey P, Warren RM, et al. (2001). Expression, characterization and subcellular localization of the Mycobacterium tuberculosis PPE gene Rv1917c. Tuberculosis (Edinb) 81:305–17
   PubMed Web of Science ®Google Scholar
• Schoepf K, Prodinger WM, Glawischnig W, et al. (2012). A two-years' survey on the prevalence of tuberculosis caused by Mycobacterium caprae in Red Deer (Cervus elaphus) in the Tyrol, Austria. ISRN Vet Sci 2012:245138
   PubMedGoogle Scholar
• Shin SJ, Choi GE, Cho SN, et al. (2013). Mycobacterial genotypes are associated with clinical manifestation and progression of lung diseases caused by Mycobacterium abscessus and Mycobacterium massiliense. Clin Infect Dis 57:32–9
   PubMed Web of Science ®Google Scholar
• Shin YC, Lee H, Lee H, et al. (2000). Variable numbers of TTC repeats in Mycobacterium leprae DNA from leprosy patients and use in strain differentiation. J Clin Microbiol 38:4535–8
   PubMed Web of Science ®Google Scholar
• Shinde V, Newton H, Sakamuri RM, et al. (2009). VNTR typing of Mycobacterium leprae in South Indian leprosy patients. Lepr Rev 80:290–301
   PubMed Web of Science ®Google Scholar
• Skuce RA, McCorry TP, McCarroll JF, et al. (2002). Discrimination of Mycobacterium tuberculosis complex bacteria using novel VNTR PCR targets. Microbiology 148:519–28
   PubMed Web of Science ®Google Scholar
• Slany M, Jezek P, Bodnarova M. (2013). Fish tank granuloma caused by Mycobacterium marinum in two aquarists: two case reports. Biomed Res Int 2013:161329
   PubMedGoogle Scholar
• Smith GP. (1974). Unequal crossover and the evolution of multigene families. Cold Spring Harb Symp Quant Biol 38:507–13
   PubMedGoogle Scholar
• Smith GR, Kunes SM, Schultz DW, et al. (1981). Structure of chi hotspots of generalized recombination. Cell 24:429–36
   PubMed Web of Science ®Google Scholar
• Smith NH, Crawshaw T, Parry J, Birtles RJ. (2009). Mycobacterium microti: more diverse than previously thought. J Clin Microbiol 47:2551–9
   PubMed Web of Science ®Google Scholar
• Smith NH, Dale J, Inwald J, et al. (2003). The population structure of Mycobacterium bovis in Great Britain: clonal expansion. Proc Natl Acad Sci USA 100:15271–5
   PubMed Web of Science ®Google Scholar
• Smittipat N, Billamas P, Palittapongarnpim M, et al. (2005). Polymorphism of variable-number tandem repeats at multiple loci in Mycobacterium tuberculosis. J Clin Microbiol 43:5034–43
   PubMed Web of Science ®Google Scholar
• Smittipat N, Palittapongarnpim P. (2000). Identification of possible loci of variable number of tandem repeats in Mycobacterium tuberculosis. Tuberc Lung Dis 80:69–74
   PubMedGoogle Scholar
• Springer B, Sander P, Sedlacek L, et al. (2004). Lack of mismatch correction facilitates genome evolution in mycobacteria. Mol Microbiol 53:1601–9
   PubMed Web of Science ®Google Scholar
• Spurgiesz RS, Quitugua TN, Smith KL, et al. (2003). Molecular typing of Mycobacterium tuberculosis by using nine novel variable-number tandem repeats across the Beijing family and low-copy-number IS6110 isolates. J Clin Microbiol 41:4224–30
   PubMed Web of Science ®Google Scholar
• Srisungnam S, Rudeeaneksin J, Lukebua A, et al. (2009). Molecular epidemiology of leprosy based on VNTR typing in Thailand. Lepr Rev 80:280–9
   PubMed Web of Science ®Google Scholar
• Stragier P, Ablordey A, Durnez L, Portaels F. (2007). VNTR analysis differentiates Mycobacterium ulcerans and IS2404 positive mycobacteria. Syst Appl Microbiol 30:525–30
   PubMed Web of Science ®Google Scholar
• Stragier P, Ablordey A, Meyers WM, Portaels F. (2005). Genotyping Mycobacterium ulcerans and Mycobacterium marinum by using mycobacterial interspersed repetitive units. J Bacteriol 187:1639–47
   PubMed Web of Science ®Google Scholar
• Streisinger G, Okada Y, Emrich J, et al. (1966). Frame shift mutations and the genetic code. This paper is dedicated to Professor Theodosius Dobzhansky on the occasion of his 66th birthday. Cold Spring Harb Symp Quant Biol 31:77–84
   PubMedGoogle Scholar
• Sun G, Chen C, Li J, et al. (2011). Discriminatory potential of a novel set of Variable Number of Tandem Repeats for genotyping Mycobacterium marinum. Vet Microbiol 152:200–4
   PubMed Web of Science ®Google Scholar
• Supply P, Magdalena J, Himpens S, Locht C. (1997). Identification of novel intergenic repetitive units in a mycobacterial two-component system operon. Mol Microbiol 26:991–1003
   PubMed Web of Science ®Google Scholar
• Supply P, Mazars E, Lesjean S, et al. (2000). Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome. Mol Microbiol 36:762–71
   PubMed Web of Science ®Google Scholar
• Sutherland GR, Richards RI. (1995). Simple tandem DNA repeals and human genetic disease. Proc Natl Acad Sci USA 92:3636–41
   PubMed Web of Science ®Google Scholar
• Szalkowski AM, Anisimova M. (2013). Graph-based modeling of tandem repeats improves global multiple sequence alignment. Nucleic Acids Res 41:e162
   PubMedGoogle Scholar
• Tantivitayakul P, Panapruksachat S, Billamas P, Palittapongarnpim P. (2010). Variable number of tandem repeat sequences act as regulatory elements in Mycobacterium tuberculosis. Tuberculosis (Edinb) 90:311–18
   PubMed Web of Science ®Google Scholar
• Tautz D. (1993). Notes on the definition and nomenclature of tandemly repetitive DNA sequences. EXS 67:21–8
   PubMedGoogle Scholar
• Thibault VC, Grayon M, Boschiroli ML, et al. (2007). New variable-number tandem-repeat markers for typing Mycobacterium avium subsp. paratuberculosis and M. avium strains: comparison with IS900 and IS1245 restriction fragment length polymorphism typing. J Clin Microbiol 45:2404–10
   PubMed Web of Science ®Google Scholar
• Thompson PJ, Cousins DV, Gow BL, et al. (1993). Seals, seal trainers and mycobacterial infection. Am Rev Respir Dis 147:164–7
   PubMed Web of Science ®Google Scholar
• Tirkkonen T, Pakarinen J, Rintala E, et al. (2010). Comparison of variable-number tandem-repeat markers typing and IS1245 restriction fragment length polymorphism fingerprinting of Mycobacterium avium subsp. hominissuis from human and porcine origins. Acta Vet Scand 52:21
   PubMedGoogle Scholar
• Torres-Cruz J, van der Woude MW. (2003). Slipped-strand mispairing can function as a phase variation mechanism in Escherichia coli. J Bacteriol 185:6990–4
   PubMed Web of Science ®Google Scholar
• van Belkum A. (1999). Short sequence repeats in microbial pathogenesis and evolution. Cell Mol Life Sci 56:729–34
   PubMed Web of Science ®Google Scholar
• van Belkum A. (2007). Tracing isolates of bacterial species by multilocus variable number of tandem repeat analysis (MLVA). FEMS Immunol Med Microbiol 49:22–7
   PubMed Web of Science ®Google Scholar
• van Belkum A, Scherer S, van Alphen L, Verbrugh H. (1998). Short-sequence DNA repeats in prokaryotic genomes. Microbiol Mol Biol Rev 62:275–93
   PubMed Web of Science ®Google Scholar
• Viana-Niero C, Gutierrez C, Sola C, et al. (2001). Genetic diversity of Mycobacterium africanum clinical isolates based on IS6110-restriction fragment length polymorphism analysis, spoligotyping, and variable number of tandem DNA repeats. J Clin Microbiol 39:57–65
   PubMed Web of Science ®Google Scholar
• Viguera E, Canceill D, Ehrlich SD. (2001). In vitro replication slippage by DNA polymerases from thermophilic organism. J Mol Biol 312:323–33
   PubMed Web of Science ®Google Scholar
• Weng XM, Wen Y, Tian XJ, et al. (2006). Preliminary study on the genotyping of Mycobacterium leprae on 50 isolates from China. Zhonghua Liu Xing Bing Xue Za Zhi 27:402–5 [ in Chinese]
   PubMedGoogle Scholar
• WHO. (2014). Global tuberculosis report 2014. Available from: http://apps.who.int/iris/bitstream/10665/137094/1/9789241564809_eng.pdf?ua=1
   Google Scholar
• Wong YL, Ong CS, Ngeow YF. (2012). Molecular typing of Mycobacterium abscessus based on tandem-repeat polymorphism. J Clin Microbiol 50:3084–8
   PubMed Web of Science ®Google Scholar
• Xiao L, Liu C, Xie CC, et al. (2012). The direct repeat sequence upstream of Bacillus chitinase genes is cis-acting elements that negatively regulate heterologous expression in E. coli. Enzyme Microb Technol 50:280–6
   PubMed Web of Science ®Google Scholar
• Young SK, Ponnighaus JM, Jain S, et al. (2008). Use of short tandem repeat sequences to study Mycobacterium leprae in leprosy patients in Malawi and India. PLoS Negl Trop Dis 2:e214
   PubMedGoogle Scholar
• Zhang L, Budiawan T, Matsuoka M. (2005). Diversity of potential short tandem repeats in Mycobacterium leprae and application for molecular typing. J Clin Microbiol 43:5221–9
   PubMed Web of Science ®Google Scholar
• Zhao X, Wang Y, Pang Y. (2014). Antimicrobial susceptibility and molecular characterization of Mycobacterium intracellular in China. Infect Genet Evol 27:332–8
   PubMed Web of Science ®Google Scholar
• Zhou A, Xu Z. Sun Q, et al. (2012). Research on relationship between polymorphisms of Mtub-39 and expression of downsream genes of Mycobacterium tuberculosis. J Shanghai Jiaotong Univ 32:1415–20 [ in Chinese]
   Google Scholar
• Zumarraga JM, Bernardelli A, Bastida R, et al. (1999). Molecular characterisation of mycobacteria isolated from seals. Microbiology 145:2519–26
   PubMed Web of Science ®Google Scholar