A quantitative and efficient approach to select MIRU–VNTR loci based on accumulation of the percentage differences of strains for discriminating divergent Mycobacterium tuberculosis sublineages

References

• Niemann S, Diel R, Khechinashvili Get al.Mycobacterium tuberculosis Beijing lineage favors the spread of multidrug-resistant tuberculosis in the Republic of Georgia. J Clin Microbiol 2010;48: 3544–3550.
   PubMed Web of Science ®Google Scholar
• Stoffels K, Allix-Beguec C, Groenen Get al.From multidrug- to extensively drug-resistant tuberculosis: upward trends as seen from a 15-year nationwide study. PLoS ONE 2013;8: e63128.
   PubMed Web of Science ®Google Scholar
• Casali N, Nikolayevskyy V, Balabanova Yet al.Evolution and transmission of drug-resistant tuberculosis in a Russian population. Nat Genet 2014;46: 279–286.
   PubMed Web of Science ®Google Scholar
• Munsiff SS, Nivin B, Sacajiu Get al.Persistence of a highly resistant strain of tuberculosis in New York City during 1990-1999. J Infect Dis 2003;188: 356–363.
   PubMed Web of Science ®Google Scholar
• Glynn JR, Whiteley J, Bifani PJet al.Worldwide occurrence of Beijing/W strains of Mycobacterium tuberculosis: a systematic review. Emerg Infect Dis 2002;8: 843–849.
   PubMed Web of Science ®Google Scholar
• Merker M, Blin C, Mona Set al.Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat Genet 2015;47: 242–249.
   PubMed Web of Science ®Google Scholar
• Bifani PJ, Mathema B, Kurepina NEet al.Global dissemination of the Mycobacterium tuberculosis W-Beijing family strains. Trends Microbiol 2002;10: 45–52.
   PubMed Web of Science ®Google Scholar
• Parwati I, van Crevel R, van Soolingen D.Possible underlying mechanisms for successful emergence of the Mycobacterium tuberculosis Beijing genotype strains. Lancet Infect Dis 2010;10: 103–111.
   PubMed Web of Science ®Google Scholar
• Hanekom M, Gey van Pittius NC, McEvoy Cet al.Mycobacterium tuberculosis Beijing genotype: a template for success. Tuberculosis 2011;91: 510–523.
   PubMed Web of Science ®Google Scholar
• de Jong BC, Hill PC, Aiken Aet al.Progression to active tuberculosis, but not transmission, varies by Mycobacterium tuberculosis lineage in the Gambia. J Infect Dis 2008;198: 1037–1043.
   PubMed Web of Science ®Google Scholar
• Kato-Maeda M, Shanley CA, Ackart Det al.Beijing sublineages of Mycobacterium tuberculosis differ in pathogenicity in the guinea pig. Clin Vaccine Immunol 2012;19: 1227–1237.
   PubMed Web of Science ®Google Scholar
• Zhang Z, Lu J, Liu Met al.Genotyping and molecular characteristics of multidrug-resistant Mycobacterium tuberculosis isolates from China. J Infect 2015;70: 335–345.
   PubMed Web of Science ®Google Scholar
• Kozinska M, Augustynowicz-Kopec E.Drug resistance and population structure of Mycobacterium tuberculosis Beijing strains isolated in Poland. Pol J Microbiol 2015;64: 399–401.
   PubMed Web of Science ®Google Scholar
• Pang Y, Zhou Y, Zhao Bet al.Spoligotyping and drug resistance analysis of Mycobacterium tuberculosis strains from national survey in China. PLoS One 2012;7: e32976.
   PubMed Web of Science ®Google Scholar
• Zhang Z, Pang Y, Wang Yet al.Beijing genotype of Mycobacterium tuberculosis is significantly associated with linezolid resistance in multidrug-resistant and extensively drug-resistant tuberculosis in China. Int J Antimicrob Agents 2014;43: 231–235.
   PubMed Web of Science ®Google Scholar
• Liu BB, Lu LP, Lu Bet al.Meta analysis on the correlation between Mycobacterium tuberculosis Beijing family strains and drug resistance. Zhonghua Yu Fang Yi Xue Za Zhi 2012;46: 158–164.
   PubMedGoogle Scholar
• Jou R, Chiang CY, Huang WL.Distribution of the Beijing family genotypes of Mycobacterium tuberculosis in Taiwan. J Clin Microbiol 2005;43: 95–100.
   PubMed Web of Science ®Google Scholar
• Mathuria JP, Srivastava GN, Sharma Pet al.Prevalence of Mycobacterium tuberculosis Beijing genotype and its association with drug resistance in North India. J Infect Public Health 2017;10: 409–414.
   PubMed Web of Science ®Google Scholar
• Wang J, Liu Y, Zhang CLet al.Genotypes and characteristics of clustering and drug susceptibility of Mycobacterium tuberculosis isolates collected in Heilongjiang Province, China. J Clin Microbiol 2011;49: 1354–1362.
   PubMed Web of Science ®Google Scholar
• Mokrousov I.Mycobacterium tuberculosis phylogeography in the context of human migration and pathogen's pathobiology: insights from Beijing and Ural families. Tuberculosis 2015;95 (Suppl 1): S167–S176.
   PubMed Web of Science ®Google Scholar
• Garzelli C, Lari N, Rindi L.Genomic diversity of Mycobacterium tuberculosis Beijing strains isolated in Tuscany, Italy, based on large sequence deletions, SNPs in putative DNA repair genes and MIRU-VNTR polymorphisms. Tuberculosis 2016;97: 147–153.
   PubMed Web of Science ®Google Scholar
• Liu Q, Luo T, Dong Xet al.Genetic features of Mycobacterium tuberculosis modern Beijing sublineage. Emerg Microbes Infect 2016;5: e14.
   PubMed Web of Science ®Google Scholar
• Rindi L, Lari N, Cuccu Bet al.Evolutionary pathway of the Beijing lineage of Mycobacterium tuberculosis based on genomic deletions and mutT genes polymorphisms. Infect Genet Evol 2009;9: 48–53.
   PubMed Web of Science ®Google Scholar
• Coscolla M, Gagneux S.Consequences of genomic diversity in Mycobacterium tuberculosis. Semin Immunol 2014;26: 431–444.
   PubMed Web of Science ®Google Scholar
• Warner DF, Koch A, Mizrahi V.Diversity and disease pathogenesis in Mycobacterium tuberculosis. Trends Microbiol 2015;23: 14–21.
   PubMed Web of Science ®Google Scholar
• Chaidir L, Sengstake S, de Beer Jet al.Predominance of modern Mycobacterium tuberculosis strains and active transmission of Beijing sublineage in Jayapura, Indonesia Papua. Infect Genet Evol 2016;39: 187–193.
   PubMed Web of Science ®Google Scholar
• Li D, Dong CB, Cui JYet al.Dominant modern sublineages and a new modern sublineage of Mycobacterium tuberculosis Beijing family clinical isolates in Heilongjiang Province, China. Infect Genet Evol 2014;27: 294–299.
   PubMed Web of Science ®Google Scholar
• Ei PW, Aung WW, Lee JSet al.Molecular strain typing of Mycobacterium tuberculosis: a review of frequently used methods. J Korean Med Sci 2016;31: 1673–1683.
   PubMed Web of Science ®Google Scholar
• Witney AA, Cosgrove CA, Arnold Aet al.Clinical use of whole genome sequencing for Mycobacterium tuberculosis. BMC Med 2016;14: 46.
   PubMed Web of Science ®Google Scholar
• Kanduma E, McHugh TD, Gillespie SH.Molecular methods for Mycobacterium tuberculosis strain typing: a users guide. J Appl Microbiol 2003;94: 781–791.
   PubMed Web of Science ®Google Scholar
• Hachisu Y, Hashimoto R, Kishida Ket al.Analytical procedure of variable number of tandem repeats (VNTR) analysis and effective use of analysis results for tuberculosis control. Rinsho Byori 2013;61: 1123–1135.
   PubMedGoogle Scholar
• Mears J, Abubakar I, Cohen Tet al.Effect of study design and setting on tuberculosis clustering estimates using mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR): a systematic review. BMJ Open 2015;5: e005636.
   PubMed Web of Science ®Google Scholar
• Alonso-Rodriguez N, Martinez-Lirola M, Sanchez MLet al.Prospective universal application of mycobacterial interspersed repetitive-unit-variable-number tandem-repeat genotyping to characterize Mycobacterium tuberculosis isolates for fast identification of clustered and orphan cases. J Clin Microbiol 2009;47: 2026–2032.
   PubMed Web of Science ®Google Scholar
• de Beer JL, Kremer K, Kodmon Cet al.First worldwide proficiency study on variable-number tandem-repeat typing of Mycobacterium tuberculosis complex strains. J Clin Microbiol 2012;50: 662–669.
   PubMed Web of Science ®Google Scholar
• Streit E, Baboolal S, Akpaka PEet al.Finer characterization of Mycobacterium tuberculosis using spoligotyping and 15-loci MIRU-VNTRs reveals phylogeographical specificities of isolates circulating in Guyana and Suriname. Infect Genet Evol 2015;30: 114–119.
   PubMed Web of Science ®Google Scholar
• Luo T, Yang C, Pang Yet al.Development of a hierarchical variable-number tandem repeat typing scheme for Mycobacterium tuberculosis in China. PLoS One 2014;9: e89726.
   PubMed Web of Science ®Google Scholar
• Srilohasin P, Chaiprasert A, Tokunaga Ket al.Genetic diversity and dynamic distribution of Mycobacterium tuberculosis isolates causing pulmonary and extrapulmonary tuberculosis in Thailand. J Clin Microbiol 2014;52: 4267–4274.
   PubMed Web of Science ®Google Scholar
• Filliol I, Motiwala AS, Cavatore Met al.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: 759–772.
   PubMed Web of Science ®Google Scholar
• Liu Y, Wang S, Lu Het al.Genetic diversity of the Mycobacterium tuberculosis Beijing family based on multiple genotyping profiles. Epidemiol Infect 2016;144: 1728–1735.
   PubMed Web of Science ®Google Scholar
• Chen YY, Chang JR, Huang WFet al.Genetic diversity of the Mycobacterium tuberculosis Beijing family based on SNP and VNTR typing profiles in Asian countries. PLoS One 2012;7: e39792.
   PubMed Web of Science ®Google Scholar
• Cardoso Oelemann M, Gomes HM, Willery Eet al.The forest behind the tree: phylogenetic exploration of a dominant Mycobacterium tuberculosis strain lineage from a high tuberculosis burden country. PLoS ONE 2011;6: e18256.
   PubMed Web of Science ®Google Scholar
• Luo T, Yang C, Gagneux Set al.Combination of single nucleotide polymorphism and variable-number tandem repeats for genotyping a homogenous population of Mycobacterium tuberculosis Beijing strains in China. J Clin Microbiol 2012;50: 633–639.
   PubMed Web of Science ®Google Scholar
• Li D, Wang JL, Ji BYet al.Persistently high prevalence of primary resistance and multidrug resistance of tuberculosis in Heilongjiang Province, China. BMC Infect Dis 2016;16: 516.
   PubMed Web of Science ®Google Scholar
• Nakajima C, Tamaru A, Rahim Zet al.Simple multiplex PCR assay for identification of Beijing family Mycobacterium tuberculosis isolates with a lineage-specific mutation in Rv0679c. J Clin Microbiol 2013;51: 2025–2032.
   PubMed Web of Science ®Google Scholar
• Gagneux S, Small PM.Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infect Dis 2007;7: 328–337.
   PubMed Web of Science ®Google Scholar
• Selander RK, Caugant DA, Ochman Het al.Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl Environ Microbiol 1986;51: 873–884.
   PubMed Web of Science ®Google Scholar
• Wada T, Iwamoto T, Maeda S.Genetic diversity of the Mycobacterium tuberculosis Beijing family in East Asia revealed through refined population structure analysis. FEMS Microbiol Lett 2009;291: 35–43.
   PubMed Web of Science ®Google Scholar
• Supply P, Allix C, Lesjean Set al.Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol 2006;44: 4498–4510.
   PubMed Web of Science ®Google Scholar
• Mazars E, Lesjean S, Banuls ALet al.High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology. Proc Natl Acad Sci USA 2001;98: 1901–1906.
   PubMed Web of Science ®Google Scholar
• Jiang Y, Liu HC, Zheng Het al.19-VNTR loci used in genotyping Chinese clinical Mycobacterium tuberculosis complex strains and in association with spoligotyping. J Basic Microbiol 2013;53: 562–580.
   PubMed Web of Science ®Google Scholar
• Mokrousov I, Narvskaya O, Vyazovaya Aet al.Mycobacterium tuberculosis Beijing genotype in Russia: in search of informative variable-number tandem-repeat loci. J Clin Microbiol 2008;46: 3576–3584.
   PubMed Web of Science ®Google Scholar
• Chin PJ, Chiu CC, Jou R.Identification of Beijing lineage Mycobacterium tuberculosis with combined mycobacterial interspersed repetitive unit loci 26, 31, and ETR-A. J Clin Microbiol 2007;45: 1022–1023.
   PubMed Web of Science ®Google Scholar
• Liu R, Xing L, Peng Zet al.Usefulness of mycobacterial interspersed repetitive-unit locus PCR amplification in rapid diagnosis of Beijing lineage strain infection among pediatric tuberculosis patients. J Clin Microbiol 2011;49: 712–714.
   PubMed Web of Science ®Google Scholar
• Surikova OV, Voitech DS, Kuzmicheva Get al.Efficient differentiation of Mycobacterium tuberculosis strains of the W-Beijing family from Russia using highly polymorphic VNTR loci. Eur J Epidemiol 2005;20: 963–974.
   PubMed Web of Science ®Google Scholar
• Faksri K, Drobniewski F, Nikolayevskyy Vet al.Genetic diversity of the Mycobacterium tuberculosis Beijing family based on IS6110, SNP, LSP and VNTR profiles from Thailand. Infect Genet Evol 2011;11: 1142–1149.
   PubMed Web of Science ®Google Scholar
• Iwamoto T, Grandjean L, Arikawa Ket al.Genetic diversity and transmission characteristics of Beijing family strains of Mycobacterium tuberculosis in Peru. PLoS ONE 2012;7: e49651.
   PubMed Web of Science ®Google Scholar
• Kam KM, Yip CW, Tse LWet al.Optimization of variable number tandem repeat typing set for differentiating Mycobacterium tuberculosis strains in the Beijing family. FEMS Microbiol Lett 2006;256: 258–265.
   PubMed Web of Science ®Google Scholar
• Wada T, Iwamoto T.Allelic diversity of variable number of tandem repeats provides phylogenetic clues regarding the Mycobacterium tuberculosis Beijing family. Infect Genet Evol 2009;9: 921–926.
   PubMed Web of Science ®Google Scholar