Drug resistance to Mycobacterium tuberculosis: From the traditional Chinese view to modern systems biology

Critical Reviews in Microbiology

Volumn 41, Issue 3, 2015, Pages 399-410

  Xu, Yuhui ^a   Zhang, Zongde ^a   Sun, Zhaogang ^a  

^a CAPITAL MEDICAL UNIVERSITY   (China)

Author keywords

Drug resistance; Mycobacterium tuberculosis; Stress response; Systems biology; Traditional Chinese view

Indexed keywords

AMINOSALICYLIC ACID; ANTITOXIN; CAPREOMYCIN; ETHAMBUTOL; ISONIAZID; KANAMYCIN; PYRAZINAMIDE; QUINOLINE DERIVED ANTIINFECTIVE AGENT; RIFAMPICIN; STREPTOMYCIN; TOXIN; TUBERCULOSTATIC AGENT; TRANSCRIPTOME;

ANTIBIOTIC RESISTANCE; BACTERIAL CELL WALL; BIOMICS; CHINESE; DNA REPAIR; GENOMICS; INTERACTOMICS; METABOLOMICS; MISMATCH REPAIR; MUTATION; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS; REVIEW; TRANSCRIPTOMICS; CELL WALL; CHINA; DRUG EFFECTS; GENETICS; HUMAN; MICROBIAL SENSITIVITY TEST; MICROBIOLOGY; MULTIDRUG RESISTANCE; PHYSIOLOGY; SYSTEMS BIOLOGY; TRANSPORT AT THE CELLULAR LEVEL; TUBERCULOSIS, PULMONARY;

ANTITUBERCULAR AGENTS; BIOLOGICAL TRANSPORT; CELL WALL; CHINA; DRUG RESISTANCE, MULTIPLE, BACTERIAL; HUMANS; MICROBIAL SENSITIVITY TESTS; MYCOBACTERIUM TUBERCULOSIS; SOS RESPONSE (GENETICS); SYSTEMS BIOLOGY; TRANSCRIPTOME; TUBERCULOSIS, PULMONARY;

EID: 84941615687     PISSN: 1040841X     EISSN: 15497828     Source Type: Journal    
DOI: 10.3109/1040841X.2013.860948     Document Type: Review

References (165)

1. Adindla S, Guruprasad L. (2003), Sequence analysis corresponding to the PPE and PE proteins in Mycobacterium tuberculosis and other genomes. J Biosci 28: 169-79.
2. Alter O, Golub GH. (2004), Integrative analysis of genomescale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription. Proc Natl Acad Sci USA 101: 16577-82.
3. Amberson JB, McMahon BT, Pinner M. (1931), A clinical trial of sanocrysin in pulmonary tuberculosis. Am Rev Tuberc 24: 401-35.
4. Baek S-H, Li AH, Sassetti CM. (2011), Metabolic regulation of mycobacterial growth and antibiotic sensitivity. PLoS Biol 9: E1001065. DOI: 10.1371/journal.pbio.1001065.
5. Besra GS, Brennan PJ. (1997), The mycobacterial cell wall: Biosynthesis of arabinogalactan and lipoarabinomannan. Biochem Soc Trans 25: 845-50.
6. Beste DJ, McFadden J. (2010), System-level strategies for studying the metabolism of Mycobacterium tuberculosis. Mol Biosyst 6: 2363-72.
7. Bester M. (2009), Defining mechanisms that determine the levels of drug resistance in Mycobacterium tuberculosis [M. D. dissertation]. South Africa: Stellenbosch University.
8. Bhatt A, Molle V, Besra GS, et al. (2007), The Mycobacterium tuberculosis FAS-II condensing enzymes: Their role in mycolic acid biosynthesis, acid-fastness, pathogenesis and in future drug development. Mol Microbiol 64: 1442-54.
9. Bhowruth V, Alderwick LJ, Brown AK, et al. (2008), Tuberculosis: A balanced diet of lipids and carbohydrates. Biochem Soc Trans 36: 555-65.
10. Bi J, Wang H, Xie J. (2011), Comparative genomics of NAD(P) biosynthesis and novel antibiotic drug targets. J Cell Physiol 226: 1-40.
11. Borrell S, Gagneux S. (2011), Strain diversity, epistasis and the evolution of drug resistance in Mycobacterium tuberculosis. Clin Microbiol Infect 17: 815-20.
12. Boshoff HI, Durbach SI, Mizrahi V. (2001), DNA metabolism in Mycobacterium tuberculosis: Implications for drug resistance and strain variability. Scand J Infect Dis 33: 101-5.
13. Boshoff HIM, Myers TG, Copp BR, et al. (2004), The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: Novel insights into drug mechanisms of action. J Biol Chem 279: 40174-84.
14. Boshoff HIM, Reed MB, Barry 3rd CE, Mizrahi V. (2003), DnaE2 polymerase contributes to in vivo survival and the emergence of drug resistance in Mycobacterium tuberculosis. Cell 113: 183-93.
15. Braibant M, Gilot P, Content J. (2000), The ATP binding cassette (ABC) transport systems of Mycobacterium tuberculosis. FEMS Microbiol Rev 24: 449-67.
16. Bridge B, Sekiguch M, Tajiri T. (1996), Effect of mutY and mutM/fpg-1 mutations on starvation-Associated mutation in Escherichia coli: Implications for the role of 7,8-dihydro-8-oxoguanine. Mol Gen Genet 251: 352-7.
17. Brooks PC, Dawson LF, Rand L, Davis EO. (2006), The mycobacteriumspecific gene Rv2719c is DNA damage inducible independently of RecA. J Bacteriol 188: 6034-8.
18. Bumann D. (2009), System-level analysis of salmonella metabolism during infection. Curr Opin Microbiol 12: 559-67.
19. Chatterjee A, Saranath D, Bhatter P, Mistry N. (2013), Global transcriptional profiling of longitudinal clinical isolates of Mycobacterium tuberculosis exhibiting rapid accumulation of drug resistance. PLoS One 8: E54717.
20. Charles E, McKenna MH, Morton RF. (1955), Studies on the absorption, diffusion, and excretion of cycloserine. Antibiot Annu 3: 169-72.
21. Cole ST, Brosch R, Parkhill J, et al. (1998), Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537-44.
22. Comas I, Borrell S, Roetzer A, et al. (2011), Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nat Genet 44: 106-10.
23. Correia FF, D'Onofrio A, Rejtar T, et al. (2006), Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia coli. J Bacteriol 188: 8360-7.
24. Dawson LF, Dillury J, Davis E. (2010), RecA-independent DNA damage induction of Mycobacterium tuberculosis ruvC despite an appropriately located SOS box. J Bacteriol 192: 599-603.
25. De Rossi E, Arrigo P, Bellinzoni M, et al. (2002), The multidrug transporters belonging to major facilitator superfamily in Mycobacterium tuberculosis. Mol Med 8: 714-24.
26. Dover LG, Cerdeno-Tarraga AM, Pallen MJ, et al. (2004), Comparative cell wall core biosynthesis in the mycolated pathogens, Mycobacterium tuberculosis and Corynebacterium diphtheriae. FEMS Microbiol Rev 28: 225-50.
27. Durbach SI, Andersen SJ, Mizrahi V. (1997), SOS induction in mycobacteria: Analysis of the DNA-binding activity of a LexA-like repressor and its role in DNA damage induction of the recA gene from Mycobacterium smegmatis. Mol Microbiol 26: 643-53.
28. Durot M, Bourguignon P, Schachter V. (2008), Genome-scale models of bacterial metabolism: Reconstruction and applications. FEMS Microbiol Rev 33: 164-90.
29. Escribano I, Rodriguez JC, Llorca B, et al. (2007), Importance of the efflux pump systems in the resistance of Mycobacterium tuberculosis to fluoroquinolones and linezolid. Chemotherapy 53: 397-401.
30. Farhat MR, Shapiro BJ, Kieser KJ, et al. (2013), Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat Genet 45: 1183-9.
31. Feuerriegel S, Cox HS, Zarkua N, et al. (2009), Sequence analyses of just four genes to detect extensively drug-resistant Mycobacterium tuberculosis strains in multidrug-resistant tuberculosis patients undergoing treatment. Antimicrob Agents Chemother 53: 3353-6.
32. Fiehn O. (2001), Combining genomics, metabolome analysis, and biochemical modeling to understand metabolic networks. Comp Funct Genomics 2: 155-68.
33. Forbes M, Kuck NA, Peets EA. (1962), Mode of action of ethambutol. J Bacteriol 84: 1099-103.
34. Fraser CM, Gocayne JD, White O, et al. (1995), The minimal gene complement of Mycoplasma genitalium. Science 270: 397-403.
35. Freidlin PJ, Goldblatt D, Kaidar-Shwartz H, Rorman E. (2009), Polymorphic exact tandem repeat A (PETRA): A newly defined lineage of Mycobacterium tuberculosis in Israel originating predominantly in Sub-Saharan Africa. J Clin Microbiol 47: 4006-20.
36. Friedberg EC, Fischhaber PL. (2003), TB or not TB: How Mycobacterium tuberculosis may evade drug treatment. Cell 113: 139-40.
37. Frothingham R, Meeker-O'Connell WA. (1998), Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats. Microbiology 144: 1189-96.
38. Fu LM, Shinnick TM. (2007), Understanding the action of INH on a highly INH-resistant Mycobacterium tuberculosis strain using Genechips. Tuberculosis (Edinb) 87: 63-70.
39. Fu LM, Tai SC. (2009), The differential gene expression pattern of Mycobacterium tuberculosis in response to capreomycin and PA-824 versus first-Line TB drugs reveals stress-And PE/PPE-related drug targets. Int J Microbiol 2009: 879621.
40. Furesz S, Timball MT. (1963), The antibacterial activity of Rifamycins. Chemotherapy 12: 365-73.
41. Galagan JE, Sisk P, Stolte C, et al. (2010), TB database 2010: Overview and update. Tuberculosis (Edinb) 90: 225-35.
42. Gamulin V, Cetkovic H, Ahel I. (2004), Identification of a promoter motif regulating the major DNA damage response mechanism of Mycobacterium tuberculosis. FEMS Microbiol Lett 238: 57-63.
43. Georghiou SB, Magana M, Garfein RS, et al. (2012), Evaluation of genetic mutations associated with Mycobacterium tuberculosis resistance to amikacin, kanamycin and capreomycin: A systematic review. PLoS One 7: E33275.
44. Gillespie SH. (2002), Evolution of drug resistance in Mycobacterium tuberculosis: Clinical and molecular perspective. Antimicrob Agents Chemother 46: 267-74.
45. Gorna AE, Bowater RP, Dziadek J. (2010), DNA repair systems and the pathogenesis of Mycobacterium tuberculosis: Varying activities at different stages of infection. Clin Sci (Lond) 119: 187-202.
46. Gordon SV, Eiglmeier K, Brosch R, et al. (1999), Genomics of Mycobacterium tuberculosis and Mycobacterium leprae. In: Ratledge C, Dale J, eds. Mycobacteria: Molecular biology and virulence. Oxford: Blackwell Science Ltd, 93-109.
47. Grobbelaar M. (2012), Adaptation of the Mycobacterium tuberculosis transcriptome in response to rifampicin [MD dissertation]. South Africa: University of Stellenbosch.
48. Gupta AK, Chauhan DS, Srivastava K, et al. (2006), Estimation of efflux mediated multi-drug resistance and its correlation with expression levels of two major efflux pumps in mycobacteria. J Commun Dis 38: 246-54.
49. Gupta AK, Katoch VM, Chauhan DS, et al. (2010), Microarray analysis of efflux pump genes in multidrug-resistant Mycobacterium tuberculosis during stress induced by common anti-Tuberculous drugs. Microb Drug Resist 16: 21-8.
50. Gutierrez MC, Brisse S, Brosch R, et al. (2005), Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis. PLoS Pathog 1: E5.
51. Gygi SP, Rochon Y, Franza BR, Aebersold R. (1999), Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19: 1720-30.
52. Hegde PS, White IR, Debouck C. (2003), Interplay of transcriptomics and proteomics. Curr Opin Biotechnol 14: 647-51.
53. Hughes MA, Silva JC, Geromanos SJ, Townsend CA. (2006), Quantitative proteomic analysis of drug-induced changes in mycobacteria. J Proteome Res 5: 54-63.
54. IATDMCT Executive Committee. (2013), Definition of TDM. Available from: Http://www.iatdmct.org
55. Ilina EN, Shitikov EA, Ikryannikova LN, et al. (2013), Comparative genomic analysis of Mycobacterium tuberculosis drug resistant strains from Russia. PLoS One 8: E56577.
56. Ishii N, Tomita, M. (2009), Multi-omics data-driven systems biology of E. Coli. In: Lee SY, ed. Systems biology and biotechnology of Escherichia coli. Dordrecht, Netherlands: Springer, 41-57.
57. Jack DL, Yang NM, Saier Jr. MH. (2001), The drug/metabolite transporter superfamily. Eur J Biochem 268: 3620-39.
58. James P. (1997), Protein identification in the post-genome era: The rapid rise of proteomics. Q Rev Biophys 30: 279-333.
59. Jiang X, Zhang W, Gao F, et al. (2006), Comparison of the proteome of isoniazid-resistant and -susceptible strains of Mycobacterium tuberculosis. Microb Drug Resist 12: 231-8.
60. Jiang X, Zhang W, Zhang Y, et al. (2008), Assessment of efflux pump gene expression in a clinical isolate Mycobacterium tuberculosis by real-Time reverse transcription PCR. Microb Drug Resist 14: 7-11.
61. Jones D, Metzger HJ, Schatz A, Waksman SA. (1944), Control of Gramnegative bacteria in experimental animals by streptomycin. Science 100: 103-5.
62. Kandpal R, Saviola B, Felton J. (2009), The era of omics unlimited. Biotechniques 46: 351-5.
63. Kim TY, Kim HU, Lee SY. (2010), Metabolite-centric approaches for the discovery of antibacterials using genome-scale metabolic networks. Metabol Eng 12: 105-11.
64. Koch R. (1932), Die Aetiologie der Tuberkulose. J Mol Med 11: 490-2.
65. Koch R. (1952), Tuberculosis etiology. Dtsch Gesundheitsw 7: 457-65.
66. Koonin EV, Galperin MY. (1997), Prokaryotic genomes: The emerging paradigm of genome-based microbiology. Curr Opin Genet Dev 7: 757-63.
67. Köser CU, Bryant JM, Becq J, et al. (2013), Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis. N Engl J Med 369: 290-2.
68. Kuroda T, Tsuchiya T. (2009), Multidrug efflux transporters in the MATE family. Biochim Biophys Acta 1794: 763-8.
69. Li X-Z, Nikaido H. (2004), Efflux-mediated drug resistance in bacteria. Drugs 64: 159-204.
70. Li X-Z, Nikaido H. (2009), Efflux-mediated drug resistance in bacteria: An update. Drugs 69: 1555-623.
71. Li X-Z, Zhang L, Nikaido H. (2004), Efflux pump-mediated intrinsic drug resistance in Mycobacterium smegmatis. Antimicrob Agents Chemother 48: 2415-23.
72. Little JW. (1982), Control of the SOS regulatory system by the level of RecA protease. Biochimie 64: 585-9.
73. Liu CH, Li HM, Lu N, et al. (2012), Genomic sequence based scanning for drug resistance-Associated mutations and evolutionary analysis of multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis. J Infect 65: 412-22.
74. Lubelski J, Konings WN, Driessen AJ. (2007), Distribution and physiology of ABC-Type transporters contributing to multidrug resistance in bacteria. Microbiol Mol Biol Rev 71: 463-76.
75. Magdalena J, Vachée A, Supply P, Locht C. (1998), Identification of a new DNA region specific for members of Mycobacterium tuberculosis complex. J Clin Microbiol 36: 937-43.
76. Manca C, Lyashchenko K, Colangeli R, Gennaro ML. (1997), MTC28, a novel 28-kilodalton proline-rich secreted antigen specific for the Mycobacterium tuberculosis complex. Infect Immun 65: 4951-7.
77. Mathys V, Wintjens R, Lefevre P, et al. (2009), Molecular genetics of para-Aminosalicylic acid resistance in clinical isolates and spontaneous mutants of Mycobacterium tuberculosis. Antimicrob Agents Chemother 53: 2100-9.
78. Mc DW, Ormond L, Muschenheim C, et al. (1954), Pyrazinamideisoniazid in tuberculosis. Am Rev Tuberc 69: 319-33.
79. McNeil M, Daffe M, Brennan PJ. (1990), Evidence for the nature of the link between the arabinogalactan and peptidoglycan of mycobacterial cell walls. J Biol Chem 265: 18200-6.
80. McNeil MR, Brennan PJ. (1991), Structure, function and biogenesis of the cell envelope of mycobacteria in relation to bacterial physiology, pathogenesis and drug resistance; some thoughts and possibilities arising from recent structural information. Res Microbil 142: 451-63.
81. Michaels ML, Miller JH. (1992), The GO system protects organisms from the mutagenic effects of the spontaneous lesion, 8-hydroxyguanine (7,8-dihydro-8-oxoguanine), J Bacteriol 174: 6321-5.
82. Minnikin DE, Minnikin SM, Goodfellow M, Stanford JL. (1982), The mycolic acids of Mycobacterium chelonei. J Gen Microbiol 128: 817-22.
83. Mishra AK. (2009), Biochemical and molecular characterisation of cell wall glycosyltransferases in Mycobacterium tuberculosis [PhD dissertation]. University of Birmingham.
84. Mizrahi V, Andersen SJ. (1998), DNA repair in Mycobacterium tuberculosis. What have we learnt from the genome sequence? Mol Microbiol 29: 1331-9.
85. Mizrahi V, Dawes SS, Rubin H. (2000), DNA replication. In: Hatfull GF, Jacobs Jr. WR, eds. Molecular genetics of mycobacteria. Washington, DC: ASM Press, 159-72.
86. Modrich P, Lahue R. (1996), Mismatch repair in replication fidelity, genetic recombination and cancer biology. Annu Rev Biochem 65: 101-33.
87. Mootha VK, Bunkenborg J, Olsen JV, et al. (2003a), Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 115: 629-40.
88. Mootha VK, Lepage P, Miller K, et al. (2003b), Identification of a gene causing human cytochrome C oxidase deficiency by integrative genomics. Proc Natl Acad Sci USA 100: 605-10.
89. Movahedzadeh F, Colston MJ, Davis EO. (1997), Determination of DNA sequences required for regulated Mycobacterium tuberculosis RecA expression in response to DNA-damaging agents suggests that two modes of regulation exist. J Bacteriol 179: 3509-18.
90. Moyed HS, Bertrand KP. (1983), hipA, a newly recognized gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis. J Bacteriol 155: 768-75.
91. Moyed HS, Broderick SH. (1986), Molecular cloning and expression of hipA, a gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis. J Bacteriol 166: 399-403.
92. Munro SA, Lewin SA, Smith HJ, et al. (2007), Patient adherence to tuberculosis treatment: A systematic review of qualitative research. PLoS Med 4: E238.
93. Muschenheim C, Mc DW, Mc CR, et al. (1954), Pyrazinamide-isoniazid in tuberculosis. I. Results in 58 patients with pulmonary lesions one year after the start of therapy. Am Rev Tuberc 70: 743-7.
94. Nagley MM. (1949), Para-Aminosalicylic acid. Practitioner 163: 459-66.
95. Nagley MM, Logg MH. (1949), Para-Amino-salicylic acid in pulmonary tuberculosis. Lancet 1: 913-16.
96. Ng KP, Yew SM, Chan CL, et al. (2013), Draft genome sequence of the first isolate of extensively drug-resistant (XDR) Mycobacterium tuberculosis in Malaysia. Genome Announc 1: E00056-12. doi: 10.1128/genomeA.00056-12.
97. Niemann S, Köser CU, Gagneux S, et al. (2009), Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints. PLoS One 4: E7407.
98. O'Sullivan DM, Hinds J, Butcher PD, et al. (2008), Mycobacterium tuberculosis DNA repair in response to subinhibitory concentrations of ciprofloxacin. J Antimicrob Chemother 62: 1199-202.
99. Oda S, Kuraoka I, Maehara Y. (2007), DNA repair as a determinant of tumour chemosensitivity. Gan To Kagaku Ryoho 34: 347-57.
100. Pablos-Mendez A, Raviglione MC, Laszlo A, et al. (1998), Global surveillance for antituberculosis-drug resistance, 1994-1997. World Health Organization-International Union against Tuberculosis and Lung Disease Working Group on Anti-Tuberculosis Drug Resistance Surveillance. N Engl J Med 338: 1641-9.
101. Paluch-Oles J, Koziol-Montewka M, Magrys A. (2009), Mutations in the rpoB gene of rifampin-resistant Mycobacterium tuberculosis isolates from Eastern Poland. New Microbiol 2: 147-52.
102. Pao SS, Paulsen IT, Saier Jr. MH. (1998), Major facilitator superfamily. Microbiol Mol Biol Rev 62: 1-34.
103. Parsons LM, Driscoll JR, TaberHW, Salfinger M. (1997), Drug resistance in tuberculosis. Infect Dis Clin North Am 11: 905-28.
104. Pasca MR, Guglierame P, Arcesi F, et al. (2004), Rv2686c-Rv2687c-Rv2688c, an ABC fluoroquinolone efflux pump in Mycobacterium tuberculosis. Antimicrob Agents Chemother 48: 3175-8.
105. Pasca MR, Guglierame P, De Rossi E, et al. (2005), mmpL7 gene of Mycobacterium tuberculosis is responsible for isoniazid efflux in Mycobacterium smegmatis. Antimicrob Agents Chemother 49: 4775-7.
106. Pitaksajjakul P, Wongwit W, Punprasit W, et al. (2005), Mutations in the gyrA and gyrB genes of fluoroquinolone-resistant Mycobacterium tuberculosis from TB patients in Thailand. Southeast Asian J Trop Med Public Health 36: 228-37.
107. Plinke C, Cox HS, Kalon S, et al. (2009), Tuberculosis ethambutol resistance: Concordance between phenotypic and genotypic test results. Tuberculosis 89: 448-52.
108. Poulet S, Cole ST. (1995), Characterization of the highly abundant polymorphic GC-rich-repetitive sequence (PGRS) present in Mycobacterium tuberculosis. Arch Microbiol 163: 87-95.
109. Provvedi R, Boldrin F, Falciani F, et al. (2009), Global transcriptional response to vancomycin in Mycobacterium tuberculosis. Microbiology 155: 1093-102.
110. Raamsdonk LM, Teusink B, Broadhurst D, et al. (2001), A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat Biotechnol 19: 45-50.
111. Radmacher E, Stansen KC, Besra GS, et al. (2005), Ethambutol, a cell wall inhibitor of Mycobacterium tuberculosis, elicits L-glutamate efflux of Corynebacterium glutamicum. Microbiology (Reading, Engl.) 151: 1359-68.
112. Ramage HR, Connolly LE, Cox JS. (2009), Comprehensive functional analysis of Mycobacterium tuberculosis toxin-Antitoxin systems: Implications for pathogenesis, stress responses, and evolution. PLoS Genet 5: E1000767.
113. Raman K, Rajagopalan P, Chandra N. (2005), Flux balance analysis of mycolic acid pathway: Targets for anti-Tubercular drugs. PLoS Comput Biol 1: E46.
114. Ramon-Garcia S, Martin C, De Rossi E, Aínsa JA. (2007), Contribution of the Rv2333c efflux pump (the Stp protein) from Mycobacterium tuberculosis to intrinsic antibiotic resistance in Mycobacterium bovis BCG. J Antimicrob Chemother 59: 544-7.
115. Rand L, Hinds J, Springer B, et al. (2003), The majority of inducible DNA repair genes in Mycobacterium tuberculosis are induced independently of RecA. Mol Microbiol 50: 1031-42.
116. Safi H, Lingaraju S, Amin A, et al. (2013), Evolution of high-level ethambutol-resistant tuberculosis through interacting mutations in decaprenylphosphoryl-b-D-Arabinose biosynthetic and utilization pathway genes. Nat Genet 45: 1190-7.
117. Sancar A. (1994), Mechanisms of DNA excision repair. Science 266: 1954-6.
118. Schatz A, Bugie E, Waksman SA. (1944), Streptomycin, a substance exhibiting antibiotic activity against Gram-positive and Gram-negative bacteria. Proc Exp Biol Med 437: 3-6.
119. Schumacher MA, Piro KM, Xu W, et al. (2009), Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB. Science 323: 396-401.
120. Seeger MA, Diederichs K, Eicher T, et al. (2008), The AcrB efflux pump: Conformational cycling and peristalsis lead to multidrug resistance. Curr Drug Targets 9: 729-49.
121. Sharma P, Kumar B, Gupta Y, et al. (2010), Proteomic analysis of streptomycin resistant and sensitive clinical isolates of Mycobacterium tuberculosis. Proteome Sci 8: 59. doi: 10.1186/1477-5956-8-59.
122. Siddiqi N, Das R, Pathak N, et al. (2004), Mycobacterium tuberculosis isolate with a distinct genomic identity overexpresses a Tap-like efflux pump. Infection 32: 109-11.
123. Singh OV, Nagaraj NS. (2006), Transcriptomics, proteomics and interactomics: Unique approaches to track the insights of bioremediation. Brief Funct Genomic Proteomic 4: 355-62.
124. Sirgel FA, Tait M, Warren RM, et al. (2012), Mutations in the rrs A1401G gene and phenotypic resistance to amikacin and capreomycin in Mycobacterium tuberculosis. Microb Drug Resist 18: 193-7.
125. Snider Jr. DE, La Montagne JR. (1994), The neglected global tuberculosis problem: A report of the 1992 World Congress on Tuberculosis. J Infect Dis 169: 1189-96.
126. Springer B, Sander P, Sedlacek L, et al. (2004), Lack of mismatch correction facilitates genome evolution in mycobacteria. Mol Microbiol 53: 1601-9.
127. Srivastava S, Pasipanodya JG, Meek C, et al. (2011), Multidrug-resistant tuberculosis not due to noncompliance but to between-patient pharmacokinetic variability. J Infect Dis 204: 1951-9.
128. Steenken Jr. W, Wolinsky E. (1952a), Antituberculous properties of hydrazines of isonicotinic acid (rimifon, marsilid), Am Rev Tuberc 65: 365-75.
129. Steenken Jr. W, Wolinsky E. (1952b), Isoniazid in experimental tuberculosis. Trans Annu Meet Natl Tuberc Assoc 48: 425-30.
130. Sun G, Luo T, Yang C, et al. (2012), Dynamic population changes in Mycobacterium tuberculosis during acquisition and fixation of drug resistance in patients. J Infect Dis 206: 1724-33.
131. Supply P, Allix C, Lesjean S, et al. (2006), Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variablenumber tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol 44: 4498-510.
132. Takayama K, Kilburn JO. (1989), Inhibition of synthesis of arabinogalactan by ethambutol in Mycobacterium smegmatis. Antimicrob Agents Chemother 33: 1493-9.
133. Telenti A, Honoré N, Bernasconi C, et al. (1997), Genotypic assessment of isoniazid and rifampin resistance in Mycobacterium tuberculosis: A blind study at reference laboratory level. J Clin Microbiol 35: 719-23.
134. Telenti A, Philipp WJ, Sreevatsan S, et al. (1997), The emb operon, a gene cluster of Mycobacterium tuberculosis involved in resistance to ethambutol. Nat Med 3: 567-70.
135. The World Health Organization (WHO), (2013), Global tuberculosis report 2012. Available from: Http://apps.who.int/iris/bitstream/10665/75938/1/9789241564502-eng.pdf [last accessed May 2013].
136. Thiele I, Jamshidi N, Fleming RM, Palsson BO. (2009), Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: A knowledge base, its mathematical formulation, and its functional characterization. PLoS Comput Biol 5: E1000312.
137. Tompsett R, Mc Jr. CR, Ormond L, et al. (1954), The influence of pyrazinamide-isoniazid on M. tuberculosis in animals and man. Trans Assoc Am Physicians 67: 224-31.
138. Tram NV, Bach NH, Anh NT, et al. (2012), Preliminary remarks on assembly whole genome sequencing of MDR M. tuberculosis isolated in Vietnam. J Infect Dev Ctries 6: 95-6.
139. Trauger SA, Kalisak E, Kalisiak J, et al. (2008), Correlating the transcriptome, proteome, and metabolome in the environmental adaptation of a hyperthermophile. J Proteome Res 7: 1027-35.
140. Tseng TT, Gratwick KS, Kollman J, et al. (1999), The RND permease superfamily: An ancient, ubiquitous and diverse family that includes human disease and development proteins. J Mol Microbiol Biotechnol 1: 107-25.
141. Ulger M, Aslan G, Emekdas G, et al. (2009), Investigation of rpsL and rrs gene region mutations in streptomycin resistant Mycobacterium tuberculosis complex isolates. Mikrobiyol Bul 43: 115-20.
142. Velayati AA, Farnia P, Ibrahim TA, et al. (2009), Differences in cell wall thickness between resistant and nonresistant strains of Mycobacterium tuberculosis: Using transmission electron microscopy. Chemotherapy 55: 303-7.
143. Velayati AA, Farnia P, Merza MA, et al. (2010), New insight into extremely drug-resistant tuberculosis: Using atomic force microscopy. Eur Respir J 36: 1490-3.
144. Vilchèze C, Wang F, Arai M, et al. (2006), Transfer of a point mutation in Mycobacterium tuberculosis inhA resolves the target of isoniazid. Nat Med 12: 1027-9
145. Waddell SJ, Butche PD. (2010), Use of DNA arrays to study transcriptional responses to antimycobacterial compounds. Methods Mol Biol 642: 75-91.
146. Waddell SJ, Stabler RA, Laing K, et al. (2004), The use of microarray analysis to determine the gene expression profiles of Mycobacterium tuberculosis in response to anti-bacterial compounds. Tuberculosis (Edinb) 84: 263-74.
147. Wang Q, Yue J, Zhang L, et al. (2007), A newly identified 191A/C mutation in the Rv2629 gene that was significantly associated with rifampin resistance in Mycobacterium tuberculosis. J Proteome Res 6: 4564-71.
148. Wang R, Marcotte EM. (2008), The proteomic response of Mycobacterium smegmatis to anti-Tuberculosis drugs suggests targeted pathways. J Proteome Res 7: 855-65.
149. Wang Y, Huang Y, Xue C, et al. (2011), ClpR protein-like regulator specifically recognizes RecA protein-independent promoter motif and broadly regulates expression of DNA damage-inducible genes in mycobacteria. J Biol Chem 286: 1159-67.
150. Warner DF, Mizrahi V. (2013), Complex genetics of drug resistance in Mycobacterium tuberculosis. Nat Genet 45: 1107-8.
151. Watanabe M, Aoyagi Y, Ridell M, Minnikin DE. (2001), Separation and characterization of individual mycolic acids in representative mycobacteria. Microbiology 147: 1825-37.
152. Wilkins MR, Pasquali C, Appel RD, et al. (1996), From proteins to proteomes: Large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology (NY) 14: 61-5.
153. Wilson M, DeRisi J, Kristensen HH, et al. (1999), Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization. Proc Natl Acad Sci USA 96: 12833-8.
154. Wu W, Zheng H, Zhang L, et al. (2013), A genome-wide analysis of multidrug-resistant and extensively drug-resistant strains of Mycobacterium tuberculosis Beijing genotype. Mol Genet Genomics 288: 425-36.
155. Xu P, Li X, Zhao M, et al. (2009), Prevalence of fluoroquinolone resistance among tuberculosis patients in Shanghai, China. Antimicrob Agents Chemother 53: 3170-2.
156. Yang C. (2007), Primary studies on the genetic stability and proteome of Mycobacterium tuberculosis rifampin-depending strain [M. D. dissertation]. Chinese Academy of Military Medical Sciences, China (in Chinese).
157. Yüksel P, Tansel O. (2009), Characterization of pncA mutations of pyrazinamide-resistant Mycobacterium tuberculosis in Turkey. New Microbiol 32: 153-8.
158. Zambrano MM, Hernández-Neuta G, Hernández-Neuta I, et al. (2012), Genomic variability of Mycobacterium tuberculosis, understanding tuberculosis. In: Pere-Joan Cardona, ed. Deciphering the secret life of the bacilli. Catalonia: InTech, 37-57.
159. Zeng L, Shi T, Zhao Q, Xie J. (2013), Mycobacterium sulfur metabolism and implications for novel drug targets. Cell Biochem Biophys 65: 77-83.
160. Zhang H, Li D, Zhao L, et al. (2013), Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance. Nat Genet 45: 1255-60.
161. Zhang W, Li F, Nie L. (2010), Integrating multiple 'omics' analysis for microbial biology: Application and methodologies. Microbiology 56: 287-301.
162. Zhang Y, Yew WW. (2009), Mechanisms of drug resistance in Mycobacterium tuberculosis. Int J Tuberc Lung Dis 13: 1320-30.
163. Zhang Y, Chen C, Liu J, et al. (2011), Complete genome sequences of Mycobacterium tuberculosis strains CCDC5079 and CCDC5080, which belong to the Beijing family. J Bacteriol 193: 5591-2.
164. Zhao X, Yu H, Yu S, et al. (2006), Hydrogen peroxide-mediated isoniazid activation catalyzed by Mycobacterium tuberculosis catalase-peroxidase (KatG) and its S315T mutant. Biochemistry 45: 4131-40.
165. Zhu C, Zhao Y, Huang X, et al. (2013), Quantitative proteomic analysis of streptomycin resistant and sensitive clinical isolates of Mycobacterium tuberculosis. Wei Sheng Wu Xue Bao 53: 154-63.