MUBII-TB-DB: A database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Flandrois, Jean Pierre ^a   Lina, Gérard ^b,c   Dumitrescu, Oana ^b,c  

^a UNIVERSITÉ LYON 1   (France)

^b CENTRE INTERNATIONAL DE RECHERCHE EN INFECTIOLOGIE   (France)

^c HOSPICES CIVILS DE LYON   (France)

Author keywords

Antibiotics; Mutation database; Sequence database; Tuberculosis; Web

Indexed keywords

ANTIBIOTICS; BIOINFORMATICS; DATABASE SYSTEMS; DNA SEQUENCES; DRUG THERAPY; GENE ENCODING; HEALTH RISKS; MOLECULAR BIOLOGY; POLYMERASE CHAIN REACTION; PROTEINS;

ANTIBIOTIC RESISTANCE; CLIENT-SERVER MODELS; MYCOBACTERIUM TUBERCULOSIS; PROTEIN TRANSLATION; SEQUENCE DATABASE; STRUCTURED DATABASE; TUBERCULOSIS; WEB;

QUERY PROCESSING;

BACTERIA (MICROORGANISMS); MYCOBACTERIUM TUBERCULOSIS;

BACTERIAL DNA; TUBERCULOSTATIC AGENT;

ANTIBIOTIC RESISTANCE; ARTICLE; CHEMISTRY; DNA SEQUENCE; DRUG EFFECT; GENETIC DATABASE; GENETICS; HUMAN; MOLECULAR GENETICS; MUTATION; MYCOBACTERIUM TUBERCULOSIS; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT;

ANTITUBERCULAR AGENTS; BASE SEQUENCE; DATABASES, GENETIC; DNA, BACTERIAL; DRUG RESISTANCE, BACTERIAL; HUMANS; MOLECULAR SEQUENCE DATA; MUTATION; MYCOBACTERIUM TUBERCULOSIS; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 84899490207     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-107     Document Type: Article

References (29)

1. Comas I, Coscolla M, Luo T, Borrell S, Holt KE, Kato-Maeda M, Parkhill J, Malla B, Berg S, Thwaites G, Yeboah-Manu D, Bothamley G, Mei J, Wei L, Bentley S, Harris SR, Niemann S, Diel R, Aseffa A, Gao Q, Young D, Gagneux S. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet 2013, 45(10):1176-1182. 10.1038/ng.2744, 3800747, 23995134.
2. Wilson LG. Commentary: Medicine, population, and tuberculosis. Int J Epidemiol 2005, 34:521-524.
3. Abubakar I, Pimpin L, Ariti C, Beynon R, Mangtani P, Sterne J, Fine P, Smith P, Lipman M, Elliman D, Watson J, Drumright L, Whiting P, Vynnycky E, Rodrigues L. Systematic review and meta-analysis of the current evidence on the duration of protection by bacillus Calmette-Guérin vaccination against tuberculosis. Health Technol Assess 2013, 17:1-372.
4. Colditz GA. Efficacy of BCG Vaccine in the Prevention of Tuberculosis Meta-analysis of the Published Literature. JAMA 1994, 271:698. 10.1001/jama.1994.03510330076038, 8309034.
5. Boehme CC, Saacks S, O'Brien RJ. The changing landscape of diagnostic services for tuberculosis. Semin Respir Crit Care Med 2013, 34:17-31. 10.1055/s-0032-1333468, 23460003.
6. World Health Organization WHO Global tuberculosis report 2012 2012, Geneva, Switzerland: Word Health Organization, World Health Organization.
7. Sotgiu G, Centis R, D'Ambrosio L, Tadolini M, Castiglia P, Migliori GB. Do we need a new Fleming époque: The nightmare of drug-resistant tuberculosis. Int J Mycobacteriology 2013, 2:123-125.
8. Lynch JB. Multidrug-resistant Tuberculosis. Med Clin North Am 2013, 97(4):553-579. ix-x, 10.1016/j.mcna.2013.03.012, 23809714.
9. Wilson ML. Rapid diagnosis of Mycobacterium tuberculosis infection and drug susceptibility testing. Arch Pathol Lab Med 2013, 137:812-819. 10.5858/arpa.2011-0578-RA, 23721277.
10. Horne DJ, Pinto LM, Arentz M, Lin S-YG, Desmond E, Flores LL, Steingart KR, Minion J. Diagnostic accuracy and reproducibility of WHO-endorsed phenotypic drug susceptibility testing methods for first-line and second-line antituberculosis drugs. J Clin Microbiol 2013, 51:393-401. 10.1128/JCM.02724-12, 3553871, 23152548.
11. Piersimoni C, Mustazzolu A, Giannoni F, Bornigia S, Gherardi G, Fattorini L. Prevention of false resistance results obtained in testing the susceptibility of Mycobacterium tuberculosis to pyrazinamide with the Bactec MGIT 960 system using a reduced inoculum. J Clin Microbiol 2013, 51:291-294. 10.1128/JCM.01838-12, 3536208, 23100351.
12. Falzon D, Jaramillo E, Schünemann HJ, Arentz M, Bauer M, Bayona J, Blanc L, Caminero JA, Daley CL, Duncombe C, Fitzpatrick C, Gebhard A, Getahun H, Henkens M, Holtz TH, Keravec J, Keshavjee S, Khan AJ, Kulier R, Leimane V, Lienhardt C, Lu C, Mariandyshev A, Migliori GB, Mirzayev F, Mitnick CD, Nunn P, Nwagboniwe G, Oxlade O, Palmero D, et al. WHO guidelines for the programmatic management of drug-resistant tuberculosis: 2011 update. Eur Respir J 2011, 38:516-528. 10.1183/09031936.00073611, 21828024.
13. Heym B, Cole ST. Multidrug resistance in Mycobacterium. Int J Antimicrob Agents 1997, 8:61-70. 10.1016/S0924-8579(96)00356-1, 18611785.
14. Warner DF, Mizrahi V. Complex genetics of drug resistance in Mycobacterium tuberculosis. Nat Genet 2013, 45:1107-1108. 10.1038/ng.2769, 24071843.
15. Musser JM. Antimicrobial agent resistance in mycobacteria: molecular genetic insights Antimicrobial Agent Resistance in Mycobacteria: Molecular Genetic Insights. Clin Microbiol 1995, 8:496-514.
16. Almeida Da Silva PEA, Palomino JC. Molecular basis and mechanisms of drug resistance in Mycobacterium tuberculosis: classical and new drugs. J Antimicrob Chemother 2011, 66:1417-1430. 10.1093/jac/dkr173, 21558086.
17. Zhang Y, Yew WW. STATE OF THE ART Mechanisms of drug resistance in Mycobacterium tuberculosis. Int J Tuberc Lung Dis 2009, 13:1320-1330.
18. Kontsevaya I, Ignatyeva O, Nikolayevskyy V, Balabanova Y, Kovalyov A, Kritsky A, Matskevich O, Drobniewski F. Diagnostic accuracy of the genotype MTBDRsl assay for rapid diagnosis of extensively drug-resistant tuberculosis in HIV-coinfected patients. J Clin Microbiol 2013, 51:243-248. 10.1128/JCM.02513-12, 3536261, 23152552.
19. Alonso M, Palacios JJ, Herranz M, Penedo A, Menéndez A, Bouza E, García de Viedma D. Isolation of Mycobacterium tuberculosis strains with a silent mutation in rpoB leading to potential misassignment of resistance category. J Clin Microbiol 2011, 49:2688-2690. 10.1128/JCM.00659-11, 3147855, 21562104.
20. Campbell PJ, Morlock GP, Sikes RD, Dalton TL, Metchock B, Starks AM, Hooks DP, Cowan LS, Plikaytis BB, Posey JE. Molecular detection of mutations associated with first- and second-line drug resistance compared with conventional drug susceptibility testing of Mycobacterium tuberculosis. Antimicrob Agents Chemother 2011, 55:2032-2041. 10.1128/AAC.01550-10, 3088277, 21300839.
21. Feuerriegel S, Oberhauser B, George AG, Dafae F, Richter E, Rüsch-Gerdes S, Niemann S. Sequence analysis for detection of first-line drug resistance in Mycobacterium tuberculosis strains from a high-incidence setting. BMC Microbiol 2012, 12:90. 10.1186/1471-2180-12-90, 3404943, 22646308.
22. 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 T, 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 X-E, Bi L. Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance. Nat Genet 2013, 45:1255-1260. 10.1038/ng.2735, 23995137.
23. Sandgren A, Strong M, Muthukrishnan P, Weiner BK, Church GM, Murray MB. Tuberculosis drug resistance mutation database. PLoS Med 2009, 6:e2. 10.1371/journal.pmed.1000002, 2637921, 19209951.
24. Cole S, Brosch R, Parkhill J, Garnier T. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 1998, 393:537-544. 10.1038/31159, 9634230.
25. Tatusova TA, Madden TL. BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 1999, 174:247-250. 10.1111/j.1574-6968.1999.tb13575.x, 10339815.
26. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410. 10.1016/S0022-2836(05)80360-2, 2231712.
27. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
28. Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 2008, 9:286-298. 10.1093/bib/bbn013, 18372315.
29. Rice P, Longden I, Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet 2000, 16:2-3.