Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology

BMC Genomics

Stephen J O’Brien⁶  Alla L Lapidus⁷  Olga V Narvskaya³  Anna A Vyazovaya³  Igor V Mokrousov³  Elena Y Nosova⁵  Yulia D Isaeva⁵  Peter K Yablonsky²  Olga A Manicheva²  Vyacheslav Y Zhuravlev²  Vadim M Govorun⁴  Elena N Ilina⁴  Elena S Kostryukova⁴  Irina Y Karpova⁴  Dmitry S Ischenko¹  Egor A Shitikov⁴  Serguei A Simonov⁶  Pavel V Dobrynin⁶  Mikhail S Rotkevich⁶  Marina V Shulgina²  Ekaterina N Chernyaeva⁶ 

[1] Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Russia;St. Petersburg Institute of Phthisiopulmonology, 2-4 Ligovskiy prospect, St. Petersburg, Russia;St. Petersburg Pasteur Institute, 14 Mira ul., St. Petersburg, Russia;Research Institute of Physical-Chemical Medicine, 1a Malaya Pirogovskaya ul, Moscow, Russia;Moscow Scientific-Practical Center of Treatment of Tuberculosis of Moscow Healthcare, 10 Stromynka ul., Moscow, Russia;St. Petersburg State University, Theodosius Dobzhansky Center for Genome Bioinformatics, 41 Sredniy prospect, St. Petersburg, Russia;St. Petersburg Academic University, 8/3 Khlopina ui., St. Petersburg, Russia

关键词: Database;    Whole genome sequencing;    Genetic diversity;    Mutation;    Genome variations;    Mycobacterium tuberculosis;   

Others  :  1217427
DOI  :  10.1186/1471-2164-15-308

 received in 2013-09-26, accepted in 2014-04-15,  发布年份 2014

【 摘 要 】

Background

Tuberculosis (TB) poses a worldwide threat due to advancing multidrug-resistant strains and deadly co-infections with Human immunodeficiency virus. Today large amounts of Mycobacterium tuberculosis whole genome sequencing data are being assessed broadly and yet there exists no comprehensive online resource that connects M. tuberculosis genome variants with geographic origin, with drug resistance or with clinical outcome.

Description

Here we describe a broadly inclusive unifying Genome-wide Mycobacterium tuberculosis Variation (GMTV) database, (http://mtb.dobzhanskycenter.org webcite) that catalogues genome variations of M. tuberculosis strains collected across Russia. GMTV contains a broad spectrum of data derived from different sources and related to M. tuberculosis molecular biology, epidemiology, TB clinical outcome, year and place of isolation, drug resistance profiles and displays the variants across the genome using a dedicated genome browser. GMTV database, which includes 1084 genomes and over 69,000 SNP or Indel variants, can be queried about M. tuberculosis genome variation and putative associations with drug resistance, geographical origin, and clinical stages and outcomes.

Conclusions

Implementation of GMTV tracks the pattern of changes of M. tuberculosis strains in different geographical areas, facilitates disease gene discoveries associated with drug resistance or different clinical sequelae, and automates comparative genomic analyses among M. tuberculosis strains.

【 授权许可】

   
2014 Chernyaeva et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

【 参考文献 】

• [1]World Health Organization: Global Tuberculosis Report 2012. France: WHO; 2012. Available: http://who.int/tb/publications/global_report/gtbr12_main.pdf webcite. Accessed 15 April 2014
• [2]Phillips L: Infectious disease: TB’s revenge. Nature 2013, 493(7430):14-16. doi:10.1038/493014a
• [3]Ross BC, Raios K, Jackson K, Dwyer B: Molecular cloning of a highly repeated DNA element from Mycobacterium tuberculosis and its use as an epidemiological tool. J Clin Microbiol 1992, 30(4):942-946.
• [4]van Embden JD, Cave MD, Crawford JT, Dale JW, Eisenach KD, Gicquel B, Hermans P, Martin C, McAdam R, Shinnick TM, Small PM: Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J Clin Microbiol 1993, 31(2):406-409.
• [5]Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S, Bunschoten A, Molhuizen H, Shaw R, Goyal M, van Embden J: Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol 1997, 35(4):907-914.
• [6]Frothingham R, Meeker-O’Connell WA: Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats. Microbiology 1998, 144(Pt 5):1189-1196.
• [7]Mazars E, Lesjean S, Banuls AL, Gilbert M, Vincent V, Gicquel B, Tibayrenc M, Locht C, Supply P: High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology. Proc Natl Acad Sci U S A 2001, 98(4):1901-1906.
• [8]Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, Varhol R, Birol I, Lem M, Sharma MK, Elwood K, Jones SJ, Brinkman FS, Brunham RC, Tang P: Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med 2011, 364(8):730-739.
• [9]Walker TM, Monk P, Grace Smith E, Peto TE: Contact investigations for outbreaks of Mycobacterium tuberculosis: advances through whole genome sequencing. Clin Microbiol Infect 2013. doi:10.1111/1469-0691.12183. Epub ahead of print
• [10]Roetzer A, Diel R, Kohl TA, Rückert C, Nübel U, Blom J, Wirth T, Jaenicke S, Schuback S, Rüsch-Gerdes S, Supply P, Kalinowski J, Niemann S: Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study. PLoS Med 2013, 10(2):e1001387. doi:10.1371/journal.pmed.1001387. Epub 2013 Feb 12
• [11]Das S, Roychowdhury T, Kumar P, Kumar A, Kalra P, Singh J, Singh S, Prasad HK, Bhattacharya A: Genetic heterogeneity revealed by sequence analysis of Mycobacterium tuberculosis isolates from extra-pulmonary tuberculosis patients. BMC Genomics 2013, 14:404. doi:10.1186/1471-2164-14-404 BioMed Central Full Text
• [12]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.
• [13]Filliol I, Motiwala AS, Cavatore M, Qi W, Hazbón MH, Bobadilla del Valle M, Fyfe J, García-García L, Rastogi N, Sola C, Zozio T, Guerrero MI, León CI, Crabtree J, Angiuoli S, Eisenach KD, Durmaz R, Joloba ML, Rendón A, Sifuentes-Osornio J, Ponce de León 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. [Erratum in: J Bacteriol 2006, 188(8):3162–3163]
• [14]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. Epub 2006 Feb 13
• [15]Comas I, Chakravartti J, Small PM, Galagan J, Niemann S, Kremer K, Ernst JD, Gagneux S: Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nat Genet 2010, 42(6):498-503. doi:10.1038/ng.590. Epub 2010 May 23
• [16]Homolka S, Projahn M, Feuerriegel S, Ubben T, Diel R, Nübel U, Niemann S: High resolution discrimination of clinical Mycobacterium tuberculosis complex strains based on single nucleotide polymorphisms. PLoS One 2012, 7(7):e39855. doi:10.1371/journal.pone.0039855. Epub 2012 Jul 2
• [17]Ioerger TR, Koo S, No EG, Chen X, Larsen MH, Jacobs WR Jr, 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. doi:10.1371/journal.pone.0007778
• [18]Ilina EN, Shitikov EA, Ikryannikova LN, Alekseev DG, Kamashev DE, Malakhova MV, Parfenova TV, Afanas’ev MV, Ischenko DS, Bazaleev NA, Smirnova TG, Larionova EE, Chernousova LN, Beletsky AV, Mardanov AV, Ravin NV, Skryabin KG, Govorun VM: Comparative genomic analysis of Mycobacterium tuberculosis drug resistant strains from Russia. PLoS One 2013, 8(2):e56577. doi:10.1371/journal.pone.0056577. Epub 2013 Feb 20
• [19]Lew JM, Kapopoulou A, Jones LM, Cole ST: TubercuList–10 years after. Tuberculosis (Edinb) 2011, 91(1):1-7. doi:10.1016/j.tube.2010.09.008. Epub 2010 Oct 25. PubMed PMID: 20980199
• [20]Reddy TB, Riley R, Wymore F, Montgomery P, DeCaprio D, Engels R, Gellesch M, Hubble J, Jen D, Jin H, Koehrsen M, Larson L, Mao M, Nitzberg M, Sisk P, Stolte C, Weiner B, White J, Zachariah ZK, Sherlock G, Galagan JE, Ball CA, Schoolnik GK: TB database: an integrated platform for tuberculosis research. Nucleic Acids Res 2009, 37(Database issue):D499-D508. doi:10.1093/nar/gkn652. Epub 2008 Oct3. PubMed PMID: 18835847; PubMed Central PMCID: PMC2686437
• [21]Vishnoi A, Srivastava A, Roy R, Bhattacharya A: MGDD: Mycobacterium tuberculosis genome divergence database. BMC Genomics 2008, 9:373. doi:10.1186/1471-2164-9-373 BioMed Central Full Text
• [22]Gillespie JJ, Wattam AR, Cammer SA, Gabbard JL, Shukla MP, Dalay O, Driscoll T, Hix D, Mane SP, Mao C, Nordberg EK, Scott M, Schulman JR, Snyder EE, Sullivan DE, Wang C, Warren A, Williams KP, Xue T, Yoo HS, Zhang C, Zhang Y, Will R, Kenyon RW, Sobral BW: PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect Immun 2011, 79(11):4286-4298. doi:10.1128/IAI.00207-11. Epub 2011 Sep 6
• [23]Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M: KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2012, 40(Database issue):D109-D114. doi:10.1093/nar/gkr988. Epub 2011 Nov 10. PubMed PMID: 22080510; PubMed Central PMCID: PMC3245020
• [24]Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28(1):27-30. PubMed PMID: 10592173; PubMed Central PMCID: PMC102409
• [25]Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9(4):357-359. doi:10.1038/nmeth.1923
• [26]Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup: The sequence alignment/map (SAM) format and SAMtools. Bioinformatics 2009, 25:2078-2079.
• [27]Danecek P, Auton A, Abecasis G, Albers C, Banks E, DePristo M, Handsaker R, Lunter G, Marth G, Sherry S, McVean G, Durbin R, 1000 Genomes Project Analysis Group: The variant call format and VCFtools. Bioinformatics 2011, 27(15):2156-2158. doi:10.1093/bioinformatics/btr330. Epub 2011 Jun 7
• [28]Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH: JBrowse: a next-generation genome browser. Genome Res 2009, 19(9):1630-1638. doi:10.1101/gr.094607.109. Epub 2009 Jul 1
• [29]Westesson O, Skinner M, Holmes I: Visualizing next-generation sequencing data with JBrowse. Brief Bioinform 2013, 14(2):172-177. doi:10.1093/bib/bbr078. Epub 2012 Mar 12
• [30]NCBI Sequence Read Archive [http://www.ncbi.nlm.nih.gov/Traces/sra/ webcite]
• [31]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. doi:10.1101/gr.128678.111. Epub 2012 Jan 31
• [32]Casali N, Nikolayevskyy V, Balabanova Y, Harris SR, Ignatyeva O, Kontsevaya I, Corander J, Bryant J, Parkhill J, Nejentsev S, Horstmann RD, Brown T, Drobniewski F: Evolution and transmission of drug-resistant tuberculosis in a Russian population. Nat Genet 2014, 46(3):279-286. doi:10.1038/ng.2878. Epub 2014 Jan
• [33]Brudey K, Driscoll JR, Rigouts L, Prodinger WM, Gori A, Al-Hajoj SA, Allix C, Aristimuño L, Arora J, Baumanis V, Binder L, Cafrune P, Cataldi A, Cheong S, Diel R, Ellermeier C, Evans JT, Fauville-Dufaux M, Ferdinand S, Garcia de Viedma D, Garzelli C, Gazzola L, Gomes HM, Guttierez MC, Hawkey PM, van Helden PD, Kadival GV, Kreiswirth BN, Kremer K, Kubin M, et al.: Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol 2006, 6:23. BioMed Central Full Text