BIGSdb: Scalable analysis of bacterial genome variation at the population level

BMC Bioinformatics - Tập 11 Số 1 - 2010
Keith A. Jolley1, Martin Maiden1
1Department of Zoology, University of Oxford, Oxford,#R# UK.

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Pettersson E, Lundeberg J, Ahmadian A: Generations of sequencing technologies. Genomics 2009, 93(2):105–111. 10.1016/j.ygeno.2008.10.003

Roumagnac P, Weill FX, Dolecek C, Baker S, Brisse S, Chinh NT, Le TA, Acosta CJ, Farrar J, Dougan G, et al.: Evolutionary history of Salmonella typhi . Science 2006, 314(5803):1301–1304. 10.1126/science.1134933

Baker S, Holt K, van de Vosse E, Roumagnac P, Whitehead S, King E, Ewels P, Keniry A, Weill FX, Lightfoot D, et al.: High-throughput genotyping of Salmonella enterica serovar Typhi allowing geographical assignment of haplotypes and pathotypes within an urban District of Jakarta, Indonesia. J Clin Microbiol 2008, 46(5):1741–1746. 10.1128/JCM.02249-07

Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX, Goodhead I, Rance R, Baker S, Maskell DJ, Wain J, et al.: High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi . Nat Genet 2008, 40(8):987–993. 10.1038/ng.195

Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK, Chantratita N, Gardete S, Tavares A, Day N, Lindsay JA, et al.: Evolution of MRSA during hospital transmission and intercontinental spread. Science 2010, 327(5964):469–474. 10.1126/science.1182395

Lewis T, Loman NJ, Bingle L, Jumaa P, Weinstock GM, Mortiboy D, Pallen MJ: High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak. J Hosp Infect 2010, 75(1):37–41. 10.1016/j.jhin.2010.01.012

Gilmour MW, Graham M, Van Domselaar G, Tyler S, Kent H, Trout-Yakel KM, Larios O, Allen V, Lee B, Nadon C: High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak. BMC Genomics 2010, 11: 120.

Beres SB, Carroll RK, Shea PR, Sitkiewicz I, Martinez-Gutierrez JC, Low DE, McGeer A, Willey BM, Green K, Tyrrell GJ, et al.: Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics. Proc Natl Acad Sci USA 2010, 107(9):4371–4376. 10.1073/pnas.0911295107

Maiden MCJ, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, et al.: Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 1998, 95(6):3140–3145. 10.1073/pnas.95.6.3140

Maiden MC: Multilocus Sequence Typing of Bacteria. Annu Rev Microbiol 2006, 60: 561–588. 10.1146/annurev.micro.59.030804.121325

Jolley KA, Brehony C, Maiden MC: Molecular typing of meningococci: recommendations for target choice and nomenclature. FEMS Microbiol Rev 2007, 31(1):89–96. 10.1111/j.1574-6976.2006.00057.x

Dingle KE, McCarthy ND, Cody AJ, Peto TE, Maiden MC: Extended sequence typing of Campylobacter spp., United Kingdom. Emerg Infect Dis 2008, 14(10):1620–1622. 10.3201/eid1410.071109

Jolley KA, Chan MS, Maiden MC: mlstdbNet - distributed multi-locus sequence typing (MLST) databases. BMC Bioinformatics 2004, 5(1):86. 10.1186/1471-2105-5-86

Jolley KA, Maiden MC: AgdbNet - antigen sequence database software for bacterial typing. BMC Bioinformatics 2006, 7: 314. 10.1186/1471-2105-7-314

Aanensen DM, Spratt BG: The multilocus sequence typing network: mlst.net. Nucleic Acids Res 2005, (33 Web Server):W728–733. 10.1093/nar/gki415

Keim P, Price LB, Klevytska AM, Smith KL, Schupp JM, Okinaka R, Jackson PJ, Hugh-Jones ME: Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis . J Bacteriol 2000, 182(10):2928–2936. 10.1128/JB.182.10.2928-2936.2000

mod_perl home page[ http://perl.apache.org/ ]

Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, et al.: The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002, 12(10):1611–1618. 10.1101/gr.361602

Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000, 16(6):276–277. 10.1016/S0168-9525(00)02024-2

jQuery home page[ http://jquery.com/ ]

Perl/Javascript MD5 secure user authentication home page[ http://perl-md5-login.sourceforge.net/ ]

Paul Johnston's home page[ http://pajhome.org.uk/ ]

Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389–3402. 10.1093/nar/25.17.3389

Didelot X, Falush D: Inference of bacterial microevolution using multilocus sequence data. Genetics 2007, 175(3):1251–1266. 10.1534/genetics.106.063305

Neisseria MLST website[ http://pubmlst.org/neisseria/ ]

Neisseria.org meningococcal typing website[ http://neisseria.org/nm/typing/ ]

Maiden MC, Stuart JM, Group UMC: Carriage of serogroup C meningococci 1 year after meningococcal C conjugate polysaccharide vaccination. Lancet 2002, 359(9320):1829–1831. 10.1016/S0140-6736(02)08679-8

Zerbino DR, Birney E: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18(5):821–829. 10.1101/gr.074492.107

Brehony C, Wilson DJ, Maiden MC: Variation of the factor H-binding protein of Neisseria meningitidis . Microbiology 2009, 155: 4155–4169. 10.1099/mic.0.027995-0

Taha MK, Vazquez JA, Hong E, Bennett DE, Bertrand S, Bukovski S, Cafferkey MT, Carion F, Christensen JJ, Diggle M, et al.: Target gene sequencing to characterize the penicillin G susceptibility of Neisseria meningitidis . Antimicrob Agents Chemother 2007, 51(8):2784–2792. 10.1128/AAC.00412-07

Streptococci genomes demonstration website[ http://pubmlst.org/streptococci/ ]

Jones N, Bohnsack JF, Takahashi S, Oliver KA, Chan MS, Kunst F, Glaser P, Rusniok C, Crook DW, Harding RM, et al.: Multilocus Sequence Typing System for Group B Streptococcus. J Clin Microbiol 2003, 41(6):2530–2536. 10.1128/JCM.41.6.2530-2536.2003

Do T, Jolley KA, Maiden MC, Gilbert SC, Clark D, Wade WG, Beighton D: Population structure of Streptococcus oralis . Microbiology 2009, 155(Pt 8):2593–2602. 10.1099/mic.0.027284-0

Enright MC, Spratt BG: A multilocus sequence typing scheme for Streptococcus pneumoniae : identification of clones associated with serious invasive disease. Microbiology 1998, 144(11):3049–3060. 10.1099/00221287-144-11-3049

Enright MC, Spratt BG, Kalia A, Cross JH, Bessen DE: Multilocus sequence typing of Streptococcus pyogenes and the relationships between emm type and clone. Infect Immun 2001, 69(4):2416–2427. 10.1128/IAI.69.4.2416-2427.2001

King SJ, Leigh JA, Heath PJ, Luque I, Tarradas C, Dowson CG, Whatmore AM: Development of a multilocus sequence typing scheme for the pig pathogen Streptococcus suis : identification of virulent clones and potential capsular serotype exchange. J Clin Microbiol 2002, 40(10):3671–3680. 10.1128/JCM.40.10.3671-3680.2002

Coffey TJ, Pullinger GD, Urwin R, Jolley KA, Wilson SM, Maiden MC, Leigh JA: First insights into the evolution of Streptococcus uberis : a multilocus sequence typing scheme that enables investigation of its population biology. Appl Environ Microbiol 2006, 72(2):1420–1428. 10.1128/AEM.72.2.1420-1428.2006

Webb K, Jolley KA, Mitchell Z, Robinson C, Newton JR, Maiden MC, Waller A: Development of an unambiguous and discriminatory multilocus sequence typing scheme for the Streptococcus zooepidemicus group. Microbiology 2008, 154(Pt 10):3016–3024. 10.1099/mic.0.2008/018911-0

Bishop CJ, Aanensen DM, Jordan GE, Kilian M, Hanage WP, Spratt BG: Assigning strains to bacterial species via the internet. BMC Biology 2009, 7: 3. 10.1186/1741-7007-7-3

Holden MT, Heather Z, Paillot R, Steward KF, Webb K, Ainslie F, Jourdan T, Bason NC, Holroyd NE, Mungall K, et al.: Genomic evidence for the evolution of Streptococcus equi : host restriction, increased virulence, and genetic exchange with human pathogens. PLoS Pathogens 2009, 5(3):e1000346. 10.1371/journal.ppat.1000346

Pearson WR: Effective protein sequence comparison. Meth Enzymol 1996, 266: 227–258. full_text

Stalker J, Gibbins B, Meidl P, Smith J, Spooner W, Hotz HR, Cox AV: The Ensembl Web site: mechanics of a genome browser. Genome Res 2004, 14(5):951–955. 10.1101/gr.1863004

Davidsen T, Beck E, Ganapathy A, Montgomery R, Zafar N, Yang Q, Madupu R, Goetz P, Galinsky K, White O, et al.: The comprehensive microbial resource. Nucleic Acids Res 2009, (38 Database):D340–345.

Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC: The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2009, (38 Database):D346–354.

Nielsen LN, Sheppard SK, McCarthy ND, Maiden MC, Ingmer H, Krogfelt KA: MLST clustering of Campylobacter jejuni isolates from patients with gastroenteritis, reactive arthritis and Guillain-Barre syndrome. J Appl Microbiol 2009.

Sheppard SK, Dallas JF, Strachan NJ, MacRae M, McCarthy ND, Wilson DJ, Gormley FJ, Falush D, Ogden ID, Maiden MC, et al.: Campylobacter genotyping to determine the source of human infection. Clin Infect Dis 2009, 48(8):1072–1078. 10.1086/597402

Sheppard SK, Dallas JF, MacRae M, McCarthy ND, Sproston EL, Gormley FJ, Strachan NJ, Ogden ID, Maiden MC, Forbes KJ: Campylobacter genotypes from food animals, environmental sources and clinical disease in Scotland 2005/6. Int J Food Microbiol 2009, 134(1–2):96–103. 10.1016/j.ijfoodmicro.2009.02.010

Baldwin A, Loughlin M, Caubilla-Barron J, Kucerova E, Manning G, Dowson C, Forsythe S: Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes. BMC Microbiology 2009, 9: 223. 10.1186/1471-2180-9-223

Arvand M, Feil EJ, Giladi M, Boulouis HJ, Viezens J: Multi-locus sequence typing of Bartonella henselae isolates from three continents reveals hypervirulent and feline-associated clones. PLoS One 2007, 2(12):e1346. 10.1371/journal.pone.0001346

Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J: ACT: the Artemis Comparison Tool. Bioinformatics 2005, 21(16):3422–3423. 10.1093/bioinformatics/bti553

Carver T, Berriman M, Tivey A, Patel C, Bohme U, Barrell BG, Parkhill J, Rajandream MA: Artemis and ACT: Viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 2008, 24(23):2672–2676. 10.1093/bioinformatics/btn529

Darling AC, Mau B, Blattner FR, Perna NT: Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004, 14(7):1394–1403. 10.1101/gr.2289704

Pandya GA, Holmes MH, Petersen JM, Pradhan S, Karamycheva SA, Wolcott MJ, Molins C, Jones M, Schriefer ME, Fleischmann RD, et al.: Whole genome single nucleotide polymorphism based phylogeny of Francisella tularensis and its application to the development of a strain typing assay. BMC Microbiology 2009, 9: 213. 10.1186/1471-2180-9-213

Foster JT, Beckstrom-Sternberg SM, Pearson T, Beckstrom-Sternberg JS, Chain PS, Roberto FF, Hnath J, Brettin T, Keim P: Whole-genome-based phylogeny and divergence of the genus Brucella . J Bacteriol 2009, 191(8):2864–2870. 10.1128/JB.01581-08

Pearson T, Okinaka RT, Foster JT, Keim P: Phylogenetic understanding of clonal populations in an era of whole genome sequencing. Infect Genet Evol 2009, 9(5):1010–1019. 10.1016/j.meegid.2009.05.014

Kennedy AD, Otto M, Braughton KR, Whitney AR, Chen L, Mathema B, Mediavilla JR, Byrne KA, Parkins LD, Tenover FC, et al.: Epidemic community-associated methicillin-resistant Staphylococcus aureus : recent clonal expansion and diversification. Proc Natl Acad Sci USA 2008, 105(4):1327–1332. 10.1073/pnas.0710217105

Jolley KA, Feil EJ, Chan MS, Maiden MC: Sequence type analysis and recombinational tests (START). Bioinformatics 2001, 17(12):1230–1231. 10.1093/bioinformatics/17.12.1230

Feil EJ, Li BC, Aanensen DM, Hanage WP, Spratt BG: eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J Bacteriol 2004, 186(5):1518–1530. 10.1128/JB.186.5.1518-1530.2004

Francisco AP, Bugalho M, Ramirez M, Carrico JA: Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach. BMC Bioinformatics 2009, 10: 152. 10.1186/1471-2105-10-152

Pritchard JK, Stephens M, Donnelly P: Inference of population structure using multilocus genotype data. Genetics 2000, 155(2):945–959.

Gil R, Silva FJ, Pereto J, Moya A: Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev 2004, 68(3):518–537. 10.1128/MMBR.68.3.518-537.2004

Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, et al.: The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 2005, 33(17):5691–5702. 10.1093/nar/gki866

Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Anderson I, Lykidis A, Mavromatis K, et al.: The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res 2010, (38 Database):D382–390. 10.1093/nar/gkp887