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Genome Sequencing of Listeria monocytogenes

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Listeria monocytogenes

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1157))

Abstract

Genome sequencing is a key technology in microbiology. A genome sequence is the prerequisite for understanding the molecular basis of a given phenotype; this is of particular importance for pathogens. Particularly for the foodborne pathogen Listeria monocytogenes, which is an important model organism in infection biology, genome sequencing has proven to be invaluable in advancing our understanding of its virulence mechanisms and epidemiology. In this chapter, current technologies and software tools for genome sequencing and genome analysis of L. monocytogenes are described.

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References

  1. Allerberger F, Wagner M (2010) Listeriosis: a resurgent foodborne infection. Clin Microbiol Infect 16:16–23

    Article  CAS  PubMed  Google Scholar 

  2. Swaminathan B, Gerner-Smidt P (2007) The epidemiology of human listeriosis. Microbes Infect 9:1236–1243

    Article  PubMed  Google Scholar 

  3. Fleming DW, Cochi SL, MacDonald KL, Brondum J, Hayes PS, Plikaytis BD, Holmes MB, Audurier A, Broome CV, Reingold AL (1985) Pasteurized milk as a vehicle of infection in an outbreak of listeriosis. N Engl J Med 312:404–407

    Article  CAS  PubMed  Google Scholar 

  4. Schlech WF 3rd, Lavigne PM, Bortolussi RA, Allen AC, Haldane EV, Wort AJ, Hightower AW, Johnson SE, King SH, Nicholls ES, Broome CV (1983) Epidemic listeriosis—evidence for transmission by food. N Engl J Med 308:203–206

    Article  PubMed  Google Scholar 

  5. Cossart P (2011) Illuminating the landscape of host-pathogen interactions with the bacterium Listeria monocytogenes. Proc Natl Acad Sci USA 108:19484–19491

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  6. Hamon M, Bierne H, Cossart P (2006) Listeria monocytogenes: a multifaceted model. Nat Rev Microbiol 4:423–434

    Article  CAS  PubMed  Google Scholar 

  7. Ivanek R, Grohn YT, Wiedmann M (2006) Listeria monocytogenes in multiple habitats and host populations: review of available data for mathematical modeling. Foodborne Pathog Dis 3:319–336

    Article  CAS  PubMed  Google Scholar 

  8. Sauders BD, Wiedmann M (2007) Ecology of Listeria species and L. monocytogenes in the natural environment. In: Ryser ET, Marth EH (eds) Listeria, listeriosis and food safety. CRC Press, Boca Raton, pp 21–53

    Google Scholar 

  9. Glaser P, Frangeul L, Buchrieser C, Rusniok C, Amend A, Baquero F, Berche P, Bloecker H, Brandt P, Chakraborty T, Charbit A, Chetouani F, Couvé E, de Daruvar A, Dehoux P, Domann E, Domínguez-Bernal G, Duchaud E, Durant L, Dussurget O, Entian KD, Fsihi H, García-del-Portillo F, Garrido P, Gautier L, Goebel W, Gómez-López N, Hain T, Hauf J, Jackson D, Jones LM, Kaerst U, Kreft J, Kuhn M, Kunst F, Kurapkat G, Madueno E, Maitournam A, Vicente JM, Ng E, Nedjari H, Nordsiek G, Novella S, de Pablos B, Pérez-Diaz JC, Purcell R, Remmel B, Rose M, Schlueter T, Simoes N, Tierrez A, Vázquez-Boland JA, Voss H, Wehland J, Cossart P (2001) Comparative genomics of Listeria species. Science 294:849–852

    CAS  PubMed  Google Scholar 

  10. Pagani I, Liolios K, Jansson J, Chen IMA, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC (2012) The Genomes OnLine Database (GOLD) v. 4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 40:D571–D579

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  11. Wilson K (2001) Preparation of genomic DNA from bacteria. Curr Protoc Mol Biol Chapter 2:Unit 2.4

    Google Scholar 

  12. Loman NJ, Constantinidou C, Chan JZ, Halachev M, Sergeant M, Penn CW, Robinson ER, Pallen MJ (2012) High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 10:599–606

    Article  CAS  PubMed  Google Scholar 

  13. MacLean D, Jones JD, Studholme DJ (2009) Application of ‘next-generation’ sequencing technologies to microbial genetics. Nat Rev Microbiol 7:287–296

    PubMed  Google Scholar 

  14. Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11:31–46

    Article  CAS  PubMed  Google Scholar 

  15. Bashir A, Klammer AA, Robins WP, Chin CS, Webster D, Paxinos E, Hsu D, Ashby M, Wang S, Peluso P, Sebra R, Sorenson J, Bullard J, Yen J, Valdovino M, Mollova E, Luong K, Lin S, LaMay B, Joshi A, Rowe L, Frace M, Tarr CL, Turnsek M, Davis BM, Kasarskis A, Mekalanos JJ, Waldor MK, Schadt EE (2012) A hybrid approach for the automated finishing of bacterial genomes. Nat Biotechnol 30:701–707

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  16. Ribeiro FJ, Przybylski D, Yin S, Sharpe T, Gnerre S, Abouelleil A, Berlin AM, Montmayeur A, Shea TP, Walker BJ, Young SK, Russ C, Nusbaum C, MacCallum I, Jaffe DB (2012) Finished bacterial genomes from shotgun sequence data. Genome Res 22:2270–2277

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  17. Nagarajan N, Pop M (2013) Sequence assembly demystified. Nat Rev Genet 14:157–167

    Article  CAS  PubMed  Google Scholar 

  18. Milne I, Bayer M, Cardle L, Shaw P, Stephen G, Wright F, Marshall D (2010) Tablet—next generation sequence assembly visualization. Bioinformatics 26:401–402

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  19. Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5:e11147

    Article  PubMed Central  PubMed  Google Scholar 

  20. Angiuoli SV, Salzberg SL (2011) Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics 27:334–342

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  21. Phillippy AM, Schatz MC, Pop M (2008) Genome assembly forensics: finding the elusive mis-assembly. Genome Biol 9:R55

    Article  PubMed Central  PubMed  Google Scholar 

  22. Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, Lajus A, Rouy Z, Roche D, Salvignol G, Scarpelli C, Médigue C (2009) MicroScope: a platform for microbial genome annotation and comparative genomics. Database (Oxford) 2009:bap021. doi:10.1093/database/bap021

    Article  Google Scholar 

  23. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75

    Article  PubMed Central  PubMed  Google Scholar 

  24. Markowitz VM, Mavromatis K, Ivanova NN, Chen IMA, Chu KC, Kyrpides NC (2009) IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 25:2271–2278

    Article  CAS  PubMed  Google Scholar 

  25. Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A (2003) GenDB—an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 31:2187–2195

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  26. Boetzer M, Pirovano W (2012) Toward almost closed genomes with GapFiller. Genome Biol 13:R56

    Article  PubMed Central  PubMed  Google Scholar 

  27. Nagarajan N, Cook C, Di Bonaventura M, Ge H, Richards A, Bishop-Lilly KA, DeSalle R, Read TD, Pop M (2010) Finishing genomes with limited resources: lessons from an ensemble of microbial genomes. BMC Genomics 11:242

    Article  PubMed Central  PubMed  Google Scholar 

  28. Galardini M, Biondi EG, Bazzicalupo M, Mengoni A (2011) CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes. Source Code Biol Med 6:11

    Article  PubMed Central  PubMed  Google Scholar 

  29. Grant JR, Arantes AS, Stothard P (2012) Comparing thousands of circular genomes using the CGView comparison tool. BMC Genomics 13:202

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  30. Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 12:402

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  31. Krzywinski M, Schlein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19:1639–1645

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  32. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J (2005) ACT: the Artemis comparison tool. Bioinformatics 21:3422–3423

    Article  CAS  PubMed  Google Scholar 

  33. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiouli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glockner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kegan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A (2008) The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 26:541–547

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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Correspondence to Stephan Schmitz-Esser .

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Schmitz-Esser, S., Wagner, M. (2014). Genome Sequencing of Listeria monocytogenes . In: Jordan, K., Fox, E., Wagner, M. (eds) Listeria monocytogenes. Methods in Molecular Biology, vol 1157. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0703-8_19

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  • DOI: https://doi.org/10.1007/978-1-4939-0703-8_19

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0702-1

  • Online ISBN: 978-1-4939-0703-8

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