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Overview: The Impact of Microbial Genomics on Food Safety

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Genomics of Foodborne Bacterial Pathogens

Part of the book series: Food Microbiology and Food Safety ((FMFS))

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Abstract

The first use of the term “genome” is attributed to Hans Winkler in his 1920 publication Verbeitung und Ursache der Parthenogenesis im Pflanzen und Tierreiche (Winkler, 1920). However, it was not until 1986 that the study of genomic concepts coalesced with the creation of a new journal by the same name (McKusick, 1997). The study of genomics was initially defined as the use or the application of “informatic tools” to study features of a sequenced genome (Strauss and Falkow, 1997). Today the field of genomics is typically considered to encompass efforts to determine the nucleic acid DNA sequence of an organism as well as the expression of genetic information using high-throughput, genome-wide methods, including transcriptomic, proteomic, and metabolomic analyses.

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References

  • Alcaine SD, Warnick LD, Wiedmann M (2007) Antimicrobial resistance in nontyphoidal Salmonella. J Food Prot 70:780–790

    CAS  Google Scholar 

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    CAS  Google Scholar 

  • Anderson S (1981) Shotgun DNA sequencing using cloned DNAse i-generated fragments. Nucleic Acids Res 9:3015–3027

    CAS  Google Scholar 

  • Archer DL, Kvenberg JE (1985) Incidence and cost of foodborne diarrhoeal disease in the United States. J Food Prot 48:887–894

    Google Scholar 

  • Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2006) Genbank. Nucleic Acids Res 34:D16–D20

    CAS  Google Scholar 

  • Bergholz TM, Wick LM, Qi W, Riordan JT, Ouellette LM, Whittam TS (2007) Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium. BMC Microbiol 7:97

    Google Scholar 

  • Best EL, Fox AJ, Owen RJ, Cheesbrough J, Bolton FJ (2007) Specific detection of Campylobacter jejuni from faeces using single nucleotide polymorphisms. Epidemiol Infect 135:839–846

    CAS  Google Scholar 

  • Blackstock WP, Weir MP (1999) Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol 17:121–127

    CAS  Google Scholar 

  • Boshoff HI, Reed MB, Barry CE 3rd, Mizrahi V (2003) Dnae2 polymerase contributes to in vivo survival and the emergence of drug resistance in Mycobacterium tuberculosis. Cell 113:183–193

    CAS  Google Scholar 

  • Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO, Eisenberg D (2004) Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol 5:R35

    Google Scholar 

  • Bowman MD, O’Neill JC, Stringer JR, Blackwell HE (2007) Rapid identification of antibacterial agents effective against Staphylococcus aureus using small-molecule macroarrays. Chem Biol 14:351–357

    CAS  Google Scholar 

  • Bunning VK, Lindsay JA, Archer DL (1997) Chronic health effects of microbial foodborne disease. World Health Stat Q 50:51–56

    CAS  Google Scholar 

  • Burns-Keliher L, Nickerson CA, Morrow BJ, Curtiss R 3rd (1998) Cell-specific proteins synthesized by Salmonella Typhimurium. Infect Immun 66:856–861

    CAS  Google Scholar 

  • Burns-Keliher LL, Portteus A, Curtiss R 3rd (1997) Specific detection of Salmonella Typhimurium proteins synthesized intracellularly. J Bacteriol 179:3604–3612

    CAS  Google Scholar 

  • Cash P (2003) Proteomics of bacterial pathogens. Adv Biochem Eng Biotechnol 83:93–115

    CAS  Google Scholar 

  • CDC (Centers for Disease Control and Prevention) (2007) Preliminary FoodNet data on the incidence of infection with pathogens transmitted commonly through food – 10 states, 2006. MMWR Morb Mortal Wkly Rep 56:336–339

    Google Scholar 

  • Cebula TA, Jackson SA, Brown EW, Goswami B, LeClerc JE (2005) Chips and SNPs, bugs and thugs: a molecular sleuthing perspective. J Food Prot 68:1271–1284

    CAS  Google Scholar 

  • Chan YC, Raengpradub S, Boor KJ, Wiedmann M (2007) Microarray-based characterization of the Listeria monocytogenes cold regulon in log- and stationary-phase cells. Appl Environ Microbiol 73:6484–6498

    CAS  Google Scholar 

  • Church GM (2006) Technology transfer and commercial scientific advisory roles (last revised 11/8/2006). http://arep.med.harvard.edu/gmc/tech.html

  • Cochrane G, Aldebert P, Althorpe N, Andersson M, Baker W, Baldwin A, Bates K, Bhattacharyya S, Browne P, van den Broek A, Castro M, Duggan K, Eberhardt R, Faruque N, Gamble J, Kanz C, Kulikova T, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, McHale M, McWilliam H, Mukherjee G, Nardone F, Pastor MP, Sobhany S, Stoehr P, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R (2006) EMBL nucleotide sequence database: developments in 2005. Nucleic Acids Res 34:D10–D15

    CAS  Google Scholar 

  • Cox-Foster DL, Conlan S, Holmes EC, Palacios G, Evans JD, Moran NA, Quan PL, Briese T, Hornig M, Geiser DM, Martinson V, vanEngelsdorp D, Kalkstein AL, Drysdale A, Hui J, Zhai J, Cui L, Hutchison SK, Simons JF, Egholm M, Petti JS, Lipkin WI (2007) A metagenomic survey of microbes in honey bee colony collapse disorder. Science 318:283–287

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  • Date SV, Marcotte EM (2003) Discovery of uncharacterized cellular systems by genome wide analysis of functional linkages. Nat Biotech 21:1055–1062

    CAS  Google Scholar 

  • Date SV, Marcotte EM (2005) Protein function prediction using the protein link explorer (PLEX). Bioinformatics 21:2558–2559

    CAS  Google Scholar 

  • Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27:4636–4641

    CAS  Google Scholar 

  • Dieterich G, Karst U, Fischer E, Wehland J, Jansch L (2006) Leger: knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species. Nucleic Acids Res 34:D402–D406

    CAS  Google Scholar 

  • Djikeng A, Halpin R, Kuzmickas R, Depasse J, Feldblyum J, Sengamalay N, Afonso C, Zhang X, Anderson NG, Ghedin E, Spiro DJ (2008) Viral genome sequencing by random priming methods. BMC Genomics 9:5

    Google Scholar 

  • Donaldson JR, Nanduri B, Burgess SC, Lawrence ML (2009) Comparative proteomic analysis of Listeria monocytogenes strains F2365 and EGD. Appl Environ Microbiol 75:366–373

    CAS  Google Scholar 

  • Doumith M, Cazalet C, Simoes N, Frangeul L, Jacquet C, Kunst F, Martin P, Cossart P, Glaser P, Buchrieser C (2004) New aspects regarding evolution and virulence of Listeria monocytogenes revealed by comparative genomics and DNA arrays. Infect Immun 72:1072–1083

    CAS  Google Scholar 

  • Drudy D, Mullane NR, Quinn T, Wall PG, Fanning S (2006) Enterobacter sakazakii: an emerging pathogen in powdered infant formula. Clin Infect Disease 42:996–1002

    CAS  Google Scholar 

  • Ducey TF, Page B, Usgaard T, Borucki MK, Pupedis K, Ward TJ (2007) A single nucleotide-polymorphism-based multilocus genotyping assay for subtyping lineage I isolates of Listeria monocytogenes. Appl Environ Microbiol 73:133–147

    CAS  Google Scholar 

  • Dussurget O, Cabanes D, Dehoux P, Lecuit M, Buchrieser C, Glaser P, Cossart P (2002) Listeria monocytogenes bile salt hydrolase is a PrfA-regulated virulence factor involved in the intestinal and hepatic phases of listeriosis. Mol Microbiol 45:1095–1106

    CAS  Google Scholar 

  • Esaki H, Noda K, Otsuki N, Kojima A, Asai T, Tamura Y, Takahashi T (2004) Rapid detection of quinolone-resistant Salmonella by real time SNP genotyping. J Microbiol Methods 58:131–134

    CAS  Google Scholar 

  • Eskra L, Mathison A, Splitter G (2003) Microarray analysis of mRNA levels from RAW264.7 macrophages infected with Brucella abortus. Infect Immun 71:1125–1133

    CAS  Google Scholar 

  • Fiers W, Contreras R, Duerinck F, Haegeman G, Iserentant D, Merregaert J, Min Jou W, Molemans F, Raeymaekers A, Van den Berghe A, Volckaert G, Ysebaert M (1976) Complete nucleotide sequence of bacteriophage ms2 RNA: primary and secondary structure of the replicase gene. Nature 260:500–507

    CAS  Google Scholar 

  • Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34:D247–D251

    CAS  Google Scholar 

  • Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM et al (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496–512

    CAS  Google Scholar 

  • Flint J, Duynhoven YV, Angulo FJ, DeLong SM, Braun P, Kirk M, Scallan E, Fitzgerald M, Adak GK, Sockett P, Ellis A, Hall G, Gargouri N, Walke H, Braam P (2005) Estimating the burden of acute gastroenteritis, foodborne disease, and pathogens commonly transmitted by food: an international review. Clin Infect Dis 41:698–704

    Google Scholar 

  • Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, DeBoy RT, Parker CT, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Sullivan SA, Shetty JU, Ayodeji MA, Shvartsbeyn A, Schatz MC, Badger JH, Fraser CM, Nelson KE (2005) Major structural differences and novel potential virulence mechanisms from the genomes of multiple Campylobacter species. PLoS Biol 3:e15

    Google Scholar 

  • Frishman D (2007) Protein annotation at genomic scale: the current status. Chem Rev 107:3448–3466

    CAS  Google Scholar 

  • Garg AX, Suri RS, Barrowman N, Rehman F, Matsell D, Rosas-Arellano MP, Salvadori M, Haynes RB, Clark WF (2003) Long-term renal prognosis of diarrhea-associated hemolytic uremic syndrome: a systematic review, meta-analysis, and meta-regression. JAMA 290:1360–1370

    CAS  Google Scholar 

  • Gat O, Grosfeld H, Ariel N, Inbar I, Zaide G, Broder Y, Zvi A, Chitlaru T, Altboum Z, Stein D, Cohen S, Shafferman A (2006) Search for Bacillus anthracis potential vaccine candidates by a functional genomic–-serologic screen. Infect Immun 74:3987–4001

    CAS  Google Scholar 

  • Gill SR, Pop M, DeBoy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE (2006) Metagenomic analysis of the human distal gut microbiome. Science 312:1355–1359

    CAS  Google Scholar 

  • Glaser P, Frangeul L, Buchrieser C, Rusniok C, Amend A, Baquero F, Berche P, Bloecker H, Brandt P, Chakraborty T, Charbit A, Chetouani F, Couve E, de Daruvar A, Dehoux P, Domann E, Dominguez-Bernal G, Duchaud E, Durant L, Dussurget O, Entian KD, Fsihi H, Garcia-del Portillo F, Garrido P, Gautier L, Goebel W, Gomez-Lopez 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, Perez-Diaz JC, Purcell R, Remmel B, Rose M, Schlueter T, Simoes N, Tierrez A, Vazquez-Boland JA, Voss H, Wehland J, Cossart P (2001) Comparative genomics of Listeria species. Science 294:849–852

    CAS  Google Scholar 

  • Glasner JD, Rusch M, Liss P, Plunkett G 3rd, Cabot EL, Darling A, Anderson BD, Infield-Harm P, Gilson MC, Perna NT (2006) Asap: a resource for annotating, curating, comparing, and disseminating genomic data. Nucleic Acids Res 34:D41–D45

    CAS  Google Scholar 

  • Greenbaum D, Colangelo C, Williams K, Gerstein M (2003) Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol 4:117

    Google Scholar 

  • Gresham D, Dunham MJ, Botstein D (2008) Comparing whole genomes using DNA microarrays. Nat Rev Genet 9:291–302

    CAS  Google Scholar 

  • Gygi SP, Rochon Y, Franza BR, Aebersold R (1999) Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19:1720–1730

    CAS  Google Scholar 

  • Hardy ME (2005) Norovirus protein structure and function. FEMS Microbiol Lett 253:1–8

    CAS  Google Scholar 

  • Harrington SM, Dudley EG, Nataro JP (2006) Pathogenesis of enteroaggregative Escherichia coli infection. FEMS Microbiol Lett 254:12–18

    CAS  Google Scholar 

  • Hoffmaster AR, Fitzgerald CC, Ribot E, Mayer LW, Popovic T (2002) Molecular subtyping of Bacillus anthracis and the 2001 bioterrorism-associated anthrax outbreak, United States. Emerg Infect Dis 8:1111–1116

    CAS  Google Scholar 

  • Holt LJ, Enever C, de Wildt RM, Tomlinson IM (2000) The use of recombinant antibodies in proteomics. Curr Opin Biotechnol 11:445–449

    CAS  Google Scholar 

  • Hommais F, Pereira S, Acquaviva C, Escobar-Paramo P, Denamur E (2005) Single nucleotide polymorphism phylotyping of Escherichia coli. Appl Environ Microbiol 71:4784–4792

    CAS  Google Scholar 

  • Hu H, Lan R, Reeves PR (2006) Adaptation of multilocus sequencing for studying variation within a major clone: evolutionary relationships of Salmonella enterica serovar Typhimurium. Genetics 172:743–750

    CAS  Google Scholar 

  • Hung DT, Shakhnovich EA, Pierson E, Mekalanos JJ (2005) Small-molecule inhibitor of Vibrio cholerae virulence and intestinal colonization. Science 310:670–674

    CAS  Google Scholar 

  • Hyytia-Trees EK, Cooper K, Ribot EM, Gerner-Smidt P (2007) Recent developments and future prospects in subtyping of foodborne bacterial pathogens. Future Microbiol 2:175–185

    Google Scholar 

  • Imirzalioglu C, Hain T, Chakraborty T, Domann E (2008) Hidden pathogens uncovered: metagenomic analysis of urinary tract infections. Andrologia 40:66–71

    CAS  Google Scholar 

  • Jay JM (2003) A review of recent taxonomic changes in seven genera of bacteria commonly found in foods. J Food Prot 66:1304–1309

    CAS  Google Scholar 

  • Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32:D277–D280

    CAS  Google Scholar 

  • Kazmierczak MJ, Mithoe SC, Boor KJ, Wiedmann M (2003) Listeria monocytogenes sigma B regulates stress response and virulence functions. J Bacteriol 185:5722–5734

    CAS  Google Scholar 

  • Kingsley RA, Msefula CL, Thomson NR, Kariuki S, Holt KE, Gordon MA, Harris D, Clarke L, Whitehead S, Sangal V, Marsh K, Achtman M, Molyneux ME, Cormican M, Parkhill J, MacLennan CA, Heyderman RS, Dougan G (2009) Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. Genome Res 19:2279–2287

    CAS  Google Scholar 

  • LaFramboise T (2009) Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances. Nucleic Acids Res 37:4181–4193

    CAS  Google Scholar 

  • Lecuit M, Sonnenburg JL, Cossart P, Gordon JI (2007) Functional genomic studies of the intestinal response to a foodborne enteropathogen in a humanized gnotobiotic mouse model. J Biol Chem 282:15065–15072

    CAS  Google Scholar 

  • Lehner A, Tasara T, Stephan R (2004) 16S rRNA gene based analysis of Enterobacter sakazakii strains from different sources and development of a PCR assay for identification. BMC Microbiol 4:43

    Google Scholar 

  • Lillehoj HS, Kim CH, Keeler CL Jr, Zhang S (2007) Immunogenomic approaches to study host immunity to enteric pathogens. Poult Sci 86:1491–1500

    CAS  Google Scholar 

  • Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC (2008) The genomes on line database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 36:D475–D479

    CAS  Google Scholar 

  • Liu XS (2007) Getting started in tiling microarray analysis. PLoS Comput Biol 3:1842–1844

    CAS  Google Scholar 

  • Liu JM, Livny J, Lawrence MS, Kimball MD, Waldor MK, Camilli A (2009) Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing. Nucleic Acids Res 37. doi:10.1093/nar/gkp080

    Google Scholar 

  • Maltsev N, Glass E, Sulakhe D, Rodriguez A, Syed MH, Bompada T, Zhang Y, D’Souza M (2006) PUMA2 – grid-based high-throughput analysis of genomes and metabolic pathways. Nucleic Acids Res 34:D369–D372

    CAS  Google Scholar 

  • Manganelli R, Voskuil MI, Schoolnik GK, Smith I (2001) The Mycobacterium tuberculosis ECF sigma factor sigmaE: role in global gene expression and survival in macrophages. Mol Microbiol 41:423–437

    CAS  Google Scholar 

  • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y-J, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim J-B, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380

    CAS  Google Scholar 

  • Mastronicolis SK, Boura A, Karaliota A, Magiatis P, Arvanitis N, Litos C, Tsakirakis A, Paraskevas P, Moustaka H, Heropoulos G (2006) Effect of cold temperature on the composition of different lipid classes of the foodborne pathogen Listeria monocytogenes: focus on neutral lipids. Food Microbiol 23:184–194

    CAS  Google Scholar 

  • McKusick VA (1997) Genomics: structural and functional studies of genomes. Genomics 45:244–249

    CAS  Google Scholar 

  • Mead PS, Slutsker L, Dietz V, McCaig LF, Bresee JS, Shapiro C, Griffin PM, Tauxe RV (1999) Food-related illness and death in the United States. Emerg Infect Dis 5:607–625

    CAS  Google Scholar 

  • Mehta S (2006) Neuromuscular disease causing acute respiratory failure. Respir Care 51:1016–1021

    Google Scholar 

  • Moorhead SM, Dykes GA, Cursons RT (2003) An SNP-based PCR assay to differentiate between Listeria monocytogenes lineages derived from phylogenetic analysis of the sigB gene. J Microbiol Methods 55:425–432

    CAS  Google Scholar 

  • Nagayama K (1997) Protein arrays: concepts and subjects. Adv Biophys 34:3–23

    CAS  Google Scholar 

  • Nakamura, Maeda, Miron, Yoh, Izutsu, Kataoka, Honda, Yasunaga, Nakaya, Kawai, Hayashizaki, Horii, Iida, 2008] Nakamura S, Maeda N, Miron IM, Yoh M, Izutsu K, Kataoka C, Honda T, Yasunaga T, Nakaya T, Kawai J, Hayashizaki Y, Horii T, Iida T (2008) Metagenomic diagnosis of bacterial infections. Emerg Infect Dis 14:1784–1786

    Google Scholar 

  • Nelson KE, Fouts DE, Mongodin EF, Ravel J, DeBoy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT, Peterson J, White O, Nelson WC, Nierman W, Beanan MJ, Brinkac LM, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Haft DH, Selengut J, Van Aken S, Khouri H, Fedorova N, Forberger H, Tran B, Kathariou S, Wonderling LD, Uhlich GA, Bayles DO, Luchansky JB, Fraser CM (2004) Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic Acids Res 32:2386–2395

    CAS  Google Scholar 

  • Newell DG (2005) Campylobacter concisus: an emerging pathogen? Eur J Gastroenterol Hepatol 17:1013–1014

    Google Scholar 

  • Noller AC, McEllistrem MC, Pacheco AG, Boxrud DJ, Harrison LH (2003) Multilocus variable-number tandem repeat analysis distinguishes outbreak and sporadic Escherichia coli O157:H7 isolates. J Clin Microbiol 41:5389–5397

    CAS  Google Scholar 

  • Nygard K, Lindstedt BA, Wahl W, Jensvoll L, Kjelso C, Molbak K, Torpdahl M, Kapperud G (2007) Outbreak of Salmonella Typhimurium infection traced to imported cured sausage using MLVA-subtyping. Euro Surveill 12:E0703155

    Google Scholar 

  • Octavia S, Lan R (2007) Single-nucleotide-polymorphism typing and genetic relationships of Salmonella enterica serovar Typhi isolates. J Clin Microbiol 45:3795–3801

    CAS  Google Scholar 

  • Okubo K, Sugawara H, Gojobori T, Tateno Y (2006) DDBJ in preparation for overview of research activities behind data submissions. Nucleic Acids Res 34:D6–D9

    CAS  Google Scholar 

  • Oldiges M, Lutz S, Pflug S, Schroer K, Stein N, Wiendahl C (2007) Metabolomics: current state and evolving methodologies and tools. Appl Microbiol Biotechnol 76:495–511

    CAS  Google Scholar 

  • Oliver HF, Orsi RH, Ponnala L, Keich U, Wang W, Sun Q, Cartinhour SW, Filiatrault MJ, Wiedmann M, Boor KJ (2009) Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs. BMC Genomics 10:641

    Google Scholar 

  • Ollinger J, Bowen B, Wiedmann M, Boor KJ, Bergholz TM (2009) Listeria monocytogenes {sigma}B modulates PrfA-mediated virulence factor expression. Infect Immun 77:2113–2124

    CAS  Google Scholar 

  • Olsen SJ, MacKinnon LC, Goulding JS, Bean NH, Slutsker L (2000) Surveillance for foodborne-disease outbreaks – United States, 1993–1997. MMWR CDC Surveill Summ 49:1–62

    CAS  Google Scholar 

  • Raengpradub S, Wiedmann M, Boor KJ (2008) Comparative analysis of the {sigma}B-dependent stress responses in Listeria monocytogenes and Listeria innocua strains exposed to selected stress conditions. Appl Envir Microbiol 74:158–171

    CAS  Google Scholar 

  • Rajashekara G, Eskra L, Mathison A, Petersen E, Yu Q, Harms J, Splitter G (2006) Brucella: functional genomics and host–pathogen interactions. Anim Health Res Rev 7:1–11

    Google Scholar 

  • Raskin DM, Seshadri R, Pukatzki SU, Mekalanos JJ (2006) Bacterial genomics and pathogen evolution. Cell 124:703–714

    CAS  Google Scholar 

  • Rasooly A, Herold KE (2008) Food microbial pathogen detection and analysis using DNA microarray technologies. Foodborne Pathog Dis 5:531–550

    CAS  Google Scholar 

  • Razzaq S (2006) Hemolytic uremic syndrome: an emerging health risk. Am Fam Physician 74:991–996

    Google Scholar 

  • Read TD, Salzberg SL, Pop M, Shumway M, Umayam L, Jiang L, Holtzapple E, Busch JD, Smith KL, Schupp JM, Solomon D, Keim P, Fraser CM (2002) Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 296:2028–2033

    CAS  Google Scholar 

  • Reen FJ, Boyd EF, Porwollik S, Murphy BP, Gilroy D, Fanning S, McClelland M (2005) Genomic comparisons of Salmonella enterica serovar Dublin, Agona, and Typhimurium strains recently isolated from milk filters and bovine samples from Ireland, using a Salmonella microarray. Appl Environ Microbiol 71:1616–1625

    CAS  Google Scholar 

  • Riedel K, Lehner A (2007) Identification of proteins involved in osmotic stress response in Enterobacter sakazakii by proteomics. Proteomics 7:1217–1231

    CAS  Google Scholar 

  • Ronaghi M, Karamohamed S, Pettersson B, Uhlen M, Nyren P (1996) Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem 242:84–89

    CAS  Google Scholar 

  • Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547

    CAS  Google Scholar 

  • Rothberg JM, Leamon JH (2008) The development and impact of 454 sequencing. Nat Biotechnol 26:1117–1124

    CAS  Google Scholar 

  • Rudi K, Holck AL (2003) Real-time closed tube single nucleotide polymorphism (SNP) quantification in pooled samples by quencher extension (qext). Nucleic Acids Res 31:e117

    Google Scholar 

  • Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M (1977a) Nucleotide sequence of bacteriophage phi x174 DNA. Nature 265:687–695

    CAS  Google Scholar 

  • Sanger F, Nicklen S, Coulson AR (1977b) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci 74:5463–5467

    CAS  Google Scholar 

  • Schloss PD, Handelsman J (2003) Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14:303–310

    CAS  Google Scholar 

  • Schoolnik GK (2002) Functional and comparative genomics of pathogenic bacteria. Curr Opin Microbiol 5:20–26

    CAS  Google Scholar 

  • Schuster SC (2008) Next-generation sequencing transforms today’s biology. Nat Methods 5:16–18

    CAS  Google Scholar 

  • Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728–1732

    CAS  Google Scholar 

  • Skovgaard N (2007) New trends in emerging pathogens. Int J Food Microbiol 120:217–224

    Google Scholar 

  • Smith JL (2001) A review of hepatitis E virus. J Food Prot 64:572–586

    CAS  Google Scholar 

  • Smith LM, Sanders JZ, Kaiser RJ, Hughes P, Dodd C, Connell CR, Heiner C, Kent SB, Hood LE (1986) Fluorescence detection in automated DNA sequence analysis. Nature 321:674–679

    CAS  Google Scholar 

  • Stears RL, Martinsky T, Schena M (2003) Trends in microarray analysis. Nat Med 9:140–145

    CAS  Google Scholar 

  • Stothard P, Wishart DS (2006) Automated bacterial genome analysis and annotation. Curr Opin Microbiol 9:505–510

    CAS  Google Scholar 

  • Strauss EJ, Falkow S (1997) Microbial pathogenesis: genomics and beyond. Science 276:707–712

    CAS  Google Scholar 

  • Suen G, Arshinoff BI, Taylor RG, Welch RD (2007) Practical applications of bacterial functional genomics. Biotechnol Genet Eng Rev 24:213–242

    CAS  Google Scholar 

  • Tartof SY, Solberg OD, Riley LW (2007) Genotypic analyses of uropathogenic Escherichia coli based on fimH single nucleotide polymorphisms (SNPs). J Med Microbiol 56:1363–1369

    CAS  Google Scholar 

  • Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28:33–36

    CAS  Google Scholar 

  • Tauxe RV (2002) Emerging foodborne pathogens. Int J Food Microbiol 78:31–41

    CAS  Google Scholar 

  • Toh M, Moffitt MC, Henrichsen L, Raftery M, Barrow K, Cox JM, Marquis CP, Neilan BA (2004) Cereulide, the emetic toxin of Bacillus cereus, is putatively a product of nonribosomal peptide synthesis. J Appl Microbiol 97:992–1000

    CAS  Google Scholar 

  • Toledo-Arana A, Dussurget D, Nikitas G, Sesto N, Guet-Revillet H, Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy M, Vergassola M, Nahori MA, Soubigou G, Régnault B, Coppée JY, Lecuit M, Johansson J, Cossart P (2009) The Listeria transcriptional landscape from saprophytism to virulence. Nature 459:950–956

    CAS  Google Scholar 

  • Toner B (2005) Harvard’ s church calls for open source, non-anonymous personal genome project. Genome Web Daily News, 14 Nov. http://www.genomeweb.com/issues/news/125128-1.html

  • Torpdahl M, Sorensen G, Ethelberg S, Sando G, Gammelgard K, Porsbo LJ (2006) A regional outbreak of S. Typhimurium in Denmark and identification of the source using MLVA typing. Euro Surveill 11:134–136

    CAS  Google Scholar 

  • Tsang RS (2002) The relationship of Campylobacter jejuni infection and the development of Guillain–Barre syndrome. Curr Opin Infect Dis 15:221–228

    Google Scholar 

  • Umejiego NN, Gollapalli D, Sharling L, Volftsun A, Lu J, Benjamin NN, Stroupe AH, Riera TV, Striepen B, Hedstrom L (2008) Targeting a prokaryotic protein in a eukaryotic pathogen: identification of lead compounds against cryptosporidiosis. Chem Biol 15:70–77

    CAS  Google Scholar 

  • Vallenet D, Labarre L, Rouy Z, Barbe V, Bocs S, Cruveiller S, Lajus A, Pascal G, Scarpelli C, Medigue C (2006) MAGE: a microbial genome annotation system supported by synteny results. Nucleic Acids Res 34:53–65

    CAS  Google Scholar 

  • Vazquez-Boland JA, Dominguez-Bernal G, Gonzalez-Zorn B, Kreft J, Goebel W (2001) Pathogenicity islands and virulence evolution in Listeria. Microbes Infect 3:571–584

    CAS  Google Scholar 

  • Voelkerding KV, Dames SA, Durtschi JD (2009) Next-generation sequencing: from basic research to diagnostics. Clin Chem 55:641–650

    CAS  Google Scholar 

  • Walter G, Bussow K, Cahill D, Lueking A, Lehrach H (2000) Protein arrays for gene expression and molecular interaction screening. Curr Opin Microbiol 3:298–302

    CAS  Google Scholar 

  • Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63

    CAS  Google Scholar 

  • Welch RA, Burland V, Plunkett G 3rd, Redford P, Roesch P, Rasko D, Buckles EL, Liou SR, Boutin A, Hackett J, Stroud D, Mayhew GF, Rose DJ, Zhou S, Schwartz DC, Perna NT, Mobley HL, Donnenberg MS, Blattner FR (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci 99:17020–17024

    CAS  Google Scholar 

  • Widdowson MA, Sulka A, Bulens SN, Beard RS, Chaves SS, Hammond R, Salehi ED, Swanson E, Totaro J, Woron R, Mead PS, Bresee JS, Monroe SS, Glass RI (2005) Norovirus and foodborne disease, United States, 1991–2000. Emerg Infect Dis 11:95–102

    Google Scholar 

  • Wilkinson M (2007) ABI launch SOLiD gene sequencer. Labtechnologist.com (7/11/2007). http://www.labtechnologist.com/news/ng.asp?id=77192-applied-biosystems-abi-dna-sequencing-solid

  • Widdowson MA, Jaspers WJ, van der Poel WH, Verschoor F, de Roda Husman AM, Winter HL, Zaaijer HL, Koopmans M (2003) Cluster of cases of acute hepatitis associated with hepatitis E virus infection acquired in the Netherlands. Clin Infect Dis 36:29–33

    Google Scholar 

  • Winkler H (1920) Verbeitung und Ursache der Parthenogenesis im Pflanzen und Tierreiche. Springer, Jena

    Google Scholar 

  • WHO (World Health Organization) (2007) Food safety and foodborne illness. Fact Sheet No. 327

    Google Scholar 

  • van Belkum A, Scherer S, van Alphen L, Verbrugh H (1998) Short-sequence DNA repeats in prokaryotic genomes. Microbiol Mol Biol Rev 62:275–293

    Google Scholar 

  • von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P (2005) String: known and predicted protein–protein associations, integrated and transferred across organisms. Nucleic Acids Res 33:D433–D437

    Google Scholar 

  • Zhu H, Snyder M (2001) Protein arrays and microarrays. Curr Opin Chem Biol 5:40–45

    CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Food Science, Cornell University, Ithaca, NY, 14853, USA

    Sara R. Milillo, Martin Wiedmann & Karin Hoelzer

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  1. Sara R. Milillo
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  2. Martin Wiedmann
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  3. Karin Hoelzer
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Correspondence to Karin Hoelzer .

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  1. Dept. Food Science, Cornell University, Stocking Hall 116, Ithaca, 14853, New York, USA

    Martin Wiedmann

  2. National Center for Food Safety &, Technology, Illinois Institute of Technology, S. Archer Rd. 6502, Summit, 60501, Illinois, USA

    Wei Zhang

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Milillo, S.R., Wiedmann, M., Hoelzer, K. (2011). Overview: The Impact of Microbial Genomics on Food Safety. In: Wiedmann, M., Zhang, W. (eds) Genomics of Foodborne Bacterial Pathogens. Food Microbiology and Food Safety. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-7686-4_1

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