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Genomics of food-borne bacterial pathogens

Published online by Cambridge University Press:  01 November 2007

Jerry M. Wells  and
Marjon H. J. Bennik
Jerry M. Wells*
Affiliation:
Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK
Marjon H. J. Bennik
Affiliation:
Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK
*
*Corresponding author: Dr Jerry Wells, fax +44 1603 207732, email [email protected]
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Abstract

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Despite continued efforts to prevent and control food-borne illness it remains a major cause of morbidity and mortality throughout the world. The problem is made worse by the continuous threat from emerging pathogens that can evolve to adapt to the different environments resulting from ongoing changes in farming or food production. The present review discusses the impact of genomics and post-genomic technologies on research in the area of food-borne bacterial pathogens. Genomics research is moving at a fast pace and these are exciting times for microbial research. The genome sequences of approximately ninety bacterial genomes have recently been completed and genome sequences are already available for several food-borne pathogens and closely related species. Comparative genomics is providing new insights into mechanisms of bacterial evolution and has helped in determining virulence factors of pathogens. Genomics has also provided tools such as DNA microarrays that can be used to examine the genetic composition and whole genome expression profiles of bacterial strains by hybridisation of fluorescently labelled DNA. This is helping to identify genes associated with particular phenotypes such as virulence and host preference, and to identify genes in uncharacterised genomes of closely related organisms. Microarrays are also being developed for the detection of food-borne pathogens and investigation of the evolutionary relationship between different species of bacteria. The review concludes with a discussion of the use of functional genomics tools to investigate bacterial responses to environmental stresses and also host–pathogen interactions. These research areas will be valuable in designing future strategies for controlling food-borne pathogens.

Keywords

Food-borne pathogensDNA microarraysGenomicsHost–microbe interactionsStress response
Type
Research Article
Information
Nutrition Research Reviews , Volume 16 , Issue 1 , June 2003 , pp. 21 - 35
Copyright
Copyright © CABI Publishing 2003

References

Adak, GK, Long, SM & O'Brien, SJ (2002) Trends in the indigenous foodborne disease and deaths, England and Wales: 1992–2000. Gut 51, 832–841.CrossRefGoogle Scholar
Arfin, SM, Long, AD, Ito, ET, Tolleri, L, Riehle, MM, Paegle, EES & Hatfield, GW (2000) Global gene expression profiling in Escherichia coli K12. The effects of integration host factor. Journal of Biological Chemistry 275, 29672–29684.CrossRefGoogle ScholarPubMed
Alm, RA, Ling, LS, Moir, DT, King, BL, Brown, ED, Doig, PC, Smith, DR, Noonan, B, Guild, BC, deJonge, BL, Carmel, G & Tummino, PJ et al. (1999) Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397, 176–180.Google ScholarPubMed
Antelmann, H, Tjalsma, H, Voigt, B, Ohlmeier, S, Bron, S, Maarten van Dijl, J & Hecker, M (2001) A proteomic view on genome-based signal peptide predictions. Genome Research 11, 1484–1502.CrossRefGoogle ScholarPubMed
Arnold, CN, McElhanon, J, Lee, A, Leonhart, R & Siegele, DA (2001) Global analysis of Escherichia coli gene expression during the acetate-induced acid tolerance response. Journal of Bacteriology 183, 2178–2186.CrossRefGoogle ScholarPubMed
Bacon, DJ, Alm, RA, Burr, DH, Hu, L, Kopecko, DJ, Ewing, CP, Trust, TJ & Guerry, P (2000) Involvement of a plasmid in virulence of Campylobacter jejuni 81–176. Infection and Immunity 68, 4384–4390.CrossRefGoogle ScholarPubMed
Balaban, N & Rasooly, A (2000) Staphylococcal enterotoxins. International Journal of Food Microbiology 61, 1–10.CrossRefGoogle ScholarPubMed
Bammert, GF & Fostel, JM (2000) Genome-wide expression patterns in Saccharomyces cerevisiae: a comparison of drug treatments and genetic alterations affecting biosynthesis of ergosterol. Antimicrobial Agents and Chermotherapy 44, 1255–1265.CrossRefGoogle ScholarPubMed
Bavykin, SG, Akowski, JP, Zakhariev, VM, Barsky, VE, Perov, AN & Mirzabekov, AD (2001) Portable system for microbial sample preparation and oligonucleotide microarray analysis. Applied and Environmental Microbiology 67, 922–928.CrossRefGoogle ScholarPubMed
Bayliss, CD, Field, D & Moxon, ER (2001) The simple sequence contingency loci of Haemophilus influenzae and Neisseria meningitidis. Journal of Clinical Investigation 107, 657–662.CrossRefGoogle ScholarPubMed
Belcher, CE, Drenkow, J, Kehoe, B, Gingeras, TR, McNamara, N, Lemjabbar, H, Basbaum, C & Relman, DA (2000) From the cover: the transcriptional responses of respiratory epithelial cells to Bordetella pertussis reveal host defensive and pathogen counter-defensive strategies. Proceedings of the National Academy of Sciences USA 97, 13847–13852.CrossRefGoogle Scholar
Berndt, P, Hobohm, U & Langen, H (1999) Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints. Electrophoresis 20, 3521–3526.3.0.CO;2-8>CrossRefGoogle ScholarPubMed
Blankenhorn, D, Phillips, J & Slonczewski, JL (1999) Acid- and base-induced proteins during aerobic and anaerobic growth of Escherichia coli revealed by two-dimensional gel electrophoresis. Journal of Bacteriology 181, 2209–2216.CrossRefGoogle ScholarPubMed
Blattner, FR, Plunkett, G III, Bloch, CA, Perna, NT, Burland, V, Riley, M, Collado-Vides, J, Glasner, JD, Rode, CK, Mayhew, GF, Gregor, J & Davis, NW et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277, 1453–1474.CrossRefGoogle ScholarPubMed
Blohm, DH & Guiseppi-Elie, A (2001) New developments in microarray technology. Current Opinion in Biotechnology 12, 41–47.CrossRefGoogle ScholarPubMed
Blomfield, IC (2001) The regulation of pap and type 1 fimbriation in Escherichia coli. Advances in Microbial Physiology 45, 1–49.CrossRefGoogle ScholarPubMed
Bottone, EJ (1999) Yersinia enterocolitica: overview and epidemiologic correlates. Microbes and Infection 1, 323–333.CrossRefGoogle ScholarPubMed
Bowtell, DD (1999) Options available – from start to finish – for obtaining expression data by microarray. Nature Genetics 21, 25–32.CrossRefGoogle ScholarPubMed
Brenner, S, Johnson, M, Bridgham, J, Golda, G, Lloyd, DH, Johnson, D, Luo, S, McCurdy, S, Foy, M, Ewan, M, Roth, R & George, D (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotechnology 18, 630–634.CrossRefGoogle ScholarPubMed
Brenner, SE (1999) Errors in genome annotation. Trends in Genetics 15, 132–133.CrossRefGoogle ScholarPubMed
Bryan, FL (1982) Diseases Transmitted by Foods – A Classification and Summary. Atlanta: GA: Centers for Disease Control.Google Scholar
Call, DR, Brockman, FJ & Chandler, DP (2001) Detecting and genotyping Escherichia coli O157:H7 using multiplexed PCR and nucleic acid microarrays. International Journal of Food Microbiology 67, 71–80.CrossRefGoogle ScholarPubMed
Call, DR, Borucki, MK & Besser, TE (2003) Mixed-genome microarrays reveal multiple serotype and lineage-specific differences among strains of Listeria monocytogenes. Journal of Clinical Microbiology 41, 632–639.CrossRefGoogle ScholarPubMed
Chalker, RB & Blaser, MJ (1988) A review of human salmonellosis: III. Magnitude of Salmonella infection in the United States. Review of Infectious Diseases 10, 111–124.CrossRefGoogle ScholarPubMed
Chart, H, Frost, JA, Oza, A, Thwaites, R, Gillanders, S & Rowe, B (1996) Heat-stable serotyping antigens expressed by strains of Campylobacter jejuni are probably capsular and not long-chain lipopolysaccharide. Journal of Applied Bacteriology 81, 635–640.CrossRefGoogle Scholar
Cheung, VG, Morley, M, Aguilar, F, Massimi, A, Kucherlapati, R & Childs, G (1999) Making and reading microarrays. Nature Genetics Review 21, 15–19.CrossRefGoogle ScholarPubMed
Cho, JC & Tiedje, JM (2001) Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Applied and Environmental Microbiology 67, 3677–3682.CrossRefGoogle ScholarPubMed
Cho, JC & Tiedje, JM (2002) Quantitative detection of microbial genes by using DNA microarrays. Applied and Environmental Microbiology 68, 1425–1430.CrossRefGoogle ScholarPubMed
Chu, S, DeRisi, J, Eisen, M, Mulholland, J, Botstein, D, Brown, PO & Herskowitz, I (1998) The transcriptional program of sporulation in budding yeast. Science 282, 699–705.CrossRefGoogle ScholarPubMed
Coombes, BK & Mahony, JB (2001) cDNA array analysis of altered gene expression in human endothelial cells in response to Chlamydia pneumoniae infection. Infection and Immunity 69, 1420–1427.CrossRefGoogle ScholarPubMed
Corbeil, J, Sheeter, D, Rought, S, Du, P, Ferguson, M, Masys, DR, Welsh, JB, Fink, JL, Sasik, R, Huang, D, Drenkow, J, Richman, DD & Gingeras, T (1999) Magnitude and specificity of temporal gene expression during HIV-1 infection of a CD4+ T cell. Nature Genetics 23, 39–40.CrossRefGoogle Scholar
Cotter, PA & Miller, JF (1998) In vivo and ex vivo regulation of bacterial virulence gene expression. Current Opinion in Microbiology 1, 17–26.CrossRefGoogle ScholarPubMed
Day, WAJ, Fernandez, RE & Maurelli, AT (2001) Pathoadaptive mutations that enhance virulence: genetic organization of the cadA regions of Shigella spp. Infection and Immunity 69, 7471–7480.CrossRefGoogle ScholarPubMed
DeRisi, J (2000) Overview of nucleic acid arrays. In Current Protocols in Molecular Biology. pp. 22.1.1–22.3.6 [Ausubel, FA, editor]. New York: NY: John Wiley & Sons.Google Scholar
Diehn, M & Relman, DA (2001) Comparing functional genomic datasets: lessons from DNA microarray analyses of host-pathogen interactions Current Opinion in Microbiology 4, 95–101.CrossRefGoogle ScholarPubMed
Dorrell, N, Mangan, JA, Laing, KG, Hinds, J, Linton, D, Al-Ghusein, H, Barrell, BG, Parkhill, J, Stoker, NG, Karlyshev, AV, Butcher, PD & Wren, BW (2001) Whole genome comparison of Campylobacter jejuni human isolates using a low-cost microarray reveals extensive genetic diversity. Genome Research 11, 1706–1715.CrossRefGoogle ScholarPubMed
Duche, O, Tremoulet, F, Glaser, P & Labadie, J (2002) Salt stress proteins induced in. Listeria monocytogenes. Applied and Environmental Microbiology 68, 1491–1498.CrossRefGoogle ScholarPubMed
Eckmann, L, Smith, JR, Housley, MP, Dwinell, MB & Kagnoff, MF (2000) Analysis by high density cDNA arrays of altered gene expression in human intestinal epithelial cells in response to infection with the invasive enteric bacteria salmonella. Journal of Biological Chemistry 275, 14084–14094.CrossRefGoogle ScholarPubMed
Edwards, AE, Olsen, GJ & Maloy, SR (2002) Comparative genomics of closely related salmonellae. Trends in Microbiology 10, 94–99.CrossRefGoogle ScholarPubMed
Eriksson, S, Lucchini, S, Thompson, A, Rhen, M & Hinton, JC (2003) Unravelling the biology of macrophage infection by gene expression profiling of intracellular Salmonella enterica. Molecular Microbiology 47, 103–118.CrossRefGoogle ScholarPubMed
Ezzell, JW Jr, Abshire, TG, Little, SF, Lidgerding, BC & Brown, C (1990) Identification of Bacillus anthracis by using monoclonal antibody to cell wall galactose-N-acetylglucosamine polysaccharide. Journal of Clinical Microbiology 28, 223–231.CrossRefGoogle ScholarPubMed
Fang, FC, Libby, SJ, Buchmeier, NA, Loewen, PC, Switala, J, Harwood, J & Guiney, DG (1992) The alternative sigma factor KatF (RpoS) regulates Salmonella virulence. Proceedings of the National Academy of Sciences USA 96, 7502–7507.CrossRefGoogle Scholar
Fawcett, P, Eichenberger, P, Losick, R & Youngman, P (2000) The transcriptional profile of early to middle sporulation in Bacillus subtilis. Proceedings of the National Academy of Sciences USA 97, 8063–8068.CrossRefGoogle ScholarPubMed
Fodor, SP, Read, JL, Pirrung, MC, Stryer, L, Lu, AT & Solas, D (1991) Light-directed spatially addressable parallel chemical synthesis Science 251, 767–773.CrossRefGoogle ScholarPubMed
Fox, AJ, Gilbart, J & Morgan, S (1990) Analytical microbiology: a perspective. In Analytical Microbiology Methods: Chromatography and Mass Spectrometry, pp. 1–17 [Fox, A, Larsson, L, Morgan, SL and Odham, G, editors]. New York: NY: Plenum Press.CrossRefGoogle Scholar
Frangeul, L, Nelson, KE, Buchrieser, C, Danchin, A, Glaser, P & Kunst, F (1999) Cloning and assembly strategies in microbial genome projects. Microbiology 145, 2625–2634.CrossRefGoogle ScholarPubMed
Fraser, CM & Fleischmann, RD (1997) Strategies for whole microbial genome sequencing and analysis. Electrophoresis 18, 1207–1216.CrossRefGoogle ScholarPubMed
Gaillot, O, Pellegrini, E, Bregenholt, S, Nair, S & Berche, P (2000) The ClpP serine protease is essential for the intracellular parasitism and virulence of Listeria monocytogenes. Molecular Microbiology 35, 1286–1294.CrossRefGoogle ScholarPubMed
Geiss, GK, Bumgarner, RE, An, MC, Agy, MB, van 't Wout, AB, Hammersmark, E, Carter, VS, Upchurch, D, Mullins, JI & Katze, MG (2000) Large-scale monitoring of host cell gene expression during HIV-1 infection using cDNA microarrays. Virology 266, 8–16.CrossRefGoogle ScholarPubMed
Gertz, S, Engelmann, S, Schmid, R, Ziebandt, AK, Tischer, K, Scharf, C, Hacker, J & Hecker, M (2000) Characterization of the sigma(B) regulon in Staphylococcus aureus. Journal of Bacteriology 182, 6983–6991.CrossRefGoogle ScholarPubMed
Gingeras, TR, Ghandour, G, Wang, E, Berno, A, Small, PM, Drobniewski, F, Alland, D, Desmond, E, Holodniy, M & Drenkow, J (1998) Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays. Genome Research 8, 435–448.CrossRefGoogle ScholarPubMed
Glaser, P, Frangeul, L, Buchrieser, C, Rusniok, C, Amend, A, Baquero, F, Berche, P, Bloecker, H, Brandt, P, Chakraborty, T, Charbit, A & Chetouani, F et al. (2001) Comparative genomics of Listeria species. Science 294, 849–852.CrossRefGoogle ScholarPubMed
Granum, PE (1990) Clostridium perfringens toxins involved in food poisoning. International Journal of Food Microbiology 10, 101–111.CrossRefGoogle ScholarPubMed
Graves, DJ (1999) Powerful tools for genetic analysis come of age. Trends in Biotechnology 17, 127–134.CrossRefGoogle ScholarPubMed
Groisman, EA & Ochman, H (1996) Pathogenicity islands: bacterial evolution in quantum leaps. Cell 87, 791–794.CrossRefGoogle ScholarPubMed
Gygi, SP, Rist, B, Gerber, SA, Turecek, F, Gelb, MH & Aebersold, R (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnology 17, 994–999.CrossRefGoogle ScholarPubMed
Hacker, J, Blum-Oehler, G, Muhldorfer, I & Tschape, H (1997) Pathogenicity islands of virulent bacteria: structure function and impact on microbial evolution. Molecular Microbiology Reviews 23, 1089–1097.CrossRefGoogle ScholarPubMed
Hallet, B (2001) Playing Dr Jekyll and Mr Hyde: combined mechanisms of phase variation in bacteria. Current Opinion in Microbiology 4, 570–581.CrossRefGoogle Scholar
Hatfield, GW, Hung, SP & Baldi, P (2003) Differential analysis of DNA microarray gene expression data. Molecular Microbiology 47, 871–877.CrossRefGoogle ScholarPubMed
Hayashi, T, Makino, K, Ohnishi, M, Kurokawa, K, Ishii, K, Yokoyama, K, Han, C-G, Ohtsubo, E, Nakayama, K, Murata, T, Tanaka, M & Tobe, T et al. (2001) Complete genome sequence of Enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Research 8, 11–22.CrossRefGoogle ScholarPubMed
Hecker, M & Voelker, U (2001) General stress response of Bacillus subtilis and other bacteria. Advances in Microbial Physiology 44, 35–91.CrossRefGoogle ScholarPubMed
Helmann, JD, Wu, MF, Kobel, PA, Gamo, FJ, Wilson, M, Morshedi, MM, Navre, M & Paddon, C (2001) Global transcriptional response of Bacillus subtilis to heat shock. Journal of Bacteriology 183, 7318–7328.CrossRefGoogle ScholarPubMed
Hengge-Aronis, R (2000) The general stress response in Escherichia coli. In Bacterial Stress Responses. pp. 161–178 [Storz, G and Hengge-Aaronis, R editors]. Washington: DC: ASM Press.Google Scholar
Hengge-Aronis, R (2002) Signal transduction and regulatory mechanisms involved in control of the σS (RpoS) subunit of RNA polymerase. Microbiology and Molecular Biology Reviews 66, 373–395.CrossRefGoogle ScholarPubMed
Hommais, F, Krin, E, Laurent-Winter, C, Soutourina, O, Malpertuy, A, Le Caer, JP, Danchin, A & Bertin, P (2001) Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS. Molecular Microbiology 40, 20–36.CrossRefGoogle ScholarPubMed
Hooper, LV, Wong, MH, Thelin, A, Hansson, L, Falk, PG & Gordon, JI (2001) Molecular analysis of commensal host-microbial relationships in the intestine. Science 291, 881–884.CrossRefGoogle ScholarPubMed
Hu, L & Kopecko, DJ (1999) Campylobacter jejuni 81–176 associates with microtubules and dynein during invasion of human intestinal cells. Infection and Immunity 67, 4171–4182.CrossRefGoogle ScholarPubMed
Hughes, TR, Marton, MJ, Jones, AR, Roberts, CJ, Stoughton, R, Armour, CD, Bennett, HA, Coffey, E, Dai, H, He, YD, Kidd, MJ & King, AM (2000) Functional discovery via a compendium of expression profiles. Cell 102, 109–126.CrossRefGoogle Scholar
Hung, SP, Baldi, P & Hatfield, GW (2002) Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein. Journal of Biological Chemistry 277, 40309–40323.CrossRefGoogle ScholarPubMed
Ibanez-Ruiz, M, Robbe-Saule, V, Hermant, D, Labrude, S & Norel, F (2000) Identification of RpoS (σS)-regulated genes in Salmonella enterica Serovar Typhimurium. Journal of Bacteriology 182, 5749–5756.CrossRefGoogle Scholar
Ichikawa, JK, Norris, A, Bangera, MG, Geiss, GK, van 't Wout, AB, Bumgarner, RE & Lory, S (2000) Interaction of Pseudomonas aeruginosa with epithelial cells: identification of differentially regulated genes by expression microarray analysis of human cDNAs. Proceedings of the National Academy of Sciences USA 97, 9659–9664.CrossRefGoogle ScholarPubMed
Israel, DA, Salama, N, Arnold, CN, Moss, SF, Ando, T, Wirth, HP, Tham, KT, Camorlinga, M, Blaser, MJ, Falkow, S & Peek, RM Jr (2001) Helicobacter pylori strain-specific differences in genetic content, identified by microarray, influence host inflammatory responses. Journal of Clinical Investigation 107, 611–620.CrossRefGoogle ScholarPubMed
Jensen, ON, Mortensen, P, Vorm, O & Mann, M (1997) Automation of matrix-assisted laser desorption/ionization mass spectrometry using fuzzy logic feedback control. Analytical Chemistry 69, 1706–1714.CrossRefGoogle ScholarPubMed
Jungblut, PR (2001) Proteome analysis of bacterial pathogens. Microbes and Infection 3, 831–840.CrossRefGoogle ScholarPubMed
Kaferstein, F & Abdussalam, M (1999) Food safety in the 21st century. Bulletin of the World Health Organization 77, 347–351.Google Scholar
Karatzas, KAG, Wouters, JA, Gahan, CGM, Hill, C, Abee, T & Bennik, MHJ (2002) A single amino acid deletion in the glycine-rich region of Ctsr effects mobility, piezotolerance, and virulence of. In Listeria monocytogenes Scott A. In Listeria Monocytogenes. – Inactivation by Essential Oils and High Pressure and Contribution of Genetic Variation to Stress Resistance, pp. 54-62. PhD Thesis. Wageningen: The Netherlands: Wageningen University.Google Scholar
Karlyshev, AV, Linton, D, Gregson, NA, Lastovica, AJ & Wren, BW (2000) Genetic and biochemical evidence of a Campylobacter jejuni capsular polysaccharide that accounts for Penner serotype specificity. Molecular Microbiology 35, 529–541.CrossRefGoogle ScholarPubMed
Kim, CC, Joyce, EA, Chan, K & Falkow, S (2002) Improved analytical methods for microarray-based genome composition analysis. Genome Biology 3, 1–16.CrossRefGoogle ScholarPubMed
Kobayashi, K, Ogura, M, Yamaguchi, H, Yoshida, K, Ogasawara, N, Tanaka, T & Fujita, Y (2001) Comprehensive DNA microarray analysis of Bacillus subtilis two-component regulatory systems. Journal of Bacteriology 183, 7365–7370.CrossRefGoogle ScholarPubMed
Kotiranta, A, Lounatmaa, K & Haapasalo, M (2000) Epidemiology and pathogenesis of Bacillus cereus infections. Microbes and Infection 2, 189–198.CrossRefGoogle ScholarPubMed
Kotloff, KL, Winickoff, JP, Ivanoff, B, Clemens, JD, Swerdlow, DL, Sansonetti, PJ, Adak, GK & Levine, MM (1999) Global burden of shigella infections: implications for vaccine development and implementation of control strategies. Bulletin of the World Health Organization 77, 651–656.Google ScholarPubMed
Lee, CA (1996) Pathogenicity islands and the evolution of bacterial pathogens. Infectious Agents and Disease 5, 1–7.Google ScholarPubMed
Lee, CY, Tai, CL, Lin, SC & Chen, YT (1994) Occurrence of plasmids and tetracycline resistance among Campylobacter jejuni and Campylobacter coli isolated from whole market chickens and clinical samples. International Journal of Food Microbiology 24, 161–170.CrossRefGoogle ScholarPubMed
Lee, ML, Kuo, FC, Whitmore, GA & Sklar, J (2000) Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proceedings of the National Academy of Sciences USA 97, 9834–9839.CrossRefGoogle ScholarPubMed
Leimgruber, RM, Malone, JP, Radabaugh, MR, LaPorte, ML, Violand, BN & Monahan, JB (2002) Development of improved cell lysis, solubilization and imaging approaches for proteomic analyses. Proteomics 2, 135–144.3.0.CO;2-1>CrossRefGoogle ScholarPubMed
Leistner, L (2000) Basic aspects of food preservation by hurdle technology. International Journal of Food Microbiology 55, 181–186.CrossRefGoogle ScholarPubMed
Lipshutz, RJ, Fodor, SP, Gingeras, TR & Lockhart, DJ (1999) High density synthetic oligonucleotide arrays. Nature Genetics Review 21, Suppl., 20–24.CrossRefGoogle ScholarPubMed
Loewen, PC, Hu, B, Strutinsky, J & Sparling, R (1998) Regulation in the rpoS regulon of Escherichia coli. Canadian Journal of Food Microbiology 44, 707–717.CrossRefGoogle ScholarPubMed
Lund, BM, Baird-Parker, TC & Gould, GW (2000) The Microbiological Safety and Quality of Food, vol. 2. Frederick, MD: Aspen Publishers.Google Scholar
McClelland, M, Sanderson, KE, Spieth, J, Clifton, SW, Latreille, P, Courtney, L, Porwollik, S, Ali, J, Dante, M, Du, F, Hou, S & Layman, D (2001) Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413, 852–856.CrossRefGoogle ScholarPubMed
Martin, GP & Trimmers, E (1997) PCR and its modifications for the detection of infectious diseases. In Nucleic Acid Amplification Technologies: Application to Disease Diagnosis. pp. 79–99 [Lee, H, Morse, S and Olsvik, O editors]. Natick, MA: Eaton Publishing.CrossRefGoogle Scholar
Maurelli, AT, Fernandez, RE, Bloch, CA, Rode, CK & Fasano, A (1998) ‘Black holes’ and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp and enteroinvasive Escherichia coli. Proceedings of the National Academy of Sciences USA 95, 3943–3948.CrossRefGoogle ScholarPubMed
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. Emerging and Infectious Diseases 5, 607–625.CrossRefGoogle ScholarPubMed
Mekalanos, JJ (1992) Environmental signals controlling expression of virulence determinants in bacteria. Journal of Bacteriology 174, 1–7.CrossRefGoogle ScholarPubMed
Meldrum, D (2000) Automation for genomics part two: sequencers microarrays and future trends. Genome Research 10, 1288–1303.CrossRefGoogle ScholarPubMed
Mishu, B, Ilyas, AA, Koski, CL, Vriesendorp, F, Cook, SD, Mithen, FA & Blaser, MJ (1993) Serologic evidence of previous Campylobacter jejuni infection in patients with the Guillain-Barre syndrome. Annals of Internal Medicine 118, 947–953.CrossRefGoogle ScholarPubMed
Moxon, ER, Rainey, PB, Nowak, MA & Lenski, RE (1994) Adaptive evolution of highly mutable loci in pathogenic bacteria. Current Biology 4, 24–33.CrossRefGoogle ScholarPubMed
Nachamkin, I, Allos, BM & Ho, T (1998) Campylobacter species and Guillain-Barre syndrome. Clinical Microbiological Reviews 11, 555–567.CrossRefGoogle ScholarPubMed
Nair, S, Fréhel, C, Nguyen, L, Escuyer, V & Berche, P (1999) ClpE, a novel member of the HSP100 family, is involved in cell division and virulence of Listeria monocytogenes. Molecular Microbiology 31, 185–196.CrossRefGoogle ScholarPubMed
Nataro, JP, Seriwatana, J, Fasano, A, Maneval, DR, Guers, LD, Noriega, F, Dubovsky, F, Levine, MM & Morris, JG Jr (1995) Identification and cloning of a novel plasmid-encoded enterotoxin of enteroinvasive Escherichia coli and Shigella strains. Infection and Immunity 63, 4721–4728.CrossRefGoogle ScholarPubMed
Niemeyer, CM & Blohm, D (1999) DNA microarrays. Angewandte Chemie (International Edition in English) 38, 2865–2869.3.0.CO;2-F>CrossRefGoogle ScholarPubMed
Ochman, H & Groisman, EA (1995) The evolution of invasion by enteric bacteria. Canadian Journal of Microbiology 41, 555–561.CrossRefGoogle ScholarPubMed
Ochman, H & Jones, IB (2000) Evolutionary dynamics of full genome content in Escherichia coli. EMBO Journal 19, 6637–6643.CrossRefGoogle ScholarPubMed
Ochman, H, Lawrence, JG & Groisman, EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299–304.CrossRefGoogle ScholarPubMed
Oda, Y, Huang, K, Cross, FR, Cowburn, D & Chait, BT (1999) Accurate quantitation of protein expression and site-specific phosphorylation. Proceedings of the National Academy of Sciences USA 96, 6591–6596.CrossRefGoogle ScholarPubMed
Oh, MK, Rohlin, L, Kao, KC & Liao, JC (2002) Global expression profiling of acetate-grown Escherichia coli. Journal of Biological Chemistry 277, 13175–13183.CrossRefGoogle ScholarPubMed
Okamoto, T, Suzuki, T & Yamamoto, N (2000) Microarray fabrication with covalent attachment of DNA using bubble jet technology. Nature Biotechnology 18, 438–441.CrossRefGoogle ScholarPubMed
Parkhill, J, Wren, BW, Mungall, K, Ketley, JM, Churcher, C, Basham, D, Chillingworth, T, Davies, RM, Feltwell, T, Holroyd, S, Jagels, K & Karlyshev, AV et al. (2000) The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature 403, 665–668.CrossRefGoogle ScholarPubMed
Peck, MW (1997) Clostridium botulinum and the safety of refrigerated processed foods of extended durability. Trends in Food Science and Technology 8, 186–192.CrossRefGoogle Scholar
Penner, JL, Hennessy, JN & Congi, RV (1983) Serotyping of Campylobacter jejuni and Campylobacter coli on the basis of thermostable antigens. European Journal of Clinical Microbiology 2, 378–383.CrossRefGoogle ScholarPubMed
Periago, PM, Van Schaik, W, Abee, T & Wouters, JA (2002) Identification of proteins involved in the heat stress response of Bacillus cereus ATCC 14579. Applied and Environmental Microbiology 68, 3486–3495.CrossRefGoogle ScholarPubMed
Perna, NT, Plunkett, G III, Burland, V, Mau, B, Glasner, JD, Rose, DJ, Mayhew, GF, Evans, PS, Gregor, J, Kirkpatrick, HA, Pósfai, G & Hackett, J et al. (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409, 529–533.CrossRefGoogle ScholarPubMed
Petersohn, A, Brigulla, M, Haas, S, Hoheisel, JD, Volker, U & Hecker, M (2001) Global analysis of the general stress response of Bacillus subtilis. Journal of Bacteriology 183, 5617–5631.CrossRefGoogle ScholarPubMed
Pomposiello, PJ, Bennik, MHJ & Demple, B (2001) Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate. Journal of Bacteriology 183, 3890–3902.CrossRefGoogle ScholarPubMed
Porwollik, S, Wong, RM & McClelland, M (2002) Evolutionary genomics of Salmonella: gene acquisitions revealed by microarray analysis. Proceedings of the National Academy of Sciences USA 99, 8956–8961.CrossRefGoogle ScholarPubMed
Price, CW (2000) Protective function and regulation of the general stress response in Bacillus subtilis and related Gram-positive bacteria. In Bacterial Stress Responses. pp. 179–197 [Storz, G and Hengge-Aaronis, R editors]. Washington: DC: ASM Press.Google Scholar
Pupo, GM, Lan, R & Reeves, PR (2000) Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proceedings of the National Academy of Sciences USA 97, 10567–10572.CrossRefGoogle ScholarPubMed
Qi, SY, Moir, A & O'Connor, CD (1996) Proteome of Salmonella typhimurium SL1344: identification of novel abundant cell envelope proteins and assignment to a two-dimensional reference map. Journal of Bacteriology 178, 5032–5038.CrossRefGoogle ScholarPubMed
Rabsch, W, Tschape, H & Baumler, AJ (2001) Non-typhoidal salmonellosis: emerging problems. Microbes and Infection 3, 237–247.CrossRefGoogle ScholarPubMed
Rhodius, V, Van Dyk, TK, Gross, C & LaRossa, RA (2002) Impact of genomic technologies on studies of bacterial gene expression. Annual Review of Microbiology 56, 599–624.CrossRefGoogle ScholarPubMed
Richmond, CS, Glasner, JD, Mau, R, Jin, H & Blattner, FR (1999) Genome-wide expression profiling in Escherichia coli K-12. Nucleic Acids Research 27, 3821–3835.CrossRefGoogle ScholarPubMed
Riehle, MM, Bennett, AF & Long, AD (2001) Genetic architecture of thermal adaptation in Escherichia coli. Proceedings of the National Academy of Sciences USA 98, 525–530.CrossRefGoogle ScholarPubMed
Rocha, EPC, Matic, I & Taddei, F (2002) Over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions?. Nucleic Acids Research 30, 1886–1894.CrossRefGoogle Scholar
Rosenberger, CM, Pollard, AJ & Finlay, BB (2001) Gene array technology to determine host responses to Salmonella. Microbes and Infection 3, 1353–1360.CrossRefGoogle ScholarPubMed
Rosenberger, CM, Scott, MG, Gold, MR, Hancock, RE & Finlay, BB (2000) Salmonella typhimurium infection and lipopolysaccharide stimulation induce similar changes in macrophage gene expression. Journal of Immunology 164, 5894–5904.CrossRefGoogle ScholarPubMed
Roth, FP, Hughes, JD, Estep, PW & Church, GM (1998) Finding DNA regulator motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nature Biotechnology 16, 939–945.CrossRefGoogle ScholarPubMed
Rouquette, C, Ripio, M-T, Pellegrini, E, Bolla, JM, Tascon, RI, Vazquez-Boland, JA & Berche, P (1996) Identification of a ClpC ATPase required for stress tolerance and in vivo survival of Listeria monocytogenes. Molecular Microbiology 21, 977–987.CrossRefGoogle ScholarPubMed
Sails, AD, Wareing, DR, Bolton, FJ, Fox, AJ & Curry, A (1998) Characterisation of 16 Campylobacter jejuni and C. coli typing bacteriophages. Journal of Medical Microbiology 47, 123–128.CrossRefGoogle Scholar
Schena, M, Shalon, D, Davis, RW & Brown, PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470.CrossRefGoogle ScholarPubMed
Schlech, WF III (2001) Foodborne listeriosis. Clinical Infection and Disease 32, 1518–1519.Google Scholar
Schuchhardt, J, Beule, D, Malik, A, Wolski, E, Eickhoff, H, Lehrach, H & Herzel, H (2000) Normalization strategies for cDNA microarrays. Nucleic Acids Research 28, E47.CrossRefGoogle ScholarPubMed
Shalon, D, Smith, SJ & Brown, PO (1996) A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Research 6, 639–645.CrossRefGoogle ScholarPubMed
Shevchenko, A, Loboda, A, Ens, W & Standing, KG (2000) MALDI quadrupole time-of-flight mass spectrometry: a powerful tool for proteomic research. Analytical Chemistry 72, 2132–2141.CrossRefGoogle ScholarPubMed
Singh-Gasson, S, Green, RD, Yue, Y, Nelson, C, Blattner, F, Sussman, MR & Cerrina, F (1999) Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nature Biotechnology 17, 974–978.CrossRefGoogle ScholarPubMed
Smelt, JPPM (1998) Recent advances in the microbiology of high pressure processing. Trends in Food Science and Technology 9, 152–158.CrossRefGoogle Scholar
Soini, H & Musser, JM (2001) Molecular diagnosis of mycobacteria. Clinical Chemistry 47, 809–814.CrossRefGoogle ScholarPubMed
Sokurenko, EV, Hasty, DL & Dykhuizen, DE (1999) Pathoadaptive mutations: gene loss and variation in bacterial pathogens. Trends in Microbiology 7, 191–195.CrossRefGoogle ScholarPubMed
Spellman, PT, Sherlock, G, Zhang, MQ, Iyer, VR, Anders, K, Eisen, MB, Brown, PO, Botstein, D & Futcher, B (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by mircoarray hybridization. Molecular Biology of the Cell 9, 3273–3297.CrossRefGoogle Scholar
Sperandio, V, Torres, AG, Giron, JA & Kaper, JB (2001) Quorum sensing is a global regulatory mechanism in enterohemorrhagic Escherichia coli 0157:H7. Journal of Bacteriology 183, 5187–5197.CrossRefGoogle Scholar
Steemers, FJ, Ferguson, JA & Walt, DR (2000) Screening unlabeled DNA targets with randomly ordered fiber-optic gene arrays. Nature Biotechnology 18, 91–94.CrossRefGoogle ScholarPubMed
Strockbine, NA, Marques, LR, Newland, JW, Smith, HW, Holmes, RK & O'Brien, AD (1986) Two toxin-converting phages from Escherichia coli O157:H7 strain 933 encode antigenically distinct toxins with similar biologic activities. Infection and Immunity 53, 135–140.CrossRefGoogle ScholarPubMed
Talaat, AM, Hunter, P & Johnston, SA (2000) Genome-directed primers for selective labeling of bacterial transcripts for DNA microarray analysis. Nature Biotechnology 18, 679–682.CrossRefGoogle ScholarPubMed
Taton, TA, Mirkin, CA & Letsinger, RL (2000) Scanometric DNA array detection with nanoparticle probes. Science 289, 1757–1760.CrossRefGoogle ScholarPubMed
Tavazoie, S, Hughes, JD, Campbell, MJ, Cho, RJ & Church, GM (1999) Systematic determination of genetic network architecture. Nature Genetics 22, 281–285.CrossRefGoogle ScholarPubMed
Tirado, C & Schmidt, K (2001) WHO surveillance programme for control of foodborne infections and intoxications: preliminary results and trends across greater Europe. World Health Organization. Journal of Infection 43, 80–84.CrossRefGoogle ScholarPubMed
van Belkum, A, Scherer, S, van Alphen, L & Verbrugh, H (1998) Short-sequence DNA repeats in prokaryotic genomes. Microbiology and Molecular Biology Reviews 62, 275–293.CrossRefGoogle ScholarPubMed
Vazquez-Boland, JA, Kuhn, M, Berche, P, Chakraborty, T, Dominguez-Bernal, G, Goebel, W, Gonzalez-Zorn, B, Wehland, J & Kreft, J (2001) Listeria pathogenesis and molecular virulence determinants. Clinical Microbiological Reviews 14, 584–640.CrossRefGoogle ScholarPubMed
Voelker, U, Maul, B & Hecker, M (1999) Expression of the σB-dependent general stress regulon confers multiple stress resistance in Bacillus subtilis. Journal of Bacteriology 181, 3942–3948.CrossRefGoogle Scholar
Volokhov, D, Rasooly, A, Chumakov, K & Chizhikov, V (2002) Identification of listeria species by microarray-based assay. Journal of Clinical Microbiology 40, 4720–4728.CrossRefGoogle ScholarPubMed
Walker, SJ, Archer, P & Banks, JG (1990) Growth of Listeria monocytogenes at refrigeration temperatures. Journal of Applied Bacteriology 68, 157–162.CrossRefGoogle ScholarPubMed
Washburn, MP & Yates, JR III (2000) Analysis of the microbial proteome. Current Opinion in Microbiology 3, 292–297.CrossRefGoogle ScholarPubMed
Wassenaar, TM & Blaser, MJ (1999) Pathophysiology of Campylobacter jejuni infections of humans. Microbes and Infection 1, 1023–1033.CrossRefGoogle ScholarPubMed
Wayne, LG, Brenner, DJ, Colwell, RR, Grimont, PAD, Kandler, MI, Krichevsky, MI & Truper, HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. International Journal of Systematic Bacteriology 37, 463–464.Google Scholar
Wei, Y, Lee, JM, Richmond, C, Blattner, FR, Rafalski, JA & LaRossa, RA (2001) High-density microarray-mediated gene expression profiling of Escherichia coli. Journal of Bacteriology 183, 545–556.CrossRefGoogle ScholarPubMed
Westin, L, Xu, X, Miller, C, Wang, L, Edman, CF & Nerenberg, M (2000) Anchored multiplex amplification on a microelectronic chip array. Nature Biotechnology 18, 199–204.CrossRefGoogle ScholarPubMed
Woese, CR (1987) Bacterial evolution. Microbiological Reviews 51, 221–271.CrossRefGoogle ScholarPubMed
Zheng, M, Wang, X, Templeton, LJ, Smulski, DR, LaRossa, RA & Storz, G (2001) DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide. Journal of Bacteriology 183, 4562–4570.CrossRefGoogle ScholarPubMed
Zhu, G, Spellman, PT, Volpe, T, Brown, PO, Botstein, D, Davis, TN & Futcher, B (2000) Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature 406, 90–94.CrossRefGoogle ScholarPubMed
Zhu, H, Cong, JP, Mamtora, G, Gingeras, T & Shenk, T (1998) Cellular gene expression altered by human cytomegalovirus: global monitoring with nucleotide arrays. Proceedings of the National Academy of Sciences USA 95, 14470–14475.CrossRefGoogle Scholar