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Bacterial Identification and Subtyping Using DNA Microarray and DNA Sequencing

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Microbial Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 881))

Abstract

The era of fast and accurate discovery of biological sequence motifs in prokaryotic and eukaryotic cells is here. The co-evolution of direct genome sequencing and DNA microarray strategies not only will identify, isotype, and serotype pathogenic bacteria, but also it will aid in the discovery of new gene functions by detecting gene expressions in different diseases and environmental conditions.

Microarray bacterial identification has made great advances in working with pure and mixed bacterial samples. The technological advances have moved beyond bacterial gene expression to include bacterial identification and isotyping. Application of new tools such as mid-infrared chemical imaging improves detection of hybridization in DNA microarrays. The research in this field is promising and future work will reveal the potential of infrared technology in bacterial identification.

On the other hand, DNA sequencing by using 454 pyrosequencing is so cost effective that the promise of $1,000 per bacterial genome sequence is becoming a reality. Pyrosequencing technology is a simple to use technique that can produce accurate and quantitative analysis of DNA sequences with a great speed. The deposition of massive amounts of bacterial genomic information in databanks is creating fingerprint phylogenetic analysis that will ultimately replace several technologies such as Pulsed Field Gel Electrophoresis. In this chapter, we will review (1) the use of DNA microarray using fluorescence and infrared imaging detection for identification of pathogenic bacteria, and (2) use of pyrosequencing in DNA cluster analysis to fingerprint bacterial phylogenetic trees.

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References

  1. 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

    Article  PubMed  CAS  Google Scholar 

  2. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, 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

    PubMed  CAS  Google Scholar 

  3. Bentley DR (2006) Whole-genome re-sequencing. Curr Opin Genet Dev 16:545–552

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  5. Chizhikov V, Rasooly A, Chumakov K, Levy DD (2001) Microarray analysis of microbial virulence factors. Appl Environ Microbiol 67:3258–3263

    Article  PubMed  CAS  Google Scholar 

  6. Al-Khaldi SF, Myers KM, Rasooly A, Chizhikov V (2004) Genotyping of Clostridium perfringens toxins using multiple oligonucleotide microarray hybridization. Mol Cell Probes 18:359–367

    Article  PubMed  CAS  Google Scholar 

  7. Al-Khaldi SF, Villanueva D, Chizhikov V (2004) Identification and characterization of Clostridium perfringens using single target DNA microarray chip. Int J Food Microbiol 91:289–296

    Article  PubMed  CAS  Google Scholar 

  8. Myers KM, Gaba J, Al-Khaldi SF (2006) Molecular identification of Yersinia enterocolitica isolated from pasteurized whole milk using DNA microarray chip hybridization. Mol Cell Probes 20:71–80

    Article  PubMed  CAS  Google Scholar 

  9. Al-Khaldi SF, Martin SA, Rasooly A, Evans JD (2002) DNA microarray technology used for studying foodborne pathogens and microbial habitats: minireview. J AOAC Int 85:906–910

    PubMed  CAS  Google Scholar 

  10. Al-Khaldi SF, Mossoba MM, Ismail AA, Fry FS (2004) Accelerating bacterial identification by infrared spectroscopy by employing microarray deposition of microorganisms. Foodborne Pathog Dis 1:172–177

    PubMed  CAS  Google Scholar 

  11. Ikeda M, Yamaguchi N, Tani K, Nasu M (2006) Rapid and simple detection of food poisoning bacteria by bead assay with a microfluidic chip-based system. J Microbiol Methods 67:241–247

    Article  PubMed  CAS  Google Scholar 

  12. Hammack TS, Jacobson AP, Andrews WH (2008) The effect of preenrichment and selective enrichment media on recovery of Salmonella Typhi from the tropical fruit mamey. J AOAC Int 91:83–91

    PubMed  CAS  Google Scholar 

  13. Hu H, Churey JJ, Worobo RW (2004) Heat treatments to enhance the safety of mung bean seeds. J Food Prot 67:1257–1260

    PubMed  Google Scholar 

  14. Inami GB, Lee SM, Hogue RW, Brenden RA (2001) Two processing methods for the isolation of Salmonella from naturally contaminated alfalfa seeds. J Food Prot 64:1240–1243

    PubMed  CAS  Google Scholar 

  15. Van Beneden CA, Keene WE, Strang RA, Werker DH, King AS, Mahon B, Hedberg K, Bell A, Kelly MT, Balan VK, Mac Kenzie WR, Fleming D (1999) Multinational outbreak of Salmonella enterica serotype Newport infections due to contaminated alfalfa sprouts. JAMA 281:158–162

    Article  PubMed  Google Scholar 

  16. Keramas G, Bang DD, Lund M, Madsen M, Bunkenborg H, Telleman P, Christensen CB (2004) Use of culture, PCR analysis, and DNA microarrays for detection of Campylobacter jejuni and Campylobacter coli from chicken feces. J Clin Microbiol 42:3985–3991

    Article  PubMed  CAS  Google Scholar 

  17. Heller LC, Jones M, Widen RH (2008) Comparison of DNA pyrosequencing with alternative methods for identification of mycobacteria. J Clin Microbiol 46:2092–2094

    Article  PubMed  Google Scholar 

  18. Bammler T, Beyer RP, Bhattacharya S, Boorman GA, Boyles A, Bradford BU, Bumgarner RE, Bushel PR, Chaturvedi K, Choi D, Cunningham ML, Deng S, Dressman HK, Fannin RD, Farin FM, Freedman JH, Fry RC, Harper A, Humble MC, Hurban P, Kavanagh TJ, Kaufmann WK, Kerr KF, Jing L, Lapidus JA, Lasarev MR, Li J, Li YJ, Lobenhofer EK, Lu X, Malek RL, Milton S, Nagalla SR, O’Malley JP, Palmer VS, Pattee P, Paules RS, Perou CM, Phillips K, Qin LX, Qiu Y, Quigley SD, Rodland M, Rusyn I, Samson LD, Schwartz DA, Shi Y, Shin JL, Sieber SO, Slifer S, Speer MC, Spencer PS, Sproles DI, Swenberg JA, Suk WA, Sullivan RC, Tian R, Tennant RW, Todd SA, Tucker CJ, Van Houten B, Weis BK, Xuan S, Zarbl H (2005) Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods 2:351–356

    Article  PubMed  Google Scholar 

  19. Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, Martinez-Murillo F, Morsberger L, Lee H, Petersen D, Quackenbush J, Scott A, Wilson M, Yang Y, Ye SQ, Yu W (2005) Multiple-laboratory comparison of microarray platforms. Nat Methods 2:345–350

    Article  PubMed  CAS  Google Scholar 

  20. Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J (2005) Independence and reproducibility across microarray platforms. Nat Methods 2:337–344

    Article  PubMed  CAS  Google Scholar 

  21. Courtney S, Mossoba ME, Hammack TS, Keys C, Al-Khaldi SF (2006) Using PCR amplification to increase the confidence level of Salmonella Typhimurium DNA microarray chip hybridization. Mol Cell Probes 20:163–171

    Article  PubMed  CAS  Google Scholar 

  22. Al-Khaldi SF, Mossoba MM (2004) Gene and bacterial identification using high-throughput technologies: genomics, proteomics, and phenomics. Nutrition 20:32–38

    Article  PubMed  CAS  Google Scholar 

  23. Kong H, Volokhov DV, George J, Ikonomi P, Chandler D, Anderson C, Chizhikov V (2007) Application of cell culture enrichment for improving the sensitivity of mycoplasma detection methods based on nucleic acid amplification technology (NAT). Appl Microbiol Biotechnol 77:223–232

    Article  PubMed  CAS  Google Scholar 

  24. Dufva M (ed) (2009) DNA microarrays for biomedical research. Humana Press, New York

    Google Scholar 

  25. Diamandis EP, Christopoulos TK (1996) Immunoassay. Academic, San Diego

    Google Scholar 

  26. Gibson G, Muse SV (2002) A primer of genome science, 3rd edn. Sinaur, Sunderland, MA

    Google Scholar 

  27. Call DR, Brockman FJ, Chandler DP (2001) Detecting and genotyping Escherichia coli O157:H7 using multiplexed PCR and nucleic acid microarrays. Int J Food Microbiol 67:71–80

    Article  PubMed  CAS  Google Scholar 

  28. Kneipp K, Kneipp H, Itzkan I, Dasari RR, Feld MS (1999) Ultrasensitive chemical analysis by Raman spectroscopy. Chem Rev 99:2957–2975

    Article  PubMed  CAS  Google Scholar 

  29. Thaxton CS, Georganopoulou DG, Mirkin CA (2006) Gold nanoparticle probes for the detection of nucleic acid targets. Clin Chim Acta 363:120–126

    Article  PubMed  CAS  Google Scholar 

  30. Mossoba MM, Al-Khaldi SF, Schoen B, Yakes BJ (2010) Nanoparticle probes and mid-infrared chemical imaging for DNA microarray detection. Appl Spectrosc 64(11):1191–1198

    Article  PubMed  CAS  Google Scholar 

  31. Hacker GW (1989) Silver-enhanced colloidal gold for light microscopy. In: Hayat MA (ed) Colloidal gold: principles, methods, and applications. Academic, San Diego, CA, pp 297–321

    Google Scholar 

  32. Bernardini M, Lee CH, Beheshti B, Prasad M, Albert M, Marrano P, Begley H, Shaw P, Covens A, Murphy J, Rosen B, Minkin S, Squire JA, Macgregor PF (2005) High-resolution mapping of genomic imbalance and identification of gene expression profiles associated with differential chemotherapy response in serous epithelial ovarian cancer. Neoplasia 7:603–613

    Article  PubMed  CAS  Google Scholar 

  33. Gerry NP, Witowski NE, Day J, Hammer RP, Barany G, Barany F (1999) Universal DNA microarray method for multiplex detection of low abundance point mutations. J Mol Biol 292:251–262

    Article  PubMed  CAS  Google Scholar 

  34. Budowle B, Allard MW, Wilson MR, Chakraborty R (2003) Forensics and mitochondrial DNA: applications, debates, and foundations. Annu Rev Genomics Hum Genet 4:119–141

    Article  PubMed  CAS  Google Scholar 

  35. Budowle B, Widen RH, Allard MW (2002) Characterization of heteroplasmy and hypervariable sites in HVI: critique of D’Eustachio’s interpretations. Forensic Sci Int 130:68–70

    Article  Google Scholar 

  36. Ou CY, Ciesielski CA, Myers G, Bandea CI, Luo CC, Korber BT, Mullins JI, Schochetman G, Berkelman RL, Economou AN et al (1992) Molecular epidemiology of HIV transmission in a dental practice. Science 256:1165–1171

    Article  PubMed  CAS  Google Scholar 

  37. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310–2314

    Article  PubMed  CAS  Google Scholar 

  38. Hillis DM, Mortiz C, Mable BK (1996) Molecular systematics, 2nd edn. Sinauer Associates, Sunderland, MA

    Google Scholar 

  39. Kitching J (1998) Cladistics—the theory and practice of parsimony, vol 2. Oxford University Press, New York, NY

    Google Scholar 

  40. Kitching IJ (1998) The theory and practice of parsimony, 2nd edn. Oxford University Press, NY

    Google Scholar 

  41. Kluge A (1989) A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst Zool 38:7–25

    Article  Google Scholar 

  42. Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, Plaut RD, Wolf AM, Watkins KL, Nierman WC, Hazen A, Cline R, Redmond C, Thwaite JE, White O, Salzberg SL, Thomason B, Friedlander AM, Koehler TM, Hanna PC, Kolsto AB, Fraser CM (2003) The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423:81–86

    Article  PubMed  CAS  Google Scholar 

  43. Hofstadler SA, Sannes-Lowery KA, Hannis JC (2005) Analysis of nucleic acids by FTICR MS. Mass Spectrom Rev 24:265–285

    Article  PubMed  CAS  Google Scholar 

  44. Sampath R, Hall TA, Massire C, Li F, Blyn LB, Eshoo MW, Hofstadler SA, Ecker DJ (2007) Rapid identification of emerging infectious agents using PCR and electrospray ionization mass spectrometry. Ann N Y Acad Sci 1102:109–120

    Article  PubMed  CAS  Google Scholar 

  45. Wise MG, Siragusa GR, Plumblee J, Healy M, Cray PJ, Seal BS (2009) Predicting Salmonella enterica serotypes by repetitive sequence-based PCR. J Microbiol Methods 76:18–24

    Article  PubMed  CAS  Google Scholar 

  46. Fitzgerald C, Collins M, van Duyne S, Mikoleit M, Brown T, Fields P (2007) Multiplex, bead-based suspension array for molecular determination of common Salmonella serogroups. J Clin Microbiol 45:3323–3334

    Article  PubMed  CAS  Google Scholar 

  47. Lienau EK, Strain E, Wang C, Zheng J, Ottesen AR, Keys CE, Hammack TS, Musser SM, Brown EW, Allard MW, Cao G, Meng J, Stones R (2011) Identification of a salmonellosis outbreak by means of molecular sequencing. N Engl J Med 364:981–982

    Article  PubMed  CAS  Google Scholar 

  48. Deng Y, Zhu XY, Kienlen T, Guo A (2006) Transport at the air/water interface is the reason for rings in protein microarrays. J Am Chem Soc 128:2768–2769

    Article  PubMed  CAS  Google Scholar 

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Acknowledgment

The use of trade, firm, or corporation names in this publication is for the information and convenience of the reader. Such use does not constitute an official endorsement or approval by the United States Food and Drug Administration of any product or service to the exclusion of others that may be suitable. E. Kurt Lienau is supported by a fellowship from the Oak Ridge Institute for Science Education.

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Authors and Affiliations

  1. Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA

    Sufian F. Al-Khaldi PhD, Marc M. Allard, E. Kurt Lienau & Eric D. Brown

  2. Division of Analytical Chemistry, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA

    Magdi M. Mossoba

Authors
  1. Sufian F. Al-Khaldi PhD
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  2. Magdi M. Mossoba
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  3. Marc M. Allard
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  4. E. Kurt Lienau
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  5. Eric D. Brown
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Corresponding author

Correspondence to Sufian F. Al-Khaldi PhD .

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Editors and Affiliations

  1. Physics & Life Sciences Directorate, Biosciences & Biotechnology Div., Lawrence Livermore National Laboratory, East Avenue 7000, Livermore, 94551, California, USA

    Ali Navid

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Al-Khaldi, S.F., Mossoba, M.M., Allard, M.M., Lienau, E.K., Brown, E.D. (2012). Bacterial Identification and Subtyping Using DNA Microarray and DNA Sequencing. In: Navid, A. (eds) Microbial Systems Biology. Methods in Molecular Biology, vol 881. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-827-6_4

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  • DOI: https://doi.org/10.1007/978-1-61779-827-6_4

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-826-9

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