Advertisement

Design of an Enterobacteriaceae Pan-Genome Microarray Chip

  • Oksana Lukjancenko
  • David W. Ussery
Part of the Communications in Computer and Information Science book series (CCIS, volume 115)

Abstract

Microarrays are a common method for evaluating genomic content of bacterial species and comparing unsequenced bacterial genomes. This technology allows for quick scans of characteristic genes and chromosomal regions, and to search for indications of horizontal transfer. A high-density microarray chip has been designed, using 116 Enterobacteriaceae genome sequences, taking into account the enteric pan-genome. Probes for the microarray were checked in silico and performance of the chip, based on experimental strains from four different genera, demonstrate a relatively high ability to distinguish those strains on genus, species, and pathotype/serovar levels. Additionally, the microarray performed well when investigating which genes were found in a given strain of interest. The Enterobacteriaceae pan-genome microarray, based on 116 genomes, provides a valuable tool for determination of the genetic makeup of unknown strains within this bacterial family and can introduce insights into phylogenetic relationships.

Keywords

Enterobacteriaceae Pan-genome DNA microarray analysis gene Escherichia coli 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Hall, B.G., Ehrlich, G.D., Hu, F.Z.: Pan-genome analysis provides much higher strain typing resolution than multi-locus sequence typing. Microbiology 156, 1060–1068 (2010)CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Sørensen, T.I., Nielsen, G.G., Andersen, P.K., Teasdale, T.W.: Genetic and environmental influences on premature death in adult adoptees. N. Engl. J. Med. 318, 727–732 (1988)CrossRefPubMedGoogle Scholar
  3. 3.
    Helms, M., Vastrup, P., Gerner-Smidt, P., Mølbak, K.: Short and long term mortality associated with foodborne bacterial gastrointestinal infections: registry based study. BMJ 326, 357 (2003)CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Ternhag, A., Törner, A., Svensson, A., Ekdahl, K., Giesecke, J.: Short- and long-term effects of bacterial gastrointestinal infections. Emerging Infect. Dis. 14, 143–148 (2008)CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Mead, P.S., Slutsker, L., Dietz, V., McCaig, L.F., Bresee, J.S., Shapiro, C., Griffin, P.M., Tauxe, R.V.: Food-related illness and death in the United States. Emerging Infect. Dis. 5, 607–625 (1999)CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Litrup, E., Torpdahl, M., Malorny, B., Huehn, S., Helms, M., Christensen, H., Nielsen, E.M.: DNA microarray analysis of Salmonella serotype Typhimurium strains causing different symptoms of disease. BMC Microbiol. 10, 96 (2010)CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Laupland, K.B., Schønheyder, H.C., Kennedy, K.J., Lyytikäinen, O., Valiquette, L., Galbraith, J., Collignon, P.: Salmonella enterica bacteraemia: a multi-national population-based cohort study. BMC Infect. Dis. 10, 95 (2010)CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Cheng, S., Hu, Y., Zhang, M., Sun, L.: Analysis of the vaccine potential of a natural avirulent Edwardsiella tarda isolate. Vaccine 28, 2716–2721 (2010)CrossRefPubMedGoogle Scholar
  9. 9.
    Lindberg, A.M., Ljungh, A., Ahrné, S., Löfdahl, S., Molin, G.: Enterobacteriaceae found in high numbers in fish, minced meat and pasteurised milk or cream and the presence of toxin encoding genes. Int. J. Food Microbiol. 39, 11–17 (1998)CrossRefPubMedGoogle Scholar
  10. 10.
    Musgrove, M.T., Northcutt, J.K., Jones, D.R., Cox, N.A., Harrison, M.A.: Enterobacteriaceae and related organisms isolated from shell eggs collected during commercial processing. Poult. Sci. 87, 1211–1218 (2008)CrossRefPubMedGoogle Scholar
  11. 11.
    Stiles, M.E., Ng, L.K.: Enterobacteriaceae associated with meats and meat handling. Appl. Environ. Microbiol. 41, 867–872 (1981)PubMedPubMedCentralGoogle Scholar
  12. 12.
    Wright, C., Kominos, S.D., Yee, R.B.: Enterobacteriaceae and Pseudomonas aeruginosa recovered from vegetable salads. Appl. Environ. Microbiol. 31, 453–454 (1976)PubMedPubMedCentralGoogle Scholar
  13. 13.
    Cossart, P., Sansonetti, P.J.: Bacterial invasion: the paradigms of enteroinvasive pathogens. Science 304, 242–248 (2004)CrossRefPubMedGoogle Scholar
  14. 14.
    Hornef, M.W., Wick, M.J., Rhen, M., Normark, S.: Bacterial strategies for overcoming host innate and adaptive immune responses. Nat. Immunol. 3, 1033–1040 (2002)CrossRefPubMedGoogle Scholar
  15. 15.
    Olsson, C., Ahrné, S., Pettersson, B., Molin, G.: DNA based classification of food associated Enterobacteriaceae previously identified by biology microplates. Syst. Appl. Microbiol. 27, 219–228 (2004)CrossRefPubMedGoogle Scholar
  16. 16.
    Glasner, J.D., Marquez-Villavicencio, M., Kim, H., Jahn, C.E., Ma, B., Biehl, B.S., Rissman, A.I., Mole, B., Yi, X., Yang, C., Dangl, J.L., Grant, S.R., Perna, N.T., Charkowski, A.O.: Niche-specificity and the variable fraction of the Pectobacterium pan-genome. Mol. Plant Microbe Interact 21, 1549–1560 (2008)CrossRefPubMedGoogle Scholar
  17. 17.
    Tettelin, H., et al.: Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial ”pan-genome”. Proc. Natl. Acad. Sci. U.S.A. 102, 13950–13955 (2005)CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Lefébure, T., Stanhope, M.J.: Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol. 8, 71 (2007)CrossRefGoogle Scholar
  19. 19.
    Phillippy, A.M., Deng, X., Zhang, W., Salzberg, S.L.: Efficient oligonucleotide probe selection for pan-genomic tiling arrays. BMC Bioinformatics 10, 293 (2009)CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Pinkel, D., Segraves, R., Sudar, D., Clark, S., Poole, I., Kowbel, D., Collins, C., Kuo, W.L., Chen, C., Zhai, Y., Dairkee, S.H., Ljung, B.M., Gray, J.W., Albertson, D.G.: High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 20, 207–211 (1998)CrossRefPubMedGoogle Scholar
  21. 21.
    Wang, D.G., Fan, J.B., Siao, C.J., Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N., Winchester, E., Spencer, J., Kruglyak, L., Stein, L., Hsie, L., Topaloglou, T., Hubbell, E., Robinson, E., Mittmann, M., Morris, M.S., Shen, N., Kilburn, D., Rioux, J., Nusbaum, C., Rozen, S., Hudson, T.J., Lipshutz, R., Chee, M., Lander, E.S.: Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280, 1077–1082 (1998)CrossRefPubMedGoogle Scholar
  22. 22.
    Khodursky, A.B., Peter, B.J., Cozzarelli, N.R., Botstein, D., Brown, P.O., Yanofsky, C.: DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 97, 12170–12175 (2000)CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Wei, Y., Lee, J.M., Richmond, C., Blattner, F.R., Rafalski, J.A., LaRossa, R.A.: High-density microarray-mediated gene expression profiling of Escherichia coli. J. Bacteriol. 183, 545–556 (2001)CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Jacobsen, L., Durso, L., Conway, T., Nickerson, K.W.: Escherichia coli O157:H7 and other E. coli strains share physiological properties associated with intestinal colonization. Appl. Environ. Microbiol. 75, 4633–4635 (2009)CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Willenbrock, H., Fridlyand, J.: A comparison study: applying segmentation to array cgh data for downstream analyses. Bioinformatics 21, 4084–4091 (2005)CrossRefPubMedGoogle Scholar
  26. 26.
    Willenbrock, H., Petersen, A., Sekse, C., Kiil, K., Wasteson, Y., Ussery, D.W.: Design of a seven-genome Escherichia coli microarray for comparative genomic profiling. J. Bacteriol. 188, 7713–7721 (2006)CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Snipen, L., Almøy, T., Ussery, D.W.: Microbial comparative pan-genomics using binomial mixture models. BMC Genomics 10, 385 (2009)CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and psi-BLAST: a new generation of protein database search programs. Nucleic. Acids. Res. 25, 3389–3402 (1997)CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Hyatt, D., Chen, G., Locascio, P.F., Land, M.L., Larimer, F.W., Hauser, L.J.: Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010)CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Wernersson, R., Nielsen, H.B.: OligoWiz 2.0–integrating sequence feature annotation into the design of microarray probes. Nucleic Acids Res. 33, W611–W615 (2005)Google Scholar
  31. 31.
    Wernersson, R., Juncker, A.S., Nielsen, H.B.: Probe selection for DNA microarrays using OligoWiz. Nat. Protoc. 2, 2677–2691 (2007)CrossRefPubMedGoogle Scholar
  32. 32.
    Vejborg, R.M., Bernbom, N., Gram, L., Klemm, P.: Anti-adhesive properties of fish tropomyosins. J. Appl. Microbiol. 105, 141–150 (2008)CrossRefPubMedGoogle Scholar
  33. 33.
  34. 34.
    Gentleman, R.C., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., Hornik, K., Hothorn, T., Huber, W., Iacus, S., Irizarry, R., Leisch, F., Li, C., Maechler, M., Rossini, A.J., Sawitzki, G., Smith, C., Smyth, G., Tierney, L., Yang, J.Y.H., Zhang, J.: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004)CrossRefGoogle Scholar
  35. 35.
    Do, J.H., Choi, D.: Normalization of microarray data: single-labeled and dual-labeled arrays. Mol. Cells 22, 254–261 (2006)PubMedGoogle Scholar
  36. 36.
    Willenbrock, H., Hallin, P.F., Wassenaar, T.M., Ussery, D.W.: Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray. Genome Biol. 8, 267 (2007)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Oksana Lukjancenko
    • 1
  • David W. Ussery
    • 1
  1. 1.Center for Biological Sequence Analysis, Department of Systems BiologyThe Technical University of DenmarkKongens LyngbyDenmark

Personalised recommendations