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Uropathogenic Escherichia coli: An Ideal Resource for DNA Microarray Probe Designing

  • Payam Behzadi
  • Elham Behzadi
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10209)

Abstract

Uropathogenic Escherichia coli (UPEC) is the most important bacterial agent causing urinary tract infections (UTIs) in patients around the world. The UTIs rank second among different types of infectious diseases. So, there is an urgent need to have a rapid and accurate diagnostic method for detecting UTIs. DNA microarray is an advanced pan-genomic technique which can be used as a rapid and accurate diagnostic method with high specificity and sensitivity. Designing a collection of DNA microarray probes enables us to have a sharp methodology for detection and identification of UPEC pathotypes. For this reason, the authors of the present review literature have tried to represent a vast range of availabilities regarding UPEC recognition by DNA microarray probe designing.

UPEC encompasses a wide range of virulence genes which are contributed to UTIs. This characteristic makes UPEC an ideal resource for DNA microarray probe designing to have a reliable UTIs diagnostic method.

Besides, UPEC possesses different pathogenic strains which are distributed worldwide. And individual strain has its particular conserved sequences within the virulence genes. In other word, DNA microarray probes can be designed for specific UPEC strains within different geographical regions.

In conclusion, UPEC is a living accessible genomic treasure which can be used for designing a diversity of DNA microarray probes with a high specificity and sensitivity.

Keywords

Microarray Urinary tract infection Uropathogenic Escherichia coli Probe Pangenome 

Notes

Acknowledgements

We are obliged to Shahr-e-Qods Branch, Islamic Azad University as the financial supporter of this paper for presenting in IWBBIO 2017, Granada, Spain.

We also have special thanks to Profs. Ignacio Rojas and Francisco Ortuño for their kind helps and collaborations.

References

  1. 1.
    Behzadi, P., Behzadi, E.: The microbial agents of urinary tract infections at central laboratory of Dr. Shariati Hospital, Tehran, Iran. Turkiye Klinikleri J. Med. Sci. 28(4), 445–449 (2008)Google Scholar
  2. 2.
    Behzadi, P., Behzadi, E., Ranjbar, R.: Urinary tract infections and Candida albicans. Cent. Eur. J. Urol. 68(1), 96–101 (2015)Google Scholar
  3. 3.
    Jahandeh, N., et al.: Uropathogenic Escherichia coli virulence genes: invaluable approaches for designing DNA microarray probes. Cent. Eur. J. Urol. 68, 452–458 (2014)Google Scholar
  4. 4.
    Subashchandrabose, S., Mobley, H.L.T.: Virulence and fitness determinants of Uropathogenic Escherichia coli. Microbiology Spectr. 3(4) (2015)Google Scholar
  5. 5.
    Matuszewski, M.A., et al.: Uroplakins and their potential applications in urology. Cent. Eur. J. Urol. 69(3), 252–257 (2016)MathSciNetGoogle Scholar
  6. 6.
    Behzadi, E., Behzadi, P.: The role of toll-like receptors (TLRs) in urinary tract infections (UTIs). Cent. Eur. J. Urol. 69, 404–410 (2016)Google Scholar
  7. 7.
    Torres, A.G.: Escherichia coli in the Americas. Springer, Cham (2016)CrossRefGoogle Scholar
  8. 8.
    Behzadi, P., Behzadi, E., Ranjbar, R.: IL-12 family cytokines: general characteristics, pathogenic microorganisms, receptors, and signalling pathways. Acta Microbiol. Immunol. Hung. 63(1), 1–25 (2016)CrossRefGoogle Scholar
  9. 9.
    Snipen, L.G., Ussery, D.W.: A domain sequence approach to pangenomics: applications to Escherichia coli. F1000Research 1, 19 (2013)Google Scholar
  10. 10.
    Mira, A., et al.: The bacterial pan-genome: a new paradigm in microbiology. Int. Microbiol. 13(2), 45–57 (2010)Google Scholar
  11. 11.
    Sharma, A.: Can “Pan-Genomics” demystify the designation of “Bacterial Species”. SM J. Bioinform. Proteomics 1(1), 1001 (2016)Google Scholar
  12. 12.
    Behzadi, P., Behzadi, E., Ranjbar, R.: Basic Modern Molecular Biology, 1st edn. Persian Science & Research Publisher, Tehran (2014)Google Scholar
  13. 13.
    Behzadi, P., Behzadi, E.: Environmental Microbiology, 1st edn. Niktab Publisher, Tehran (2007)Google Scholar
  14. 14.
    Mira, A., Klasson, L., Andersson, S.G.: Microbial genome evolution: sources of variability. Curr. Opin. Microbiol. 5(5), 506–512 (2002)CrossRefGoogle Scholar
  15. 15.
    Genome/Escherichia coli (2017). https://www.ncbi.nlm.nih.gov/genome/?term=Escherichia+coli. Accessed 10 Feb 2017
  16. 16.
    Gene/Escherichia coli: National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, USA (2017)Google Scholar
  17. 17.
    Hu, P., et al.: Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7(4), e1000096 (2009)CrossRefGoogle Scholar
  18. 18.
    Cho, B.-K., et al.: The transcription unit architecture of the Escherichia coli genome. Nat. Biotechnol. 27(11), 1043–1049 (2009)CrossRefGoogle Scholar
  19. 19.
    Behzadi, P., et al.: Microarray long oligo probe designing for Escherichia coli: an in-silico DNA marker extraction. Cent. Eur. J. Urol. 69, 105–111 (2016)CrossRefGoogle Scholar
  20. 20.
    Behzadi, P., Behzadi, E., Ranjbar, R.: Microarray probe set: biology, bioinformatics and biophysics. Alban. Med. J. 2, 78–83 (2015)Google Scholar
  21. 21.
    Behzadi, P., Behzadi, E., Ranjbar, R.: Microarray data analysis. Alban. Med. J. 4, 84–90 (2014)Google Scholar
  22. 22.
    Ranjbar, R., Behzadi, P., Mammina, C.: Respiratory Tularemia: Francisella tularensis and microarray probe designing. Open Microbiol. J. 10, 176–182 (2016)CrossRefGoogle Scholar
  23. 23.
    Behzadi, P., Ranjbar, R., Alavian, S.M.: Nucleic acid-based approaches for detection of viral hepatitis. Jundishapur J. Microbiol. 8, e17449 (2015)CrossRefGoogle Scholar
  24. 24.
    Behzadi, P., Ranjbar, R.: Microarray long oligo probe designing for Bacteria: an in silico pan-genomic research. Alban. Med. J. 2, 5–11 (2016)Google Scholar
  25. 25.
    Lukjancenko, O., Wassenaar, T.M., Ussery, D.W.: Comparison of 61 sequenced Escherichia coli genomes. Microb. Ecol. 60(4), 708–720 (2010)CrossRefGoogle Scholar
  26. 26.
    Mao, B.-H., et al.: Identification of Escherichia coli genes associated with urinary tract infections. J. Clin. Microbiol. JCM 50(2), 449–456 (2011)CrossRefGoogle Scholar
  27. 27.
    MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, CAMS&PUMC, Beijing, China: Virulence factors of pathogenic bacteria, 28 October 2016. http://www.mgc.ac.cn/cgi-bin/VFs/compvfs.cgi?Genus=Escherichia. Accessed 12 Feb 2017
  28. 28.
    Baby, S., Karnaker, V.K., Geetha, R.: Adhesins of Uropathogenic Escherichia coli (UPEC). Int. J. Med. Microbiol. Trop. Dis. 2(1), 10–18 (2016)Google Scholar
  29. 29.
    Zalewska, B., et al.: A surface-exposed DraD protein of Uropathogenic Escherichia coli bearing Dr fimbriae may be expressed and secreted independently from DraC usher and DraE adhesin. Microbiology 151(7), 2477–2486 (2005)CrossRefGoogle Scholar
  30. 30.
    Cordeiro, M.A., et al.: Curli fimbria: an Escherichia coli adhesin associated with human cystitis. Braz. J. Microbiol. 47(2), 414–416 (2016)CrossRefGoogle Scholar
  31. 31.
    Kwak, M.-J., et al.: Genome sequence of Escherichia coli NCCP15653, a group D strain isolated from a diarrhea patient. Gut Pathog. 8(1), 7 (2016)CrossRefMathSciNetGoogle Scholar
  32. 32.
    Wurpel, D.J., et al.: Comparative proteomics of Uropathogenic Escherichia coli during growth in human urine identify UCA-like (UCL) fimbriae as an adherence factor involved in biofilm formation and binding to uroepithelial cells. J. Proteomics 131, 177–189 (2016)CrossRefGoogle Scholar
  33. 33.
    Archer, C.T., et al.: The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli. BMC Genom. 12(1), 9 (2011)CrossRefGoogle Scholar
  34. 34.
    Roos, V., Klemm, P.: Global gene expression profiling of the asymptomatic bacteriuria Escherichia coli strain 83972 in the human urinary tract. Infect. Immun. 74(6), 3565–3575 (2006)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  1. 1.Department of Microbiology, College of Basic SciencesShahr-e-Qods Branch, Islamic Azad UniversityTehranIran

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