Bacterial identification and subtyping using DNA microarray and DNA sequencing

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

Research output: Chapter in Book/Report/Conference proceedingChapter

7 Scopus citations

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.

Original languageEnglish (US)
Title of host publicationMicrobial Systems Biology
Subtitle of host publicationMethods and Protocols
PublisherHumana Press Inc.
Pages73-95
Number of pages23
ISBN (Print)9781617798269
DOIs
StatePublished - Jan 1 2012

Publication series

NameMethods in Molecular Biology
Volume881
ISSN (Print)1064-3745

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

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  • Cite this

    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 Microbial Systems Biology: Methods and Protocols (pp. 73-95). (Methods in Molecular Biology; Vol. 881). Humana Press Inc.. https://doi.org/10.1007/978-1-61779-827-6_4