IDENTIFICATION OF NEW TARGET SEQUENCES FOR PCR DETECTION OF VIBRIO PARAHAEMOLYTICUS BY GENOME COMPARISON
Article first published online: 2 MAR 2009
© 2009, The Author(s). Journal compilation © 2009, Wiley Periodicals, Inc.
Journal of Rapid Methods & Automation in Microbiology
Volume 17, Issue 1, pages 67–79, March 2009
How to Cite
ZHU, D.-S., ZHOU, M., FAN, Y.-L. and SHI, X.-M. (2009), IDENTIFICATION OF NEW TARGET SEQUENCES FOR PCR DETECTION OF VIBRIO PARAHAEMOLYTICUS BY GENOME COMPARISON. Journal of Rapid Methods & Automation in Microbiology, 17: 67–79. doi: 10.1111/j.1745-4581.2009.00158.x
- Issue published online: 2 MAR 2009
- Article first published online: 2 MAR 2009
- Accepted for Publication May 2, 2008
A genome comparison method was used to identify specific target sequences for the polymerase chain reaction (PCR) detection of Vibrio parahaemolyticus, and the CDS value of this bacterium was compared with that of 139 other bacterial genomes. It was found that 20 CDS of V. parahaemolyticus were relatively specific according to their E value in BLAST (a new tool for comparing protein and nucleotide sequences), and four of them were selected for the design of PCR primers. There were positive amplification products of these four pairs of primers from nine V. parahaemolyticus strains, whereas there were no amplification products from nine other Vibrionaceae strains and four non-Vibrionaceae strains. An evaluation of detection sensitivities revealed that these four pairs of primers can be used in a PCR assay for the detection of V. parahaemolyticus.
An automatic BLAST method was developed in this study, by which species-specific sequences can be screened out rapidly. In this way, new and specific genes of Vibrio parahaemolyticus were identified to be used as target sequences for PCR detection. In terms of acceptable specificity and sensitivity, the four pairs of primers were selected by screening, which can be applied in PCR assays and other molecular methods. These kinds of methods might become commercial detection products in the new future. In addition, this method for searching specific DNA sequences can also be used for the mining specific sequences in other genus and species, such as Salmonella, Staphylococcus, etc.