Microarray detection of food-borne pathogens using specific probes prepared by comparative genomics

In order to design a method for the accurate detection and identification of food-borne pathogens, we used comparative genomics to select 70-mer oligonucleotide probes specific for 11 major food-borne pathogens (10 overlapping probes per pathogen) for use in microarray analysis. We analyzed the hybr...

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Bibliographic Details
Published in:Biosensors & bioelectronics 2008-10, Vol.24 (2), p.238-246
Main Authors: Kim, Hyun-Joong, Park, Si-Hong, Lee, Tae-Ho, Nahm, Baek-Hie, Kim, Young-Rok, Kim, Hae-Yeong
Format: Article
Language:English
Subjects:
Biological and medical sciences
Biosensors
Biotechnology
Chromosome Mapping - methods
Comparative genomics
Detection
DNA Probes - genetics
DNA, Bacterial - analysis
DNA, Bacterial - genetics
Food Analysis - methods
Food Contamination - analysis
Food Microbiology
Food-borne pathogens
Fundamental and applied biological sciences. Psychology
Methods. Procedures. Technologies
Oligonucleotide Array Sequence Analysis - methods
Oligonucleotide microarray
Specific probe
Various methods and equipments
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Summary:In order to design a method for the accurate detection and identification of food-borne pathogens, we used comparative genomics to select 70-mer oligonucleotide probes specific for 11 major food-borne pathogens (10 overlapping probes per pathogen) for use in microarray analysis. We analyzed the hybridization pattern of this constructed microarray with the Cy3-labeled genomic DNA of various food-borne pathogens and other bacteria. Our microarray showed a highly specific hybridization pattern with the genomic DNA of each food-borne pathogen; little unexpected cross-hybridization was observed. Microarray data were analyzed and clustered using the GenePix Pro 6.0 and GeneSpring GX 7.3.1 programs. The analyzed dendrogram revealed the discriminating power of constructed microarray. Each food-borne pathogen clustered according to its hybridization specificity and non-pathogenic species were discriminated from pathogenic species. Our method can be applied to the rapid and accurate detection and identification of food-borne pathogens in the food industry. In addition, this study demonstrates that genome sequence comparison and DNA microarray analysis have a powerful application in epidemiologic and taxonomic studies, as well as in the food safety and biodefense fields.
ISSN:0956-5663
1873-4235
DOI:10.1016/j.bios.2008.03.019