Development of DNA microarray for pathogen detection

2004 ◽  
Vol 9 (2) ◽  
pp. 93-99 ◽  
Author(s):  
Seung Min Yoo ◽  
Ki Chang Keum ◽  
So Young Yoo ◽  
Jun Yong Choi ◽  
Kyung Hee Chang ◽  
...  
Keyword(s):  
Dna Microarray ◽  
Pathogen Detection

scholarly journals Nucleic Acid Amplification Strategies for DNA Microarray-Based Pathogen Detection

2004 ◽  
Vol 70 (5) ◽  
pp. 3047-3054 ◽  
Author(s):  
Gary J. Vora ◽  
Carolyn E. Meador ◽  
David A. Stenger ◽  
Joanne D. Andreadis
Keyword(s):  
Nucleic Acid ◽  
Multiplex Pcr ◽  
Dna Microarray ◽  
Pathogen Detection ◽  
Pcr Amplification ◽  
Environmental Water ◽  
Nucleic Acid Amplification ◽  
Klenow Fragment ◽  
Front End ◽  
Random Amplification

ABSTRACT DNA microarray-based screening and diagnostic technologies have long promised comprehensive testing capabilities. However, the potential of these powerful tools has been limited by front-end target-specific nucleic acid amplification. Despite the sensitivity and specificity associated with PCR amplification, the inherent bias and limited throughput of this approach constrain the principal benefits of downstream microarray-based applications, especially for pathogen detection. To begin addressing alternative approaches, we investigated four front-end amplification strategies: random primed, isothermal Klenow fragment-based, φ29 DNA polymerase-based, and multiplex PCR. The utility of each amplification strategy was assessed by hybridizing amplicons to microarrays consisting of 70-mer oligonucleotide probes specific for enterohemorrhagic Escherichia coli O157:H7 and by quantitating their sensitivities for the detection of O157:H7 in laboratory and environmental samples. Although nearly identical levels of hybridization specificity were achieved for each method, multiplex PCR was at least 3 orders of magnitude more sensitive than any individual random amplification approach. However, the use of Klenow-plus-Klenow and φ29 polymerase-plus-Klenow tandem random amplification strategies provided better sensitivities than multiplex PCR. In addition, amplification biases among the five genetic loci tested were 2- to 20-fold for the random approaches, in contrast to >4 orders of magnitude for multiplex PCR. The same random amplification strategies were also able to detect all five diagnostic targets in a spiked environmental water sample that contained a 63-fold excess of contaminating DNA. The results presented here underscore the feasibility of using random amplification approaches and begin to systematically address the versatility of these approaches for unbiased pathogen detection from environmental sources.

DNA Microarray-based Detection of Bacteria in Samples Containing Antibiotics: Effect of Antibiotics on the Performance of Pathogen Detection Assays

2021 ◽  
Vol 26 (3) ◽  
pp. 447-455
Author(s):  
So Youn Shin ◽  
Dong Min Kim ◽  
Yeonggyu Jo ◽  
June Myung Kim ◽  
Seung Min Yoo
Keyword(s):  
Dna Microarray ◽  
Pathogen Detection

scholarly journals DNA microarrays for pathogen detection and characterisation

2006 ◽  
Vol 27 (2) ◽  
pp. 68
Author(s):  
Philippa Jack ◽  
David Boyle
Keyword(s):  
Dna Microarray ◽  
Clinical Microbiology ◽  
Pathogen Detection ◽  
Dna Microarrays ◽  
Pcr Amplification ◽  
Specific Primer ◽  
Pathogen Discovery ◽  
Primer Sets ◽  
Major Factors ◽  
Diagnostic Microbiology

DNA microarrays have three main potential diagnostic uses in clinical microbiology: detection of known pathogens, pathogen typing and novel pathogen discovery. Although DNA microarray platforms offer the ability to screen for a large number of agents in parallel, sensitivity is dependent on the ability to obtain adequate amounts of pathogen nucleic acids from collected samples. In general, high levels of sensitivity require a PCR amplification step using specific primer sets, subsequently reducing the overall scope of the microarray assay. At present, relatively high costs, restricted sample throughput capabilities and validation difficulties are also major factors limiting the implementation of DNA microarray assays in diagnostic microbiology laboratories.

scholarly journals Detection and Genotyping of Arcobacter and Campylobacter Isolates from Retail Chicken Samples by Use of DNA Oligonucleotide Arrays

2007 ◽  
Vol 73 (11) ◽  
pp. 3645-3655 ◽  
Author(s):  
Beatriz Quiñones ◽  
Craig T. Parker ◽  
John M. Janda ◽  
William G. Miller ◽  
Robert E. Mandrell
Keyword(s):  
Dna Microarray ◽  
Membrane Filtration ◽  
Pathogen Detection ◽  
Dna Microarrays ◽  
Pcr Amplification ◽  
Detection Sensitivity ◽  
Sensitivity Threshold ◽  
Campylobacter Coli ◽  
Oligonucleotide Arrays ◽  
High Level

ABSTRACT To explore the use of DNA microarrays for pathogen detection in food, we produced DNA oligonucleotide arrays to simultaneously determine the presence of Arcobacter and the presence of Campylobacter in retail chicken samples. Probes were selected that target housekeeping and virulence-associated genes in both Arcobacter butzleri and thermotolerant Campylobacter jejuni and Campylobacter coli. These microarrays showed a high level of probe specificity; the signal intensities detected for A. butzleri, C. coli, or C. jejuni probes were at least 10-fold higher than the background levels. Specific identification of A. butzleri, C. coli, and C. jejuni was achieved without the need for a PCR amplification step. By adapting an isolation method that employed membrane filtration and selective media, C. jejuni isolates were recovered from package liquid from whole chicken carcasses prior to enrichment. Increasing the time of enrichment resulted in the isolation of A. butzleri and increased the recovery of C. jejuni. C. jejuni isolates were further classified by using an additional subset of probes targeting the lipooligosaccharide (LOS) biosynthesis locus. Our results demonstrated that most of the C. jejuni isolates likely possess class B, C, or H LOS. Validation experiments demonstrated that the DNA microarray had a detection sensitivity threshold of approximately 10,000 C. jejuni cells. Interestingly, the use of C. jejuni sequence-specific primers to label genomic DNA improved the sensitivity of this DNA microarray for detection of C. jejuni in whole chicken carcass samples. C. jejuni was efficiently detected directly both in package liquid from whole chicken carcasses and in enrichment broths.

Inkjet Printing platforms for DNA-based pathogen detection

2018 ◽  
Vol 2018 (1) ◽  
pp. 107-112 ◽  
Author(s):  
Min Zhao ◽  
Susana Diaz Amaya ◽  
Seon-ah Jin ◽  
Li-Kai Lin ◽  
Amanda J. Deering ◽  
...  
Keyword(s):  
Inkjet Printing ◽  
Pathogen Detection
Sign in / Sign up

Export Citation Format

Share Document