scholarly journals A model of base-call resolution on broad-spectrum pathogen detection resequencing DNA microarrays

2008 ◽  
Vol 36 (10) ◽  
pp. 3194-3201 ◽  
Author(s):  
A. P. Malanoski ◽  
B. Lin ◽  
D. A. Stenger
Keyword(s):  
Broad Spectrum ◽  
Pathogen Detection ◽  
Dna Microarrays ◽  
Base Call

Apds, a Network-Ready, Broad Spectrum, Environmental Pathogen Detection System

2006 ◽  
pp. 67-75
Author(s):  
F. P. Milanovich ◽  
J. Dzenitis ◽  
B. J. Hindson ◽  
A. J. Makarewicz ◽  
M. T. McBride ◽  
...  
Keyword(s):  
Broad Spectrum ◽  
Pathogen Detection ◽  
Detection System

Functionalization of poly(dimethylsiloxane) by chemisorption of copolymers: DNA microarrays for pathogen detection

2008 ◽  
Vol 132 (1) ◽  
pp. 258-264 ◽  
Author(s):  
Marina Cretich ◽  
Valentina Sedini ◽  
Francesco Damin ◽  
Gabriele Di Carlo ◽  
Claudio Oldani ◽  
...  
Keyword(s):  
Pathogen Detection ◽  
Dna Microarrays

DNA Microarrays for Pathogen Detection

2015 ◽  
pp. 113-220 ◽  
Author(s):  
Holger Schulze ◽  
Maya Rubtsova ◽  
Till T. Bachmann
Keyword(s):  
Pathogen Detection ◽  
Dna Microarrays

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 Large scale multiplex PCR improves pathogen detection by DNA microarrays

2009 ◽  
Vol 9 (1) ◽  
pp. 1 ◽  
Author(s):  
Maria Palka-Santini ◽  
Berit E Cleven ◽  
Ludwig Eichinger ◽  
Martin Krönke ◽  
Oleg Krut
Keyword(s):  
Multiplex Pcr ◽  
Large Scale ◽  
Pathogen Detection ◽  
Dna Microarrays

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.

scholarly journals Application of Broad-Spectrum Resequencing Microarray for Genotyping Rhabdoviruses

2010 ◽  
Vol 84 (18) ◽  
pp. 9557-9574 ◽  
Author(s):  
Laurent Dacheux ◽  
Nicolas Berthet ◽  
Gabriel Dissard ◽  
Edward C. Holmes ◽  
Olivier Delmas ◽  
...  
Keyword(s):  
Broad Spectrum ◽  
Pathogen Detection ◽  
Consensus Sequence ◽  
Sequence Information ◽  
Accurate Identification ◽  
Diagnostic Assays ◽  
Detection And Identification ◽  
The Family ◽  
Nucleotide Divergence ◽  
Multiple Pathogen

ABSTRACT The rapid and accurate identification of pathogens is critical in the control of infectious disease. To this end, we analyzed the capacity for viral detection and identification of a newly described high-density resequencing microarray (RMA), termed PathogenID, which was designed for multiple pathogen detection using database similarity searching. We focused on one of the largest and most diverse viral families described to date, the family Rhabdoviridae. We demonstrate that this approach has the potential to identify both known and related viruses for which precise sequence information is unavailable. In particular, we demonstrate that a strategy based on consensus sequence determination for analysis of RMA output data enabled successful detection of viruses exhibiting up to 26% nucleotide divergence with the closest sequence tiled on the array. Using clinical specimens obtained from rabid patients and animals, this method also shows a high species level concordance with standard reference assays, indicating that it is amenable for the development of diagnostic assays. Finally, 12 animal rhabdoviruses which were currently unclassified, unassigned, or assigned as tentative species within the family Rhabdoviridae were successfully detected. These new data allowed an unprecedented phylogenetic analysis of 106 rhabdoviruses and further suggest that the principles and methodology developed here may be used for the broad-spectrum surveillance and the broader-scale investigation of biodiversity in the viral world.

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