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Series GSE30794 Query DataSets for GSE30794
Status Public on Jul 20, 2011
Title Design of a Diagnostic Pan-Pathogen Oligonucleotide Microarray including a sub-Array for Detection of Meningitis-Causing Bacterial Pathogens
Platform organism synthetic construct
Sample organisms Neisseria flavescens; Neisseria lactamica; Neisseria meningitidis; Haemophilus influenzae; Staphylococcus aureus; Streptococcus agalactiae; Streptococcus pneumoniae; Listeria monocytogenes; Homo sapiens
Experiment type Other
Summary Meningitis is a complex disease which can be caused by infection with either viral or bacterial pathogens. Viral meningitis is usually a sterile self-limiting disease with a good clinical prognosis, while bacterial meningitis is a potentially more serious disease with a higher mortality rate. Early diagnosis of bacterial meningitis is of paramount importance, as intervention with antimicrobial therapy increases the likelihood of a favourable clinical outcome. Routine diagnosis in many laboratories is still dependent to some degree on traditional methods e.g. culture, though molecular methods have been developed which can give a shorter time to diagnosis. However, there is not as yet a single test format that can detect all bacterial pathogens capable of causing meningitis. In addition, many tests e.g. real-time PCR have a finite limit for multiplexing and do not provide additional information such as strain or serogroup which is useful during outbreaks and for retrospective epidemiological surveillance. To this end we have developed a microarray probe set for detection of meningitis-associated bacterial pathogens including those in the N. meningitidis serogroups. Here we demonstrate utility of this array in specific detection of represented bacterial species and strains and in detection of pathogen signals in cerebrospinal fluid samples from patients with suspected bacterial meningitis. This method shows promise for development as a diagnostic tool; however, we discuss the technical issues encountered and suggest mechanisms to improve resolution of pathogen-specific signals in complex clinical samples.
Overall design We designed as part of a larger pan-pathogen microarray a sub-set of probes to meningitis-associated bacterial pathogens. We present here data confirming the pathogen-specificity of many of these probes and their potential use in clinical diagnosis through testing on a small number of patient clinical samples using human DNA and no added nucleic acid controls. These data are from single channel Cy3-labelled nucleic acids. Four technical replicates for each feature are included on the array.
Contributor(s) Kempsell KE, Vollmer SA, Shah S, Watson M, Elmore MJ, Telfer Brunton WA, Marsh P, Green S, Vipond R, Silman NJ
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Submission date Jul 19, 2011
Last update date Mar 23, 2012
Contact name Karen Elizabeth Kempsell
Phone ++44(0)1980 619816
Organization name UK Health Security Agency
Department Science Group
Lab Diagnostic Technologies
Street address Porton Down
City Salisbury
State/province Wiltshire
ZIP/Postal code SP4 0JG
Country United Kingdom
Platforms (1)
GPL13948 HPA Pan_Pathogen Microarray 9248- V5.1
Samples (68)
GSM764007 Bacterial nucleic acid sample BMA_HPA_001
GSM764008 Bacterial nucleic acid sample BMA_HPA_002
GSM764009 Bacterial nucleic acid sample BMA_HPA_003
BioProject PRJNA144293

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE30794_RAW.tar 52.0 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
Processed data provided as supplementary file

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