Transcriptional response to bacterial and viral pathogens in patients with acute febrile illness
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ABSTRACT:
PROVIDER: PRJNA852269 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Non-specific clinical presentation and lack of sensitive acute-phase diagnostic reagents hinder early recognitiion and manangement of systemic infections. To identify pathogen-specific features of the acute host response to infection we examined genome-wide patterns of whole blood gene expression in febrile patients with well-defined bacterial and viral infections (n=49), as well as health controls (n=12)
2022-12-01 | GSE206829 | GEO
Project description:This study aimed to use pan-viral detection microarrays to identify viruses in serum from cases of acute pediatric febrile illness in a tropical setting. Patient clinical data and serum samples were collected between 2005 and 2009 as part of an ongoing pediatric dengue virus study at the Hospital Infantil Manuel de Jesús Rivera in Managua, Nicaragua. This study focused on patients who presented with dengue-like illness but who tested negative for dengue-virus infection. We hypothesized that non-dengue viruses or previously uncharacterized viruses might be causing these illnesses. The Virochip microarray is capable of detecting known viruses and discovering novel viruses. This series includes 153 arrays corresponding to 148 cases and 5 HeLa controls. Keywords: viral detection, tropical febrile illness, dengue virus, Nicaragua, Virochip
2011-12-31 | GSE28142 | GEO
Project description:This study aimed to use pan-viral detection microarrays to identify viruses in serum from cases of acute pediatric febrile illness in a tropical setting. Patient clinical data and serum samples were collected between 2005 and 2009 as part of an ongoing pediatric dengue virus study at the Hospital Infantil Manuel de Jesús Rivera in Managua, Nicaragua. This study focused on patients who presented with dengue-like illness but who tested negative for dengue-virus infection. We hypothesized that non-dengue viruses or previously uncharacterized viruses might be causing these illnesses. The Virochip microarray is capable of detecting known viruses and discovering novel viruses. This series includes 153 arrays corresponding to 148 cases and 5 HeLa controls. Keywords: viral detection, tropical febrile illness, dengue virus, Nicaragua, Virochip From each serum sample, total nucleic acid was extracted and used to prepare a randomly-primed dsDNA library. These libraries were fluorescently labeled and hybrized to Virochip arrays.
2011-12-31 | E-GEOD-28142 | biostudies-arrayexpress
Project description:Viral infections are among the most common causes for fever without an apparent source (FWS) in young children; however, many febrile children are treated with antibiotics despite the absence of bacterial infection. Adenovirus, human herpesvirus 6 (HHV-6) and enterovirus are detected in children with FWS more often than other viral species. Virus and bacteria interact with pattern recognition receptors in circulating blood leukocytes and trigger specific host transcriptional programs that mediate immune response, and unique transcriptional signatures may be ascertained to discriminate between viral and bacterial causes for children with FWS. Microarray analyses were conducted on peripheral blood samples obtained from 51 pediatric patients with confirmed adenovirus, human herpesvirus 6 (HHV-6), enterovirus or bacterial infection. Whole blood transcriptional profiles could clearly distinguish febrile children from healthy controls, and febrile children with viral infections from afebrile children carrying the same virus. Molecular pathways regulating host immune response were the most affected in febrile children with infection. Pattern recognition programs were prominently activated in all febrile children with infection, while differential activation of transcriptional programs was observed among viral species. Interferon signaling pathway was uniquely activated in children with febrile viral infection, while a different set of pathways was uniquely activated in children with bacterial infection. Transcriptional signatures were identified and classified febrile children with viral or bacterial infection with 87% overall accuracy, an improvement from the current clinical practice of deducing from white blood cell (WBC) count status. Similar degree of accuracy was observed when we validated the signature probes on data sets from an independent study with different microarray platforms. The current study confirms the clinical utility of blood transcriptional analysis, suggests the composition of transcriptional signatures which can be used to ascertain the infectious etiology of febrile young children without an apparent source, thus limit the overuse of antibiotics on febrile children presenting with this common clinical complaint. Total RNA samples extracted from whole blood of young children were processed for hybridization onto Illumina Human-HT12 version 4 beadchips, and differential expression of the transcripts was analyzed between sick children with either viral or bacterial infection and healthy children.
2012-10-15 | E-GEOD-40396 | biostudies-arrayexpress
Project description:Viral infections are among the most common causes for fever without an apparent source (FWS) in young children; however, many febrile children are treated with antibiotics despite the absence of bacterial infection. Adenovirus, human herpesvirus 6 (HHV-6) and enterovirus are detected in children with FWS more often than other viral species. Virus and bacteria interact with pattern recognition receptors in circulating blood leukocytes and trigger specific host transcriptional programs that mediate immune response, and unique transcriptional signatures may be ascertained to discriminate between viral and bacterial causes for children with FWS. Microarray analyses were conducted on peripheral blood samples obtained from 51 pediatric patients with confirmed adenovirus, human herpesvirus 6 (HHV-6), enterovirus or bacterial infection. Whole blood transcriptional profiles could clearly distinguish febrile children from healthy controls, and febrile children with viral infections from afebrile children carrying the same virus. Molecular pathways regulating host immune response were the most affected in febrile children with infection. Pattern recognition programs were prominently activated in all febrile children with infection, while differential activation of transcriptional programs was observed among viral species. Interferon signaling pathway was uniquely activated in children with febrile viral infection, while a different set of pathways was uniquely activated in children with bacterial infection. Transcriptional signatures were identified and classified febrile children with viral or bacterial infection with 87% overall accuracy, an improvement from the current clinical practice of deducing from white blood cell (WBC) count status. Similar degree of accuracy was observed when we validated the signature probes on data sets from an independent study with different microarray platforms. The current study confirms the clinical utility of blood transcriptional analysis, suggests the composition of transcriptional signatures which can be used to ascertain the infectious etiology of febrile young children without an apparent source, thus limit the overuse of antibiotics on febrile children presenting with this common clinical complaint.
2012-10-15 | GSE40396 | GEO
Project description:Global endemic infections, such as leptospirosis, rickettsial diseases, and dengue infections present diagnostic challenges, posing a dilemma for antibiotic stewardship worldwide. The goal of this project was to identify accurate transcriptional classifiers able to discriminate between bacterial and viral illness of global pathogens.
2023-12-19 | GSE211567 | GEO
Project description:A pressing clinical challenge is identifying the etiologic basis of acute respiratory illness. Without reliable diagnostics, the uncertainty associated with this clinical entity leads to a significant, inappropriate use of antibacterials. Use of host peripheral blood gene expression data to classify individuals with bacterial infection, viral infection, or non-infection represents a complementary diagnostic approach. Patients with respiratory tract infection along with ill, non-infected controls were enrolled through the emergency department or undergraduate student health services. Whole blood was obtained to generate gene expression profiles. These profiles were then used to generate signatures of bacterial acute respiratory infection, viral acute respiratory infection, and non-infectious illness. 273 subjects were ascertained for this analysis. This included 88 patients with non-infectious illness, 115 with viral acute respiratory infection, and 70 with bacterial acute respiratory infection. Samples were obtained at the time of enrollment, which was at initial clinical presentation. Total RNA was extracted from human blood using the PAXgene Blood RNA Kit. Microarray data were generated using the GeneChip Human Genome U133A 2.0 Array. Microarrays were generated in two microarray batches with seven overlapping samples giving rise to 280 total microarray experiments.
2016-01-20 | E-GEOD-63990 | biostudies-arrayexpress
Project description:A pressing clinical challenge is identifying the etiologic basis of acute respiratory illness. Without reliable diagnostics, the uncertainty associated with this clinical entity leads to a significant, inappropriate use of antibacterials. Use of host peripheral blood gene expression data to classify individuals with bacterial infection, viral infection, or non-infection represents a complementary diagnostic approach. Patients with respiratory tract infection along with ill, non-infected controls were enrolled through the emergency department or undergraduate student health services. Whole blood was obtained to generate gene expression profiles. These profiles were then used to generate signatures of bacterial acute respiratory infection, viral acute respiratory infection, and non-infectious illness.
2016-01-20 | GSE63990 | GEO
Project description:Previously developed gene expression signatures had high predictive accuracy at distinguishing viral and bacterial infection in a South Asian cohort with ARI caused by typical and atypical pathogens.
2020-07-06 | GSE149947 | GEO
Project description:The use of microbiological cultures for diagnosing bacterial infections in young febrile infants have substantial limitations, including false positive and false negative cultures, and non-ideal turn-around times. Analysis of host genomic expression patterns (“RNA biosignatures”) in response to the presence of specific pathogens, however, may provide an alternate and potentially improved diagnostic approach. This study was designed to define bacterial and non-bacterial RNA biosignatures to distinguish these infections in young febrile infants.
2016-07-27 | GSE64456 | GEO