Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA144045 | ENA |
REPOSITORIES: ENA
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Project description:Analysis of transcriptional profiles in whole blood from patients with Staphylococcus aureus infection. The hypothesis tested is that transcriptional profile heterogeneity will reflect patient clinical heterogeneity.
2012-04-04 | GSE30119 | GEO
Project description:Methicillin-resistant Staphylococcus aureus (MRSA) infections result in more than 200,000 hospitalizations and 10,000 deaths in the United States each year and remain an important medical challenge. To better understand the transcriptome of Staphylococcus aureus USA300 NRS384, a community-acquired MRSA strain, we have conducted an RNA-Seq experiment on WT samples.
2017-11-15 | GSE102279 | GEO
Project description:Staphylococcus aureus can cause serious skin, respiratory, and other life-threatening invasive infections in humans, and methicillin-resistant S. aureus (MRSA) strains have been acquiring increasing antibiotic resistance. While MRSA was once mainly considered a hospital-acquired infection, the emergence of new strains, some of which are pandemic, has resulted in community-acquired MRSA infections that often present as serious skin infections in otherwise healthy individuals. Accordingly, defining the mechanisms that govern the activation and regulation of the immune response to MRSA is clinically important and could lead to the discovery of much needed rational targets for therapeutic intervention. Because the cytokine thymic stromal lymphopoetin (TSLP) is highly expressed by keratinocytes of the skin3, we investigated its role in host-defense against MRSA. Here we demonstrate that TSLP acts on neutrophils to increase their killing of MRSA. In particular, we show that both mouse and human neutrophils express functional TSLP receptors. Strikingly, TSLP enhances mouse neutrophil killing of MRSA in both an in vitro whole blood killing assay and an in vivo skin infection model. Similarly, TSLP acts directly on purified human blood neutrophils to reduce MRSA burden. Unexpectedly, we demonstrate that TSLP mediates these effects both in vivo and in vitro by engaging the complement C5 system. Thus, TSLP increases MRSA killing in a neutrophil- and complement-dependent manner, revealing a key connection between TSLP and the innate complement system, with potentially important therapeutic implications for control of MRSA infection.
2016-11-18 | GSE73313 | GEO
Project description:Staphylococcus aureus is a major pathogen of healthcare settings with a high rate of morbidity and mortality. S. aureus has also emerged as a serious threat in healthy individuals in the community. Increasingly, antibiotic resistant S. aureus strains, particularly methicillin resistant S. aureus (MRSA), are causing these community-acquired infections (CA-MRSA). Because of the rising incidence of antibiotic resistance, including resistance to “last resort” antibiotics, development of prophylactic vaccines for S. aureus is considered a high priority. A complete, accurate characterization of the transcriptome of the host during different types of infection would expedite S. aureus vaccine development by identifying antigens that would be optimal vaccine targets. RNA-seq (deep-sequencing of cDNA) provides an unbiased method to comprehensively and systematically define the transcriptome (the complete set of transcribed regions in a genome) of an organism in a manner that is significantly more sensitive than microarray hybridization approaches. We propose a comprehensive characterization of the host transcriptome in two different murine models of infection (systemic infection and skin and soft tissue infection (SSTI)). We believe that this research will provide insight into potential vaccine targets that are expressed at high levels in both types of infection. We also wish to determine what mouse genes are up- or down-regulated during the course of these infections in order to better characterize the host-pathogen interaction. This description of the in vivo transcriptome will give novel insight into how the host senses and responds to infection with S. aureus in different infection types, and how the host tissue responds to bacterial invasion.
2014-07-11 | GSE56227 | GEO
Project description:Staphylococcus aureus is the most common cause of hospital-acquired infection. In healthy hosts outside of the health care setting, S.aureus is a frequent colonizer of the human nose but rarely causes severe invasive infection such as bacteremia, endocarditis, or osteomyelitis. To identify genes associated with community-acquired invasive isolates, regions of genomic variability, and the S.aureus population structure, we compared 61 community-acquired invasive isolates of S.aureus and 100 nasal carriage isolates from healthy donors using a microarray spotted with PCR products representing every gene from the seven S.aureus sequencing projects. The core genes common to all strains were identified, and 10 dominant lineages of S.aureus were clearly discriminated. Each lineage carried a unique combination of hundreds of core variable (CV) genes scattered throughout the chromosome, suggesting a common ancestor but early evolutionary divergence. Many CV genes are regulators of virulence genes or known or predicted to be expressed on the bacterial surface and to interact with the host during nasal colonization and infection. Within each lineage, isolates showed substantial variation in the carriage of mobile genetic elements and their associated virulence and resistance genes, indicating frequent horizontal transfer. However, we were unable to identify any association between lineage or gene and invasive isolates. We suggest that the S.aureus gene combinations necessary for invasive disease may also be necessary for nasal colonization and that community-acquired invasive disease is strongly dependent on host factors. Data is also available from http://bugs.sgul.ac.uk/E-BUGS-33
2007-01-30 | E-BUGS-33 | biostudies-arrayexpress
Project description:Methicillin resistant Staphylococcus aureus (MRSA) is an opportunistic pathogen chief amongst bloodstream infecting pathogens. MRSA produces an array of human specific virulence factors that may contribute to immune suppression. Here, we defined the response of primary human phagocytes to infection with MRSA using RNA-Seq. We found that the overall transcriptional response to MRSA was weak both in the number of genes and the magnitude of response. Using an ex vivo bacteremia model with fresh human blood, we found that infection with live MRSA resulted in the down-regulation of genes related to innate immune response, and cytokine and chemokine signaling. This muted transcriptional response was conserved across diverse S. aureus clones but absent in heat-killed MRSA or blood infected with live Staphylococcus epidermidis. Importantly, the muted signature was also present in patients with S. aureus bacteremia. We next identified the master regulator SaeRS and the SaeRS-regulated pore-forming toxins as key mediators of transcriptional suppression. The impaired chemokine and cytokine responses were reflected by circulating protein levels in the plasma. MRSA elicits a soluble milieu that is restrictive in the recruitment of human neutrophils compared to strains lacking saeRS. Thus, MRSA blunts the inflammatory response resulting in impaired neutrophil recruitment, which could promote the survival of S. aureus during invasive infection.
2022-07-20 | GSE193219 | GEO
Project description:Staphylococcus aureus is a Gram-positive human pathogen causing a variety of human diseases in both hospital and community settings. This bacterium is so closely associated with prophages that it is rare to find S. aureus isolates without prophages. Two phages are known to be important for staphylococcal virulence: the beta-hemolysin (hlb) converting phage and the Panton-Valentine Leukocidin (PVL) converting phage. The hlb-converting phage is found in more than 90% of clinical isolates of S. aureus. This phage produces exotoxins and immune modulatory molecules, which inhibit human innate immune responses. The PVL-converting phage produces the two-component exotoxin PVL, which can kill human leucocytes. This phage is wide-spread among community-associated methicillin resistant S. aureus (CA-MRSA). It also shows strong association with soft tissue infections and necrotizing pneumonia. Several lines of evidence suggest that staphylococcal prophages increase bacterial virulence not only by providing virulence factors but also by altering bacterial gene expression: 1) Transposon insertion into prophage regulatory genes, but not into the genes of virulence factors, reduced S. aureus killing of Caenorhabditis elegans.; 2) Although the toxins and immune modulatory molecules encoded by the hlb- converting phages do not function in the murine system, deletion of ϕNM3, the hlb-converting phage in S. aureus Newman, reduced staphylococcal virulence in the murine abscess formation model. 3) In a preliminary microarray experiment, prophages in S. aureus Newman altered the expression of more than 300 genes. In this research proposal, using microarray and high-throughput quantitative RT-PCR (qRT-PCR) technologies, we will identify the effects of the two important staphylococcal phages on the gene expression of S. aureus in both in vitro and in vivo conditions. This project is intended to be completed within one year. All the data – microarray, qRT-PCR and all the primer sequences- will be made available to public 6 month after completion. Data from this project will help us to understand the role of prophages in the S. aureus pathogenesis and can lead to development of a strategy to interfere with the pathogenesis process. Following strains were grown in TSA broth: Staphylococcus aureus USA300 (reference) Staphylococcus aureus USA300 with deletion of ϕSa2usa (Query) Staphylococcus aureus USA300 with deletion of ϕSa3usa (Query) Staphylococcus aureus USA300 Prophage-free mutant (Query) Staphylococcus aureus USA300 Prophage-free mutant lysogenized with ϕSa2mw (Query) Staphylococcus aureus USA300 Prophage-free mutant lysogenized with ϕSa3usa (Query) strain: Staphylococcus aureus USA300 Prophage-free mutant lysogenized with both ϕSa2mw and ϕSa3usa (Query) RNA samples were harvested at early log, midlog and stationary phase.Samples were hybridized on aminosilane coated slides with 70-mer oligos.
2011-02-28 | E-GEOD-26623 | biostudies-arrayexpress
Project description:Sepsis is a clinical syndrome that can be caused by bacteria or fungi. Early knowledge on the nature of the causative agent is a prerequisite for targeted anti-microbial therapy. Besides currently used detection methods like blood culture and PCR-based assays, the analysis of the transcriptional response of the host to infecting organisms holds great promise. In this study, we aim to examine the transcriptional footprint of infections caused by the bacterial pathogens Staphylococcus aureus and Escherichia coli and the fungal pathogens Candida albicans and Aspergillus fumigatus in a human whole-blood model. Moreover, we use the expression information to build a random forest classifier to determine if the pathogen is bacterial, fungal or neither of the two. After normalizing the transcription intensities using stably expressed reference genes, we filtered the gene set for biomarkers of bacterial or fungal blood infections. This selection is based on differential expression and an additional gene relevance measure. In this way, we identified 38 biomarker genes, including IL6, SOCS3, and IRG1 which were already associated to sepsis by other studies. Using these genes, we trained the classifier and assessed its performance. It yielded a 96% accuracy (sensitivities >93%, specificities >97%) for a 10-fold stratified cross-validation and a 92% accuracy (sensitivities and specificities >83%) for an additional dataset comprising Cryptococcus neoformans infections. Furthermore, the noise-robustness of the classifier suggests high rates of correct class predictions on datasets of new species. In conclusion, this genome-wide approach demonstrates an effective feature selection process in combination with the construction of a well-performing classification model. Further analyses of genes with pathogen-dependent expression patterns can provide insights into the systemic host responses, which may lead to new anti-microbial therapeutic advances. Analysis of innate immune activation on the basis of gene expression of whole blood cells during ex vivo whole blood infection with bacterial (Staphylococcus aureus, Escherichia coli) and fungal pathogens (Candida albicans, Aspergillus fumigatus) in comparison to mock-treated blood.
2015-03-11 | E-GEOD-65088 | biostudies-arrayexpress
Project description:Survival and pathogenesis of Staphylococcus aureus in the host requires the ability to respond to changes. Therefore, tight regulation of gene expression via various regulators is essential. Also, the organization of genes in operons is of influence on the regulation of gene expression. Knowledge of gene expression under different conditions and the ability to accurately predict operons are important steps towards understanding the transcriptional regulation, function and pathogenesis. A whole genome Agilent microarray was developed for the highly virulent, community-acquired MSSA476.During standard growth in a defined medium, we were able to determine four basic gene expression patterns of S. aureus for both virulence and non-virulence genes. In addition, we predicted operon structures by calculating Pearson correlation coefficients of the transcriptional profiles for all adjacent probes over all time points and replicas. In this study, we have set a basis for the knowledge on gene expression of MSSA476 during growth. Moreover, the correlation of time-dependent transcriptional profiles of adjacent probes seems to be a promising approach to predict operon structures. Five separate cultures of S. aureus mssa476 were grown. Of each replicate culture, samples were taken at 1, 2, 3, 4, 5, 6 and 9 h post inoculation (p.i.). In total, this amounts to 35 samples (7 time points in 5 replicates).
2010-06-24 | E-GEOD-16488 | biostudies-arrayexpress
Project description:Young adult fer-15;fem-1 Caenorhabditis elegans were infected with Staphylococcus aureus for 8 h to determine the transcriptional host response to Staphylococcus aureus. Analysis of differential gene expression in C. elegans young adults exposed to two different bacteria: E. coli strain OP50 (control), wild-type Staphylococcus aureus RN6390. Samples were analyzed at 8 hours after exposure to the different bacteria. These studies identified C. elegans genes induced by pathogen infection. Keywords: response to pathogen infection, innate immunity, host-pathogen interactions
2010-06-12 | GSE21819 | GEO