Streptococcus pneumoniae
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ABSTRACT:
PROVIDER: PRJNA252007 | ENA |
REPOSITORIES: ENA
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Project description:Background. Pneumococcus is a major human pathogen and the polysaccharide capsule is considered its main virulence factor. Nevertheless, strains lacking a capsule, named non-typeable pneumococcus (NT), are maintained in nature and frequently colonise the human nasopharynx. Interest in these strains, not targeted by any of the currently available pneumococcal vaccines, has been rising as they seem to play an important role in the evolution of the species. Currently, there is a paucity of data regarding this group of pneumococci. Also, questions have been raised on whether they are true pneumococci. We aimed to obtain insights in the genetic content of NT and the mechanisms leading to non-typeability and to genetic diversity. Methods. A collection of 52 NT isolates representative of the lineages circulating in Portugal between 1997 and 2007, as determined by pulsed-field gel electrophoresis and multilocus sequence typing, was analysed. The capsular region was sequenced and comparative genomic hybridisation (CGH) using a microarray covering the genome of 10 pneumococcal strains was carried out. The presence of mobile elements was investigated as source of intraclonal variation. Results. NT circulating in Portugal were found to have similar capsular regions, of cps type NCC2, i.e., having aliB-like ORF1 and aliB-like ORF2 genes. The core genome of NT was essentially similar to that of encapsulated strains. Also, competence genes and most virulence genes were present. The few virulence genes absent in all NT were the capsular genes, type-I and type-II pili, choline-binding protein A (cbpA/pspC), and pneumococcal surface protein A (pspA). Intraclonal variation could not be entirely explained by the presence of prophages and other mobile elements. Conclusions. NT circulating in Portugal are a homogeneous group belonging to cps type NCC2. Our observations support the theory that they are bona-fide pneumococcal isolates that do not express the capsule but are otherwise essentially similar to encapsulated pneumococci. Thus we propose that NT should be routinely identified and reported in surveillance studies.
2014-11-24 | GSE58329 | GEO
Project description:PFGRC has developed a cost effective alternative to complete genome sequencing in order to study the genetic differences between closely related species and/or strains. The comparative genomics approach combines Gene Discovery (GD) and Comparative Genomic Hybridization (CGH) techniques, resulting in the design and production of species microarrays that represent the diversity of a species beyond just the sequenced reference strain(s) used in the initial microarray design. These species arrays may then be used to interrogate hundreds of closely related strains in order to further unravel their evolutionary relationships. The Pneumococcus are among most deadly pathogens world-wide. The infections and outbreaks caused by this pathogens is quite frequent despite existing diagnostic network and therapeutic means. Therefore, developing reliable diagnostic tools and efficient (broad-spectrum) therapeutics for Streptococcus pneumoniae remain a public health priority for every country in world today. The comparative genomics study will provide the largest hitherto genomic data sets regarding this pathogen.These large data sets will enable us as well as other members of scientific community to conduct comprehensive data mining in the form of gene association studies with statistical power and significance.
2011-08-01 | GSE29501 | GEO
Project description:PFGRC has developed a cost effective alternative to complete genome sequencing in order to study the genetic differences between closely related species and/or strains. The comparative genomics approach combines Gene Discovery (GD) and Comparative Genomic Hybridization (CGH) techniques, resulting in the design and production of species microarrays that represent the diversity of a species beyond just the sequenced reference strain(s) used in the initial microarray design. These species arrays may then be used to interrogate hundreds of closely related strains in order to further unravel their evolutionary relationships. The Pneumococcus are among most deadly pathogens world-wide. The infections and outbreaks caused by this pathogens is quite frequent despite existing diagnostic network and therapeutic means. Therefore, developing reliable diagnostic tools and efficient (broad-spectrum) therapeutics for Streptococcus pneumoniae remain a public health priority for every country in world today. The comparative genomics study will provide the largest hitherto genomic data sets regarding this pathogen.These large data sets will enable us as well as other members of scientific community to conduct comprehensive data mining in the form of gene association studies with statistical power and significance. Two hundread fifty five query strains were investigated in this study, with each query strain hybridized against the reference strain, tigr4. Each strain has a single dye experiment. Each oligo is spotted on the S.pneumoniae species microarray once. Positive controls on the array consist of oligos designed from the sequenced reference genome of S. pneumoniae and negative controls on the array consist of oligos designed from the thale cress plant, Arabidopsis thaliana.The microarrays also had Agilent internal controls.
2011-07-31 | E-GEOD-29501 | biostudies-arrayexpress
Project description:Our understanding of the synergism between S. pneumoniae and influenza virus remains incomplete. The classic dogma has been that influenza attenuates the host innate immunity and increase the susceptibility to subsequent bacterial infection. Therefore, the majority of current studies have been focusing on the interaction of S. pneumoniae and influenza in the context of host cells. By contrast, in this study, we set out to investigate the response of pneumococcus alone to virus infection. Our hypothesis was that prior to causing any damages to host cells, influenza may have induced (lethal) changes to pneumococcus cell itself. Indeed, a very recent evidence has shown that direct viral treatment to pneumococcus will increase its adhesion to macrophage cells. Here, using quantitative phosphoproteomic approach, we attempt to investigate the global alterations of S. pneumoniae phosphorylation by influenza virus challenge, and provide a landscape of synergism between the IAV and pneumococcus.
2022-12-09 | PXD016214 | Pride
Project description:Acetyl phosphate (AcP) is a small-molecule metabolite that can act as a phosphoryl group donor for response regulators of two-component regulatory systems (TCSs). Streptococcus pneumoniae (pneumococcus) synthesizes AcP by the conventional pathway involving the phosphotransacetylase and acetate kinase enzymes encoded by the pta and ackA genes, respectively. In addition, pneumococcus synthesizes copious amounts of AcP and hydrogen peroxide (H2O2) by the pyruvate oxidase enzyme encoded by spxB. To access possible roles of AcP in pneumococcal TCS regulation and metabolism, we constructed combinations of spxB, pta, and ackA mutants and determined their ATP, AcP, and H2O2 production. Epistasis and microarray experiments were consistent with a role for the AcP biosynthetic pathway in basal-level phosphorylation of WalRSpn and possibly other response regulators involved in sensing cell wall status. However, this basal phosphorylation likely does not play an active physiological role in sensing in S. pneumoniae.
2010-11-29 | GSE23404 | GEO
Project description:Our understanding of the synergism between S. pneumoniae and influenza virus remains incomplete. The classic dogma has been that influenza attenuates the host innate immunity and increase the susceptibility to subsequent bacterial infection. Therefore, the majority of current studies have been focusing on the interaction of S. pneumoniae and influenza in the context of host cells. By contrast, in this study, we set out to investigate the response of pneumococcus alone to virus infection. Our hypothesis was that prior to causing any damages to host cells, influenza may have induced (lethal) changes to pneumococcus cell itself. Indeed, a very recent evidence has shown that direct viral treatment to pneumococcus will increase its adhesion to macrophage cells. Here, using quantitative shotgun approach, we attempt to investigate the proteomic alterations of S. pneumoniae by influenza virus challenge, and provide a landscape of interactions between the IAV and pneumococcus.
2022-12-09 | PXD016122 | Pride
Project description:We report the mRNA expression profile of Streptococcus pneumoniae Type 2 D39 strain-derived mutant lacking the phpP gene encoding eukaryote-type ser/thr phosphatase . Measuring transcriptome profiling in D39Î?phpP mutants vs D39-WT pneumococcus wild-type strain
2016-10-27 | E-GEOD-74421 | biostudies-arrayexpress
Project description:we characterized the zebrafish innate immune response to pneumococcus through a whole-genome level transcriptome analysis. The analysis revealed the induction of genes coding for pro-inflammatory cytokines, chemokines, acute phase proteins, and antimicrobial peptides, indicating a well-conserved innate immune response to the human pathogen pneumococcus in zebrafish embryos. To gain understanding of the genetic factors associated with the increased risk for severe pneumococcal infection in humans, we carried out a medium-scale forward genetic screen in zebrafish. We identified a mutant fish line, which showed compromised defense against pneumococcus in septic larval infection model. Poor survival upon infection was associated with increased bacterial counts indicating defect in resistance. The transcriptome analysis of the mutant zebrafish embryos revealed otherwise normal innate immune response to pneumococcal infection but a deficient expression of a gene homologous for human C-reactive protein (CRP).
2022-11-14 | GSE112433 | GEO
Project description:Carolacton is a novel biofilm inhibitor that kills biofilm cells of Streptococcus mutans in nanomolar concentrations. Interestingly, Carolacton also inhibits growth of the clinically relevant and human pathogenic bacterium Streptococcus pneumoniae TIGR4. The cellular target of Carolacton is still unknown. Here, we adressed the differential transcription of cellular RNAs when S. pneumoniae TIGR4 was grown in the presence of Carolacton. This was done to identify transcriptional regulatory networks that are directly affected by treatment of the pneumococcus with Carolacton. In order to gain insights into the primary transcriptional response, early time-points were chosen for sampling, which should not reflect secondary responses (e.g. due to differences in growth phase, drop in pH etc.). To achieve a thorough overview over all affected cellular RNA species, such as mRNAs, small regulatory RNAs and tRNAs, and not to lose small transcripts during library preparation, RNAs were separated according to size and used to construct two separate libraries for sequencing.
2016-09-19 | GSE76979 | GEO