Streptococcus pneumoniaeis the leading cause of community-acquired pneumonia. Levofloxacin is a fluoroquinolone used for treatment of severe community-acquired pneumonia. Here, we describe the draft genome sequences ofS. pneumoniaewith emerging resistance to levofloxacin, resulting in failure of treatment of pneumococcal pneumonia. ...[more]
Project description:This SuperSeries is composed of the following subset Series: GSE31815: ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + Glucose at MID-log growth phase GSE31816: ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + GLucose at transition-phase of growth (TS) GSE31817: ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + Galactose at MID-log growth phase GSE31818: ccpA mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + galactose at transition-phase of growth (TS) Refer to individual Series
Project description:RNA sequencing was used to explore the expression of all genes in Streptococcus pneumoniae under heat stress. The pneumococcal strain 2/2 was grown in broth culture under control (37°C) and high temperature (40°C) conditions. 2/2 culture samples were taken at sequential time points and RNA was extracted and sequenced. Overall design: Streptococcus pneumoniae isolate 2/2 was cultured in seven 10 ml tubes of brain-heart infusion broth and incubated at 40°C + 5% CO2 for 6 h to mimic heat shock. The experimental control was the same isolate 2/2, also cultured in seven 10 ml tubes of brain-heart infusion broth but incubated at standard conditions of 37°C + 5% CO2. Broth cultures at five time points (2, 3, 4, 5 and 6 h of incubation) were removed and 19 ml of RNAprotect Bacteria Reagent (Qiagen) was added to stabilise the RNA. RNA was extracted from the samples using the Promega Maxwell® 16 Instrument and LEV simplyRNA Cells purification kit, following the manufacturer’s protocol. Extracted RNA samples were sent to the Oxford Genomics Centre for processing. Library preps were made using RNA-Seq Ribozero kits (Illumina, Inc) and sequencing was performed on the MiSeq (Illumina, Inc). The sequenced forward and reverse reads were paired and mapped to the S. pneumoniae strain 2/2 genome using Bowtie2 with the highest sensitivity option. Differential gene expression was analysed in Geneious version 9.1 (Biomatters Ltd) using the DESeq method. Genes with an adjusted p value <0.05 were considered to be differentially expressed.
Project description:Galactose promotes pneumococcal biofilms in vivo 15 mRNA profiles of Streptococcus pneumoniae samples that were grown under different conditions were generated using deep sequencing.
Project description:Transcriptome comparison of the Streptococcus pneumoniae D39 wild-type grown in M17 medium toD39 wild-type grown in M17 medium + 0.5% sialic acid (SM17). Overall design: Two conditions design comparison of one strain including a dye swap.
Project description:Streptococcus pneumoniae normally resides in the human nasopharynx in a non-disease state. In response to yet unknown triggers it can descend to the lower respiratory tract and/or invade the bloodstream. Regulation and activation of virulence genes play essential roles in this process of disease development. A putative transcriptional regulator in S. pneumoniae, MgrA, with homology to a virulence gene activator, mga, of Group A streptococcus (GAS) was previously identified as being required for development of pneumonia in a murine model. In this work we confirm that mgrA is required for both nasopharyngeal carriage and pneumonia. Transcriptional profiling by microarray technology through the growth course of a strain that bears a deletion of mgrA (AC1500) with that of a strain that over expresses Mgra (AC1481) is used to show that MgrA acts as a repressor of the previously characterized rlrA pathogenicity islet. This is manifested phenotypically by a decrease in adherence to epithelial cells in tissue culture since rlrA pathogenicity islet contains genes mediating adherence.
Project description:Three Microarray comparisons have been preformed in this study. 1- Transcriptome comparison of the Streptococcus pneumoniae D39 wild type grown in M17 medium + 0.5 % (w/v) NAGa (NAGaM17) to M17 medium + 0.5 % (w/v) glucose (GM17) (GSM2372597 and GSM2372598). 2- Transcriptome comparison of the Streptococcus pneumoniae D39 ΔagaR to D39 wild type grown in M17 medium + 0.5 % (w/v) glucose (GM17) (GSM2372599 and GSM2372600). 3- Transcriptome comparison of the Streptococcus pneumoniae D39 ΔccpA to D39 wild type grown in M17 medium + 0.5 % (w/v) NAGa (NAGaM17) (GSM2290636 and GSM2290637). Overall design: - Two conditions design comparison of one strain including a dye swap or Microarray comparisons 1. - One condition design comparision of two strains including a dye swap for Microarray comparisons 2 and 3.
Project description:Transcriptome Comparison of the Streptococcus pneumoniae D39 wild-type grown in CDM with 0 mM to 10mM Niacin Overall design: Two conditions design comparison of one strain including a dye swap.
Project description:Transcriptome Comparison of the Streptococcus pneumoniae D39 wild-type grown in CDM with 0 mM to 5mM Aspirin Overall design: Two conditions design comparison of one strain including a dye swap.
Project description:Transcriptome Comparison of the Streptococcus pneumoniae D39 wild-type grown in CDM with 0.03 mM to 50mM Cysteine Overall design: Two conditions design comparison of one strain including a dye swap.
Project description:Genome-wide screens have discovered a large set of essential genes in the human pathogen Streptococcus pneumoniae. However, the function of many essential genes is still unknown, hampering vaccine and drug development programs. Based on results from transposon-sequencing (Tn-Seq), we refined the list of essential genes in S. pneumoniae serotype 2 strain D39. Next, we created a knockdown library targeting all 391 potentially essential genes using CRISPR interference (CRISPRi). Using high-content microscopy screening, we searched for essential genes of unknown function with clear phenotypes in cell morphology upon CRISPRi-based depletion. We identified SPD1416 and SPD1417 (named to MurT and GatD, respectively) as essential peptidoglycan synthesis proteins and we show that SPD1198 and SPD1197 (named to TarP and TarQ, respectively) are responsible for the polymerization of teichoic acid (TA) precursors. This knowledge enabled us to reconstruct the unique pneumococcal TA biosynthetic pathway. Our CRISPRi library provides a valuable tool for characterization of pneumococcal genes and pathways and revealed several promising antibiotic targets. This RNA-Seq dataset is aimed to show that induction of the CRISPRi system very selectively represses its target gene, firefly luciferase, without other observable transcriptional effects. Overall design: Pairwise comparison of control and IPTG-induced cells (RNA-seq), analyzing the effect of CRISPRi activation on the transcriptome of Streptococcus pneumoniae. It was performed with deep sequencing, using an Illumina HiSeq 2000 machine with 51 nt single-end reads. Samples were analysed from duplicate samples. To separate CRISPRi-specific effects from general IPTG-induced effects, we compared the uninduced strains with IPTG-induced strains that either did or did not contain the single-guide RNA.