Exploring the Genomic Background of Salmonella enterica Serovar Typhi in Bangladesh
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PROVIDER: PRJEB83818 | ENA |
REPOSITORIES: ENA
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Project description:We applied an RNA capture and amplification technique, Selective Capture of Transcribed Sequences (SCOTS), and microarray hybridization to identify S. Typhi transcripts expressed in the blood of five humans infected with S. Typhi in Bangladesh. In total, we detected the expression of mRNAs for 2046 S. Typhi genes (44% of the S. Typhi genome) in human blood; expression of 912 genes was detected in all 5 patients, and expression of 1100 genes was detected in 4 or more patients. Identified transcripts were associated with the virulence-associated PhoP regulon, Salmonella pathogenicity islands, the use of alternative carbon and energy sources, synthesis and transport of iron, thiamine, and biotin, and resistance to antimicrobial peptides and oxidative stress. The most highly represented group were genes currently annotated as encoding proteins designated as hypothetical, unknown, or unclassified. Of the 2046 detected transcripts, 1320 (29% of the S. Typhi genome) had significantly different levels of detection in human blood compared to in vitro cultures; detection of 141 transcripts was significantly different in all 5 patients, and detection of 331 transcripts varied in at least 4 patients. These mRNAs encode proteins of unknown function, those involved in energy metabolism, transport and binding, cell envelope, cellular processes, and pathogenesis. We confirmed increased expression of a subset of identified mRNAs by quantitative-PCR.
2011-07-12 | GSE30565 | GEO
Project description:We applied an RNA capture and amplification technique, Selective Capture of Transcribed Sequences (SCOTS), and microarray hybridization to identify S. Typhi transcripts expressed in the blood of five humans infected with S. Typhi in Bangladesh. In total, we detected the expression of mRNAs for 2046 S. Typhi genes (44% of the S. Typhi genome) in human blood; expression of 912 genes was detected in all 5 patients, and expression of 1100 genes was detected in 4 or more patients. Identified transcripts were associated with the virulence-associated PhoP regulon, Salmonella pathogenicity islands, the use of alternative carbon and energy sources, synthesis and transport of iron, thiamine, and biotin, and resistance to antimicrobial peptides and oxidative stress. The most highly represented group were genes currently annotated as encoding proteins designated as hypothetical, unknown, or unclassified. Of the 2046 detected transcripts, 1320 (29% of the S. Typhi genome) had significantly different levels of detection in human blood compared to in vitro cultures; detection of 141 transcripts was significantly different in all 5 patients, and detection of 331 transcripts varied in at least 4 patients. These mRNAs encode proteins of unknown function, those involved in energy metabolism, transport and binding, cell envelope, cellular processes, and pathogenesis. We confirmed increased expression of a subset of identified mRNAs by quantitative-PCR. We compared transcriptional profiles of S. Typhi from the blood of infected humans to S. Typhi grown in vitro
2011-07-12 | E-GEOD-30565 | biostudies-arrayexpress
Project description:Salmonella Typhi in Bangladesh: exploration of genomic diversity and antimicrobial resistance
| PRJEB27394 | ENA
Project description:Exploring the genomic background of Salmonella enterica serovar Paratyphi A from Bangladesh using Next Generation Sequencing
| PRJEB48506 | ENA
Project description:Macrophages provide a crucial environment for Salmonella enterica serovar Typhi (S. Typhi) to multiply during typhoid fever, yet our understanding of how human macrophages and S. Typhi interact remains limited. In this study, we delve into the dynamics of S. Typhi replication within human macrophages and the resulting heterogeneous transcriptomic responses of macrophages during infection. Our study reveals key factors that influence macrophage diversity, uncovering distinct immune and metabolic pathways associated with different stages of S. Typhi intracellular replication in macrophages. Of note, we found that macrophages harboring replicating S. Typhi are skewed towards an M1 pro-inflammatory state, whereas macrophages containing non-replicating S. Typhi exhibit neither a distinct M1 pro-inflammatory nor M2 anti-inflammatory state. Additionally, macrophages with replicating S. Typhi were characterized by the increased expression of genes associated with STAT3 phosphorylation and the activation of the STAT3 transcription factor. Our results shed light on transcriptomic pathways involved in the susceptibility of human macrophages to intracellular S. Typhi replication, thereby providing crucial insight into host phenotypes that restrict and support S. Typhi infection.
2024-05-20 | GSE267899 | GEO
Project description:This study describes how Salmonella Typhi, the pathogen responsible for typhoid fever, uses similar strategies to escape immune defense responses and survive within its human host. To elucidate the early mechanisms of typhoid fever, we performed studies using healthy human intestinal tissue samples to analyze gene expression changes in human intestinal specimens and bacterial cells both separately and after colonization. Our results showed mechanistic strategies that S. Typhi uses to rearrange the cellular machinery of the host cytoskeleton to successfully invade the intestinal epithelium, promote polarized cytokine release and evade immune system activation by downregulating genes involved in antigen sampling and presentation during infection.
2018-06-15 | GSE113333 | GEO
Project description:Six sequencing libraries was prepared from S. Typhi planktonic cells and biofilm cells using Illumina HiSeq 2500 sequencing to investigate differential gene expression between the two conditions. The transcriptome was processed using Cufflinks and there were a total of 35 up-regulated genes and 29 down-regulated genes log2-fold change values of greater than 2 and less than negative 2. The differentially expressed genes were identified using BLAST and the functions was analysed. This study provides an overview of the genes that are differentially expressed in S. Typhi when it transitions from the planktonic to the biofilm phenotype. The data will provide a basis for further study is necessary to uncover the mechanisms of biofilm formation in S. Typhi and discovery of novel gene functions or pathways associated with the development of the typhoid carrier state. This data may also be used to elucidate the effect of biofilm on the virulence and pathogenicity of S. Typhi in chronic carriers.
2017-10-31 | GSE93686 | GEO
Project description:Human genetic diversity can reveal critical factors in host-pathogen interactions. This is especially useful for human-restricted pathogens like Salmonella enterica serovar Typhi (S. Typhi), the cause of Typhoid fever. One key dynamic during infection is competition for nutrients: host cells attempt to restrict intracellular replication by depriving bacteria of key nutrients or delivering toxic metabolites in a process called nutritional immunity. Here, a cellular genome-wide association study of intracellular replication by S. Typhi in nearly a thousand cell lines from around the world—and extensive follow-up using intracellular S. Typhi transcriptomics and manipulation of magnesium concentrations—demonstrates that the divalent cation channel mucolipin-2 (MCOLN2) restricts S. Typhi intracellular replication through magnesium deprivation. Our results reveal natural diversity in Mg2+ limitation as a key component of nutritional immunity against S. Typhi.
2023-01-05 | GSE222194 | GEO
Project description:Global expression profiles of Salmonella typhi grown in the supernatant of infection and within human macrophages at 0h, 2h, 8h and 24h were obtained. Stringent analytical methods were used to compare Salmonella typhi cDNAs and revealed that known virulence factors, such as the SPI-1 and SPI-2 encoded type III secretion systems, were found to be expressed as predicted during infection by Salmonella. Intracellular Typhi expressed many genes encoding antimicrobial peptides, used the glyoxylate bypass for fatty acid utilization, and, did not induce the SOS response or the oxidative stress response. Genes coding for the flagellar apparatus, chemotaxis and the iron transport system were down-regulated in vivo. The combined use of SCOTS and microarray is an effective way to determine global bacterial gene expression profiling in the context of host infection, without the need of increasing the multiplicity of infection beyond what is seen in nature. Keywords: Time course
2006-01-10 | GSE3096 | GEO
Project description:Sequencing of RNA of selected Salmonella Typhi strains from typhoid-endemic regions of Asia and Africahttp://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.htmlThese data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2015-01-20 | E-ERAD-315 | biostudies-arrayexpress