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Transcriptome RNA Sequencing Data Sets of Francisella tularensis tularensis SchuS4 upon treatment with various concentrations of Doxycycline or Ciprofloxacin antibiotics

ABSTRACT: Transcriptome RNA Sequencing Data Sets of Francisella tularensis tularensis SchuS4 upon treatment with various concentrations of Doxycycline or Ciprofloxacin antibiotics

PROVIDER: PRJNA868402 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21009101.fastq.gz	Fastqsanger.gz
	SRR21009102.fastq.gz	Fastqsanger.gz
	SRR21009103.fastq.gz	Fastqsanger.gz
	SRR21009104.fastq.gz	Fastqsanger.gz
	SRR21009105.fastq.gz	Fastqsanger.gz

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Transcriptome RNA Sequencing Data Sets of Francisella tularensis tularensis SchuS4 upon treatment with various concentrations of Doxycycline or Ciprofloxacin antibiotics

Project description:Francisella tularensis, the etiological agnet of Tularemia is a Category A select agent. Preparedness means for prompt proper antibiotic treatment are of need to prevent morbidity and mortality. While standard antimicrobial susceptibility tests are time consuming, the quantification of the changes in the expression levlels of specific mRNA markers folowing antibiotic exposure may enable a rapid determination of antimicrobial susceptibility. We submit transcriptomic data sets detailing global gene expression of F. tularensis following exposure to Doxycycline or Ciprofloxacin antibiotics.

2023-03-05 | GSE210974 | GEO

Transcriptome sequencing Data sets for human epithelial cells response during Francisella Tularensis infection.

Project description:The goal of this study is to determine the host response of human epithelial cells during infection with Francisella Tularensis. For this purpose, A549 human epithelial cell line was infected with Francisella tularensis spp. holarctica strain LVS for different times of infection, in duplicates. At different times post infection (0.5/1/3/6/12/24 hours post infection) cells were harvested and total RNA was extracted. RNA-seq libraries were constructed and sequencing of 100bp paired-end was performed on the Illumina NovaSeq 6000 system. Sequencing yielded about 22M reads per sample that were mapped to the human genome (Human: GRCh38) resulting with the identification of 21,066 transcripts. The expression of the infected samples was compared to mock sample, and RNA ratios were clustered using partitioning clustering. This approach allowed clustering of the cellular transcripts into 5 distinct classes based on similarities in temporal expression profiles. We next carried out GO term enrichment analysis for each of these five cluster. Our study represents the first detailed analysis of human epithelial response to Francisella tularensis infection, and provide a framework for comparative investigations of genes and mechanisms that may contribute to the infection.

2020-08-11 | GSE155970 | GEO

Subinhibitory concentrations of ciprofloxacin enhance antimicrobial resistance and pathogenicity of Enterococcus faecium

Project description:Enterococcus faecium has emerged as a major opportunistic pathogen for two decades, with the spread of hospital-adapted multidrug-resistant clones. Members of the intestinal microbiota, they are subjected to numerous bacterial stresses, including antibiotics at subinhibitory concentrations (SICs). Since fluoroquinolones are extensively prescribed, SICs are very likely to occur in vivo with potential effects on bacterial metabolism with subsequent modulation of opportunistic traits. The aim of the study was to evaluate globally the impact of subinhibitory concentrations (SICs) of ciprofloxacin on antimicrobial resistance and pathogenicity of E. faecium. Transcriptomic analysis was performed by RNA-seq (HiSeq 2500, Illumina) using the vanB-positive reference strain E. faecium Aus0004 in the absence or presence of ciprofloxacin SIC (0.38 mg/L, i.e. MIC 1/8). Several genetic and phenotypic tests were used for validation. In the presence of ciprofloxacin SIC, 196 genes were significantly induced whereas 286 were significantly repressed, meaning that 16.8% of the E. faecium genome was altered. Amongst upregulated genes, EFAU004_02294 (fold change of 14.3) encoded a protein (EfmQnr) homologue of Qnr proteins involved in quinolone resistance in Gram-negative bacilli. Its implication in intrinsic and adaptive FQ resistance in E. faecium was experimentally ascertained. Moreover, EFAU004_02292 coding for the collagen adhesin Acm was also induced by SIC of ciprofloxacin (fold change of 8.2), and higher adhesion capabilities were demonstrated phenotypically. Both Efmqnr and Acm determinants may play an important role in the transition from a commensal to a pathogenic state of E. faecium that resides in the gut of patients receiving a fluoroquinolone therapy.

2017-02-04 | GSE94507 | GEO

Gene expression in F. tularensis subsp. tularensis SCHU P0, P5, and P9 strains.

Project description:The microarray analysis of Francisella tularensis subsp. tularensis strains SCHU P9 (virulent) and SCHU P0/P5 (attenuated) revealed significant differences in gene expression. The results showed that 19 genes were upregulated in the virulent SCHU P9 strain, while two genes, including ftt_0965c, were significantly downregulated

2024-12-31 | GSE274776 | GEO

Transcriptome sequencing Data sets for human epithelial cells response during Francisella Tularensis infection.

Project description:Transcriptome sequencing Data sets for human epithelial cells response during Francisella Tularensis infection.

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Gene expression data from F. tularensis-exposed neutrophils

Project description:We demonstrated recently that both constitutive and FAS-triggered apoptosis of human neutrophils are profoundly impaired by Francisella tularensis, but how this is achieved is largely unknown. To test the hypothesis that changes in neutrophil gene expression contribute to this phenotype, we used human oligonucleotide microarrays to identify differentially regulated genes in cells infected with F. tularensis strain LVS compared with uninfected controls. In order to examine the effect of F. tularensis on the neutrophil transcriptome, we performed microarray expression analysis on human neutrophils treated with F. tularensis subsp. holarctica live vaccine strain (LVS).

2012-10-22 | GSE37416 | GEO

Francisella tularensis subsp. tularensis

Project description:Francisella tularensis subsp. tularensis Multiisolate

| PRJNA217354 | ENA

Comprehensive Adsorption Studies of Doxycycline and Ciprofloxacin Antibiotics by Biochars Prepared at Different Temperatures.

Project description:This paper comparatively investigated the removal efficiency and mechanisms of rice straw biochars prepared under three pyrolytic temperatures for two kinds of tetracycline and quinolone antibiotics (doxycycline and ciprofloxacin). The influencing factors of antibiotic adsorption (including biochar dosage, pH, background electrolytes, humic acid, initial antibiotics concentration, contact time, and temperature) were comprehensively studied. The results suggest that biochars produced at high-temperature [i.e., 700°C (BC700)], have higher adsorption capacity for the two antibiotics than low-temperature (i.e., 300-500°C) biochars (BC300 and BC500). Higher surface area gives rise to greater volume of micropores and mesopores, and higher graphitic surfaces of the BC700 contributed to its higher functionality. The maximum adsorption capacity was found to be in the following order: DOX > CIP. The π-π EDA interaction and hydrogen bonding might be the predominant adsorption mechanisms. Findings in this study highlight the important roles of high-temperature biochars in controlling the contamination of tetracycline and quinolone antibiotics in the environment.

| S-EPMC5880934 | biostudies-literature

Global transcriptomic analysis of Francisella tularensis SchuS4 differentially expressed genes in response to doxycycline or ciprofloxacin exposure.

Project description:ObjectiveAs part of a research aiming at presenting an alternative approach for rapid determination of antimicrobial susceptibility by quantification of changes in expression levels of specific marker genes and gene sets, cultures of the virulent bacterial strain Francisella tularensis SchuS4 were grown in the presence of inhibitory/sub-inhibitory concentrations of either ciprofloxacin or doxycycline and their transcriptomic profiles were elucidated using differential expression analysis followed by functional annotation.Data descriptionRNA sequencing was performed to identify differentially expressed genes (DEGs) in response to exposure of F. tularensis SchuS4 to either ciprofloxacin or doxycycline, the antibiotics of choice for Tularemia therapy. Accordingly, RNA samples were collected 2 h post antibiotic exposure and subjected to RNA sequence analysis. Transcriptomic quantification of RNA representing duplicated samples generated highly similar gene expression data. Exposure to sub-inhibitory concentration [0.5 x MIC (minimal inhibitory concentration)] of doxycycline or ciprofloxacin modulated the expression of 237 or 8 genes, respectively, while exposure to an inhibitory concentration (1 x MIC) resulted in the modulation of 583 or 234 genes, respectively. Amongst the genes modulated upon doxycycline exposure upregulation of 31 genes encoding for translation-functions could be distinguished, as well as downregulation of 14 genes encoding for functions involved in DNA transcription and repair. Ciprofloxacin exposure impacted differently the RNA sequence profile of the pathogen, resulting in upregulation of 27 genes encoding mainly DNA replication and repair functions, transmembrane transporters and molecular chaperons. In addition, 15 downregulated genes were involved in translation processes.

| S-EPMC10114481 | biostudies-literature

The role and mechanism of erythrocyte invasion by Francisella tularensis

Project description:Francisella tularensis, is an extremely virulent bacterium that can be transmitted naturally by blood sucking arthropods. During mammalian infection, F. tularensis infects numerous types of host cells, including erythrocytes. As erythrocytes do not undergo phagocytosis or endocytosis, it remains unknown how F. tularensis invades these cells. Furthermore, the consequence of inhabiting the intracellular space of red blood cells has not been determined. Here, we provide evidence indicating that residing within an erythrocyte enhances the ability of F. tularensis to colonize ticks following a blood meal.

2017-05-24 | GSE93233 | GEO

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