Clostridioides difficile
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA217778 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR960431_1.fastq.gz | Fastqsanger.gz | |||
| SRR960431_2.fastq.gz | Fastqsanger.gz | |||
| SRR960432_1.fastq.gz | Fastqsanger.gz | |||
| SRR960432_2.fastq.gz | Fastqsanger.gz | |||
| SRR960433_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Purpose: To determine how divergent strains of C. difficile respond to environmental changes, the transcriptomes of two historic and two recently isolated hypervirulent strains were analyzed following nutrient shift and osmotic shock. Methods: Following nutrient shift and osmotic shock, mRNA profile were determined using sequing of transcriptome in biological duplicates, using Illumina Hi-seq 2000. Results: After applying the quality control steps, for each sample, sequence reads were 90 nucleotides in length and the total number of reads per sample was ~ 26.6 million on average. Expression of more than 90% CDS was detected under the three experimental conditions combined. About 20% of these genes were indentified to be differentially expressed at 1.5 fold or more. Conclusions: Our results reveal that although C. difficile strains contain a large number of shared and strain specific genes, the majority of the differentially expressed genes were core genes. We also detected a number of transcriptionally active regions that were not part of the primary genome annotation. Some of these are likely to be small regulatory RNAs. Differential stress transcriptomes of two historic (strain 630 and 196) and two recently emerged hypervirulent strains (stain R20291 and 32g58) of C. difficile was determined by deep sequencing, in duplicate, using Illumina Hi-Seq 2000.
2013-11-06 | E-GEOD-50497 | biostudies-arrayexpress
Project description:Clostridium difficile (C. difficile) strains belonging to PCR ribotype 027, PFGE type NAP1, REA type B1 and toxinotype III, termed NAP1/027, have been implicated in the increased frequency of outbreaks of Clostridium difficile-associated diarrhoea (CDAD) in North America and Europe. The NAP1/027 strains appears to be more virulent with an increased mortality and frequency of relapse. Current European C. difficile microarrays are designed to the first sequenced and annotated C. difficile complete genome - strain 630 (ribotype 12). A high density oligonucleotide microarray was designed to C. difficile 630 (CD630) sequence and extra probes corresponding to two PCR ribotypes O27 strains C. difficile R20291 and QCD-32g58 were also included. Comparative genomic hybridisation was used to identify markers of ribotype 027 strains and markers to identify CD630. Strains hybridised to the array included the most prevalent ribotypes found in the UK and Europe (106 and 001) as well as the emerging hypervirulent ribotype 078.
2010-07-01 | E-MTAB-162 | biostudies-arrayexpress
Project description:Purpose: To determine how divergent strains of C. difficile respond to environmental changes, the transcriptomes of two historic and two recently isolated hypervirulent strains were analyzed following nutrient shift and osmotic shock. Methods: Following nutrient shift and osmotic shock, mRNA profile were determined using sequing of transcriptome in biological duplicates, using Illumina Hi-seq 2000. Results: After applying the quality control steps, for each sample, sequence reads were 90 nucleotides in length and the total number of reads per sample was ~ 26.6 million on average. Expression of more than 90% CDS was detected under the three experimental conditions combined. About 20% of these genes were indentified to be differentially expressed at 1.5 fold or more. Conclusions: Our results reveal that although C. difficile strains contain a large number of shared and strain specific genes, the majority of the differentially expressed genes were core genes. We also detected a number of transcriptionally active regions that were not part of the primary genome annotation. Some of these are likely to be small regulatory RNAs.
2013-11-06 | GSE50497 | GEO
Project description:Clostridioides difficile (formerly Clostridium difficile) colonizes the gastrointestinal tract following disruption of the microbiota and can initiate a spectrum of clinical manifestations ranging from asymptomatic to life-threatening colitis. Following antibiotic treatment, luminal oxygen concentrations increase, exposing gut microbes to potentially toxic reactive oxygen species (ROS). Though typically regarded as a strict anaerobe, C. difficile can grow at low oxygen concentrations. How the bacterium adapts to a microaerobic environment and whether those responses to oxygen are conserved amongst strains is not entirely understood. Here, two C. difficile strains (630 and CD196) were cultured in 1.5% oxygen and the transcriptional response was evaluated via RNA-sequencing. During growth in a microaerobic environment, several genes predicted to protect against oxidative stress were upregulated, including ruberythrins and rubredoxins. Genes involved in metal homeostasis were positively correlated with increasing oxygen levels and were also amongst the most differentially transcribed. These included ferrous iron transporters (feo), a zinc transporter (zupT), and predicted siderophore transporters. To directly compare the transcriptional landscape between C. difficile strains, a ‘consensus-genome’ was generated. On the basis of the identified conserved genes, basal transcriptional differences as well as variations in the response to oxygen were evaluated. While several responses were similar between the strains, there were significant differences in the abundance of transcripts for amino acid and carbohydrate metabolism. Furthermore, homologous metal homeostasis genes were similarly transcribed, but the intracellular metal concentrations significantly varied both in an oxygen-dependent and independent manner. Overall, these results indicate that C. difficile adapts to grow in a low oxygen environment through transcriptional changes, though the specific strategy employed varies between strains.
2021-05-21 | GSE173804 | GEO
Project description:The incidence of Clostridium difficile infection has been steadily rising over the past decade. Its increased rate is associated with the specific NAP1/BI/027 strains which are “hypervirulent” and have led to several large outbreaks since their emergence. However, the relation between their outbreaks and virulence regulation mechanisms remains unclear. It has been reported that the major virulence factor TcdA and TcdB in C. difficile could be repressed by cysteine. Here, we investigated functional and virulence-associated regulation of C. difficile R20291 in response to cysteine stress by using a time-resolved genome-wide transcriptional analysis. Dramatic changes of gene expression in C. difficile were revealed in functional categories related to transport, metabolism, and regulators under cysteine stress during different phases of growth.
2020-12-12 | GSE107961 | GEO
Project description:Clostridioides difficile BI/NAP1/ribotype 027 is an epidemic hypervirulent strain found worldwide, including in Latin America. We examined the genomes and exoproteomes of two multilocus sequence type (MLST) clade 2 C. difficile strains considered hypervirulent: ICC-45 (ribotype SLO231/UK[CE]821), isolated in Brazil, and NAP1/027/ST01 (LIBA5756), isolated during a 2010 outbreak in Costa Rica. C. difficile isolates were cultured and extracellular proteins were analyzed using high-performance liquid chromatography-tandem mass spectrometry. Genomic analysis revealed that these isolates shared most of the gene composition. Only 83 and 290 NAP1/027 genes were considered singletons in ICC-45 and NAP1/027, respectively. Exoproteome analysis revealed 197 proteins, of which 192 were similar in both strains. Only five proteins were exclusive to the ICC-45 strain. These proteins were involved with catalytic and binding functions and indirectly interacted with proteins related to pathogenicity. Most proteins, including TcdA, TcdB, flagellin subunit, and cell surface protein, were overrepresented in the ICC-45 strain; 14 proteins, including mature S-layer protein, were present in higher proportions in LIBA5756. These data show close similarity between the genome and proteins in the supernatant of two strains with hypervirulent features isolated in Latin America and underscore the importance of epidemiological surveillance of the transmission and emergence of new strains.
2021-07-01 | PXD026218 | Pride
Project description:Pathogenomic study of Clostridium difficile strains
| PRJNA342402 | ENA
Project description:We illustrate how metabolically distinct species of Clostridia can protect against or worsen Clostridioides difficile infection, modulating the pathogen's colonization, growth, and virulence to impact host survival. Gnotobiotic mice colonized with the amino acid fermenter Paraclostridium bifermentans survived infection while mice colonized with the butyrate-producer, Clostridium sardiniense, more rapidly succumbed. Systematic in vivo analyses revealed how each commensal altered the gut nutrient environment, modulating the pathogen's metabolism, regulatory networks, and toxin production. Oral administration of P. bifermentans rescued conventional mice from lethal C. difficile infection via mechanisms identified in specifically colonized mice. Our findings lay the foundation for mechanistically informed therapies to counter C. difficile disease using systems biologic approaches to define host-commensal-pathogen interactions in vivo.
2021-10-04 | GSE182613 | GEO
Project description:Clostridium difficile ribotype 244 Australia outbreak strains
| PRJNA277962 | ENA
Project description:Hypervirulent epidemic strains of Clostridium difficile (C. difficile), referred to as NAPI/027, express an additional virulence factor, binary toxin (CDT), and are associated with more severe disease. Emerging evidence indicates gut immunity to C. difficile is a delicate balance between protection and pathology. To identify potential therapeutic host immune targets, we conducted a transcriptome analysis of host genes altered by NAPI/027 infection and identified interleukin-33 (IL-33) as a candidate immune target. Using a murine model, we show that both endogenous IL-33 and exogenous IL-33 treatment protect from the enhanced mortality, weight-loss and tissue pathology which is characteristic of hypervirulent C. difficile. IL-33 mediated protection was elicited through type-2 innate lymphoid cells (ILC2s) and adoptive transfer of purified ILC2s was sufficient to mitigate CDI- associated mortality and weight-loss. Furthermore, dysregulated IL-33 signaling via the soluble IL-33 decoy receptor (sST2) predicted disease severity and mortality in human patients. Lastly, colonic IL-33 expression appears to be regulated by the microbiota as antibiotic- depletion of IL-33 was rescued with mouse fecal microbiota transplant (FMT) and a human fecal spore preparation (HSP). Thus, IL-33 signaling is a novel therapeutic pathway for severe CDI which can potentially be targeted with rationally designed microbial therapies.
2019-05-09 | GSE122013 | GEO