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ABSTRACT: Molecular characterisation of, and antimicrobial resistance in, Clostridioides difficile from Thailand, 2017-2018

PROVIDER: PRJNA679085 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	JADPMT01.dat.gz	Other
	JADPMT01.fasta.gz	Fasta.gz
	JADPMT01.master.dat	Other
	JADPMU01.dat.gz	Other

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Project description:Molecular epidemiology and antimicrobial resistance in clinical Clostridioides difficile isolates from Thailand during 2017-2018

| PRJEB40974 | ENA

Exogenous butyrate inhibits butyrogenic metabolism and alters virulence phenotypes in Clostridioides difficile

Project description:The gut microbiome engenders colonization resistance against the diarrheal pathogen Clostridioides difficile but the molecular basis of this colonization resistance is incompletely understood. A prominent class of gut microbiome-produced metabolites important for colonization resistance against C. difficile is short chain fatty acids (SCFAs). In particular, one SCFA (butyrate) decreases the fitness of C. difficile in vitro and is correlated with C. difficile-inhospitable gut environments, both in mice and in humans. Here, we demonstrate that butyrate-dependent growth inhibition in C. difficile occurs under conditions where C. difficile also produces butyrate as a metabolic end product. Furthermore, we show that exogenous butyrate is internalized into C. difficile cells and is incorporated into intracellular CoA pools where it is metabolized in a reverse (energetically unfavorable) direction to crotonyl-CoA and (S)-3-hydroxybutyryl-CoA and/or 4-hydroxybutyryl-CoA. This internalization of butyrate and reverse metabolic flow of butyrogenic pathway(s) in C. difficile coincides with alterations in toxin release and sporulation. Together, this work highlights butyrate as a marker of a C. difficile inhospitable environment to which C. difficile responds by releasing its diarrheagenic toxins and producing environmentally-resistant spores necessary for transmission between hosts. These findings provide foundational data for understanding the molecular and genetic basis of how C. difficile growth is inhibited by butyrate and how butyrate alters C. difficile virulence in the face of a highly competitive and dynamic gut environment.

2023-12-21 | GSE249810 | GEO

Clostridioides difficile: R20291_pMTL84151 transconjugant (C) vs. R20291_pMTL84151-03890 (T1)

Project description:Gene expression level of Clostridioides difficile (C. difficile) strain R20291 comparing control C. difficile carring pMTL84151 as vector plasmid with C. difficile conjugated with a pMTL84151-03890 gene. Goal was to determine the effects of 03890 gene conjugation on C. difficile strain R20291 gene expression.

2023-11-30 | GSE219066 | GEO

Unraveling Cecal Alterations in Clostridioides difficile Colonized Mice through a Comprehensive Metabolic Profile of 289 Compound

Project description:Unraveling Cecal Alterations in Clostridioides difficile Colonized Mice through a Comprehensive Metabolic Profile of 289 Compound

2024-07-10 | MSV000095285 | MassIVE

Dual RNA-seq identifies proteins and pathways required for Clostridioides difficile colonisation

Project description:Clostridioides difficile interactions with the gut mucosa are crucial for colonisation and establishment of infection, however key infection events during the establishment of disease are still poorly defined. To better understand the initial events that occur during C. difficile colonisation, we employed a dual RNA-sequencing approach to study the host and bacterial transcriptomic profiles during C. difficile infection in a dual-environment in vitro human gut model. Temporal changes in gene expression were analysed over 3-24h post infection and comparisons were made with uninfected controls.

2023-03-23 | E-MTAB-12660 | biostudies-arrayexpress

Global transcriptome analysis of colonic tissue during Clostridioides difficile infection

Project description:Clostridioides difficile can cause severe infections in the gastrointestinal tract and affects almost half a million people in the U.S every year. Upon establishment of infection, a strong immune response is induced. We sought to investigate the dynamics of the mucosal host response during C. difficile infection.

2023-09-13 | GSE237574 | GEO

Clostridioides difficile toxins deregulate tight junction proteins.

Project description:The Clostridioides difficile toxins TcdA and TcdB are responsible for diarrhea and colitis. The aim of this project was to explore the effects of the toxins on epithelial barrier function and the molecular mechanisms for diarrhea and inflammation. RNA-seq of toxin-treated intestinal cell monolayers was performed to describe the C. difficile-mediated effects. mRNA profiles from intestinale epithelial cells were generated by deep sequencing using Illumina NovaSeq 6000. This data provide the basis for subsequent upstream regulator analysis.

2023-11-29 | GSE232704 | GEO

Identification of DraRS in C. difficile, a two-component regulatory system that responds to lipid II interacting antibiotics

Project description:Clostridioides difficile is a Gram-positive opportunistic pathogen that results in 220,000 infections, 12,000 deaths, and upwards of $1 billion in medical costs in the US each year. C. difficile is highly resistant to a variety of antibiotics, but we have a poor understanding of how C. difficile senses and responds to antibiotic stress, and how such sensory systems affect clinical outcomes. There has been recent interest in using a daptomycin analog, Surotomycin, to treat C. difficile infections. We have identified a spontaneous C. difficile mutant that displays increased daptomycin resistance. We performed whole-genome sequencing that this mutant possessed a nonsense mutation, S605*, in draS which encodes a putative sensor histidine kinase of a two-component system (TCS). The draSS605* mutant has approximately a 4-8-fold increase in daptomycin MIC compared to WT. We found that expression of constitutively active DraRD54E in WT increases daptomycin resistance 8-16-fold and increases bacitracin resistance ~4-fold. We found that a selection of lipid II inhibiting compounds leads to increased activity of the luciferase-based reporter, PdraR-sLucopt including vancomycin, bacitracin, ramoplanin, and daptomycin. Using RNA-seq we identified the DraRS regulon. Interestingly, we found that DraRS can induce expression of the previously identified hex locus required for synthesis of a novel glycolipid produced in C. difficile. Our data suggest that induction of the hex locus by DraR explains some, but not all, of the DraR-induced daptomycin and bacitracin resistance.

2023-06-17 | GSE234961 | GEO

L-lactate supplementation influences toxin production of Clostridioides difficile via energy metabolism

Project description:Metabolomic and transcriptomic analysis of changes in the exponential and stationary phase of Clostridioides difficile after cultivation in casamino acids medium (reference) and supplemented with L-lactate and the connection to toxin production.

2021-01-31 | GSE139354 | GEO

Transcriptomic RNA-sequencing analysis of the hypervirulent Clostridioides difficile R20291 strain in response to trehalose

Project description:Clostridioides difficile, the leading cause of antibiotic-associated diarrhoea worldwide, is a genetically diverse species which can metabolise a number of nutrient sources upon colonising a dysbiotic gut environment. Trehalose, a disaccharide sugar consisting of two glucose molecules bonded by an α 1,1-glycosidic bond, has been hypothesised to be involved in the emergence of C. difficile hypervirulence due to its increased utilisation by the RT027 and RT078 strains. Using RNA-sequencing analysis, we report the identification of a putative trehalose metabolism pathway which is induced during growth in trehalose: this has not been previously described within the C. difficile species. These data demonstrate the metabolic diversity exhibited by C. difficile which warrants further investigation to elucidate the molecular basis of trehalose metabolism within this important gut pathogen.

2023-05-26 | GSE232033 | GEO

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