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Prevalence of LCT negative binary toxin positive Clostridium difficile

ABSTRACT: Prevalence of Binary Toxin Positive Clostridium difficile in Symptomatic Humans in the Absence of Epidemic Ribotype 027

PROVIDER: PRJEB19597 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1854840_1.fastq.gz	Fastqsanger.gz
	ERR1854840_2.fastq.gz	Fastqsanger.gz
	ERR1854841_1.fastq.gz	Fastqsanger.gz
	ERR1854841_2.fastq.gz	Fastqsanger.gz
	ERR1854842_1.fastq.gz	Fastqsanger.gz

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Microbiota-dependent IL-33 restricts the virulence of binary toxin expressing epidemic Clostridium difficile via ILC2s.

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.

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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.

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Project description:We used RNA-seq to conduct a genome-wide transcriptomic analysis of the C. difficile strain R20291 carrying the newly introduced M-OM-^UCD38-2 prophage. A total of 39 bacterial genes were differentially expressed in the R20291 lysogen, 26 of them being downregulated. Several of the regulated genes encode transcriptional regulators and PTS subunits involved in glucose, fructose and glucitol/sorbitol uptake and metabolism. Also of note, the presence of M-OM-^UCD38-2 upregulated the expression of a group of regulatory genes located in phi-027, a resident prophage common to most ribotype 027 isolates. The most differentially expressed gene was the conserved phase-variable cell wall protein CwpV, which was upregulated by about 20-fold in the lysogen. This is the first study describing the global response of C. difficile to the presence of a newly introduced prophage. Two strains (WT and lysogen) were subjected for RNA-seq analysis with two biological replicates each.

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