Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tracing the spread of Clostridium difficile ribotype 027 in Germany

ABSTRACT: Tracing the spread of Clostridium difficile ribotype 027 in Germany based on bacterial genome sequences

PROVIDER: PRJEB9067 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR928220_1.fastq.gz	Fastqsanger.gz
	ERR928220_2.fastq.gz	Fastqsanger.gz
	ERR928221_1.fastq.gz	Fastqsanger.gz
	ERR928221_2.fastq.gz	Fastqsanger.gz
	ERR928222_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 188

Similar Datasets

Clostridium difficile ribotype 027 resequencing

Project description:Clostridium difficile ribotype 027 resequencing

| PRJEB2207 | ENA

Clostridium difficile ribotype 027 project

Project description:Clostridium difficile ribotype 027 project

| PRJEB2134 | ENA

Tracing the Spread of Clostridium difficile Ribotype 027 in Germany Based on Bacterial Genome Sequences.

Project description:We applied whole-genome sequencing to reconstruct the spatial and temporal dynamics underpinning the expansion of Clostridium difficile ribotype 027 in Germany. Based on re-sequencing of genomes from 57 clinical C. difficile isolates, which had been collected from hospitalized patients at 36 locations throughout Germany between 1990 and 2012, we demonstrate that C. difficile genomes have accumulated sequence variation sufficiently fast to document the pathogen's spread at a regional scale. We detected both previously described lineages of fluoroquinolone-resistant C. difficile ribotype 027, FQR1 and FQR2. Using Bayesian phylogeographic analyses, we show that fluoroquinolone-resistant C. difficile 027 was imported into Germany at least four times, that it had been widely disseminated across multiple federal states even before the first outbreak was noted in 2007, and that it has continued to spread since.

| S-EPMC4596877 | biostudies-literature

C. difficile Ribotype 027 Outbreak in Bern, Switzerland

Project description:C. difficile Ribotype 027 Outbreak in Bern, Switzerland

| PRJEB37809 | ENA

WGS of Clostridioides (Clostridium) difficile ribotype 027

Project description:Molecular characterization of an outbreak of Clostridioides (Clostridium) difficile ribotype 027

| PRJEB30088 | ENA

The largely unnoticed spread of <i>Clostridioides difficile</i> PCR ribotype 027 in Germany after 2010.

Project description:In recent decades, incidence and severity of Clostridioides difficile infection (CDI) has increased dramatically, coinciding with the emergence of hypervirulent strains such as PCR ribotype 027 (RT027). Data on prevalence of distinct C. difficile strains in random CDI cases in Germany are scarce. The aim of this review was to obtain an overview of prevalence and geographical distribution of RT027 among clinical C. difficile isolates from random cases in non-outbreak settings in hospitals in Germany. For this purpose, we performed a literature review on reported cases of C. difficile RT027 in Germany between 2007 and 2019 in three databases (PubMed, Embase and LIVIVO) and conference proceedings. Studies with selection bias for RT027 (e.g. clinical severity, outbreak reports) were excluded. A total of 304 records were screened, from which 21 were included in this analysis. The nationwide prevalence of RT027 in Germany was <1% prior to 2010 but increased continuously thereafter, reaching 21.7% in 2013. The regional prevalence varied markedly between federal states, higher prevalence was reported from North Rhine-Westphalia (37.4%) and Saxony (31.8%) in 2013-2015. However, data on C. difficile RT027 were not available from almost half of the federal states and were scarce at the national level. Our data suggest a remarkable spread of RT027 in Germany during the past decade, which has remained rather unnoticed so far. A national program for molecular surveillance of C. difficile is required to monitor the changing epidemiology of CDI and to adjust the prevention and control measures.

| S-EPMC8336157 | biostudies-literature

Comparative genomic hybridization of Clostridium difficile strains to identify markers of different ribotypes

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

cdiff 027 tagged pools

Project description:Microevolution of hypervirulent clade and ribotype 027 C. difficile isolates

| PRJEB2039 | ENA

Exoproteomic analysis of two MLST clade 2 strains of Clostridioides difficile from Latin America

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

Surface layer protein A variant of Clostridium difficile PCR-ribotype 027.

Project description: Not available

| S-EPMC3204749 | biostudies-literature