European study of Escherichia coli carrying blaNDM-5 based on national whole genome sequencing data from 13 European Union / European Economic Area countries, 2012-2022
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB61153 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR11256700.fastq.gz | Fastqsanger.gz | |||
| ERR11256800.fastq.gz | Fastqsanger.gz | |||
| ERR11257200_1.fastq.gz | Fastqsanger.gz | |||
| ERR11257200_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 1613 |
Similar Datasets
Project description:Escherichia coli ST131 carrying carbapenemase genes in the European Union/European Economic Area, August 2012 – May 2024
| PRJEB81860 | ENA
Project description:Resurgence of pertussis has been observed in many countries with high vaccination coverage and clonal expansion of certain Bordetella pertussis strains has been associated with recent epidemics in Europe. It is known that vaccinations have selected strains which are different from those used for vaccine production. However, little is known about the differences in genomic content of strains circulating before the vaccination was introduced. In this study, we compared the genomes of 39 vaccine strains and old clinical isolates collected from Finland (N=5), Poland (N=14), Serbia (N=10) and the UK (N=10). The analysis included genotyping, pulsed-field gel electrophoresis (PFGE) and comparative genomic hybridisation (CGH). Compared to the strain Tohama I, the European strains analyzed have lost three major regions of difference (RD3, 5 and 29). However, difference in frequency of the absent RDs 3, 5 or 29 was observed among the four countries. Of the strains with absent RD5, half had also a duplicated region in the genome. All four RDs (RD22, 23, 24 and 26) absent in Tohama I were present in majority of the tested strains. Results obtained from PFGE analysis correlated well with those of CGH. Recently a novel pertussis toxin promoter allele (ptxP3) was described. Strains with ptxP3 have replaced resident ptxP1 strains. When the recent strains (N=22) selected from the four countries were examined, the ptxP3 allele was found in all countries except Poland. Our result indicates that at least three clusters of B. pertussis circulated in Europe in pre-vaccine era and their genomes were distinct from that of the reference strain Tohama I. Although progressive gene loss occurs in B. pertussis population with time, difference in frequency of the lost genes were observed among the countries. The observed differences in genomic content might be vaccine-driven.
2011-10-04 | GSE29579 | GEO
Project description:Non-union skeletal fractures are characterized by their inability to heal six months after injury. Left untreated, the non-union fracture may cause advanced arthritis or loss of function in the affected limb. Arrays were used to identify the mechanisms that lead to lack of skeletal repair in non-unions. These profiles are the non-union callous samples pooled from five individuals Keywords: other
2003-07-16 | GSE494 | GEO
Project description:Resurgence of pertussis has been observed in many countries with high vaccination coverage and clonal expansion of certain Bordetella pertussis strains has been associated with recent epidemics in Europe. It is known that vaccinations have selected strains which are different from those used for vaccine production. However, little is known about the differences in genomic content of strains circulating before the vaccination was introduced. In this study, we compared the genomes of 39 vaccine strains and old clinical isolates collected from Finland (N=5), Poland (N=14), Serbia (N=10) and the UK (N=10). The analysis included genotyping, pulsed-field gel electrophoresis (PFGE) and comparative genomic hybridisation (CGH). Compared to the strain Tohama I, the European strains analyzed have lost three major regions of difference (RD3, 5 and 29). However, difference in frequency of the absent RDs 3, 5 or 29 was observed among the four countries. Of the strains with absent RD5, half had also a duplicated region in the genome. All four RDs (RD22, 23, 24 and 26) absent in Tohama I were present in majority of the tested strains. Results obtained from PFGE analysis correlated well with those of CGH. Recently a novel pertussis toxin promoter allele (ptxP3) was described. Strains with ptxP3 have replaced resident ptxP1 strains. When the recent strains (N=22) selected from the four countries were examined, the ptxP3 allele was found in all countries except Poland. Our result indicates that at least three clusters of B. pertussis circulated in Europe in pre-vaccine era and their genomes were distinct from that of the reference strain Tohama I. Although progressive gene loss occurs in B. pertussis population with time, difference in frequency of the lost genes were observed among the countries. The observed differences in genomic content might be vaccine-driven. The strains were serotyped for the fimbriae, genotyped with LightCycler RT-PCR for pertussis toxin subunit 1 (ptxA), pertussis toxin promoter (ptxP) (Kallonen et al 2011, unpublished data, submitted) and pertactin (prn). The vaccine and old strains were assigned to profiles according to the PFGE results. From every PFGE profile from all countries at least 1 strain was selected and tested for CGH. Altogether 29 strains were analysed with CGH from Poland, Serbia and the United Kingdom, 12, 7 and 10, respectively. In addition 5 old previously published Finnish strains were included in the analysis as well as the reference strain Tohama I (Heikkinen et al., 2007). The hybridisations were performed as previously described (Heikkinen et al., 2007). Microarray data analysis was performed with R/Bioconductor (R Development Core Team, 2008). Print-tip-loess normalization was performed with default parameters and the gains/losses were filtered with Limma package. The regions of difference (RDs) found in this study are presented with the nomenclature defined by Brinig et al. (2006). The RDs which were not described by Brinig et al are indicated by RDs and the consequent unused number.
2011-10-03 | E-GEOD-29579 | biostudies-arrayexpress
Project description:BackgroundEstimates of the economic burden of work injuries and diseases can help policymakers prioritize occupational health and safety policies and interventions in order to best allocate scarce resources. Several attempts have been made to estimate these economic burdens at the national level, but most have not included a comprehensive list of cost components, and none have attempted to implement a standard approach across several countries. The aim of our study is to develop a framework for estimating the economic burden of work injuries and diseases and implement it for selected European Union countries.MethodsWe develop an incidence cost framework using a bottom-up approach to estimate the societal burden of work injuries and diseases and implement it for five European Union countries. Three broad categories of costs are considered-direct healthcare, indirect productivity and intangible health-related quality of life costs. We begin with data on newly diagnosed work injuries and diseases from calendar year 2015. We consider lifetime costs for cases across all categories and incurred by all stakeholders. Sensitivity analysis is undertaken for key parameters.ResultsIndirect costs are the largest part of the economic burden, then direct costs and intangible costs. As a percentage of GDP, the highest overall costs are for Poland (10.4%), then Italy (6.7%), The Netherlands (3.6%), Germany (3.3%) and Finland (2.7%). The Netherlands has the highest per case costs (€75,342), then Italy (€58,411), Germany (€44,919), Finland (€43,069) and Poland (€38,918). Costs per working-age population are highest for Italy (€4956), then The Netherlands (€2930), Poland (€2793), Germany (€2527) and Finland (€2331).ConclusionsOur framework serves as a template for estimating the economic burden of work injuries and diseases across countries in the European Union and elsewhere. Results can assist policymakers with identifying health and safety priority areas based on the magnitude of components, particularly when stratified by key characteristics such as industry, injury/disease, age and sex. Case costing can serve as an input into the economic evaluation of prevention initiatives. Comparisons across countries provide insights into the relevant performance of health and safety systems.
| S-EPMC7789331 | biostudies-literature
Project description:Whole genome sequencing data of 874 Escherichia coli isolates carrying bla NDM-5 from 13 European Union/European Economic Area countries between 2012 and June 2022 showed the predominance of sequence types ST167, ST405, ST410, ST361 and ST648, and an increasing frequency of detection. Nearly a third (30.6%) of these isolates were associated with infections and more than half (58.2%) were predicted to be multidrug-resistant. Further spread of E. coli carrying bla NDM-5 would leave limited treatment options for serious E. coli infections.
| S-EPMC10176832 | biostudies-literature
Project description:A questionnaire survey of animal and human health authorities in Europe revealed that leishmaniases are not notifiable in all countries with autochthonous cases. Few countries implement surveillance and control targeting both animal and human infections. Leishmaniases are considered emergent diseases in most countries, and lack of resources is a challenge for control.
| S-EPMC8153892 | biostudies-literature
Project description:Exchange rate pass-through (ERPT) represents a degree to which changes in nominal exchange rates are transmitted into domestic prices. European Union (EU) countries have experienced the unprecedented inflationary pressure due to high geopolitical risk events. As such, understanding the ERPT plays a crucial role. This study provides a comprehensive and up-to-date analysis of ERPT to import prices for 16 EU countries from January 2006 to December 2022. Using the panel autoregressive distributed lag (ARDL) model, our findings confirm the linear, rather than nonlinear, ERPT pattern characterized by a diminishing trend over time in the EU countries. However, the degree of pass-through varies depending on country characteristics. Specifically, countries that are highly dependent on imports experience a larger ERPT. Furthermore, the degree of pass-through to import prices is more significant and persistent during periods of high uncertainty. These findings are robust across various robust analyses including sub periods. Our findings provide that help policymakers evaluate the trade-offs between exchange rate risks and macroeconomic stability during times of high uncertainty.
| S-EPMC11361579 | biostudies-literature
Project description:Metagenomes from soil of Union Glacier (Antarctica)
| PRJNA1067332 | ENA
Project description:Analysis of 594 isolates of Escherichia coli sequence type (ST)131 and its single locus variants carrying carbapenemase genes from 17 European Union/European Economic Area countries revealed acquisition of 18 carbapenemase variants, mainly in ST131 clades A and C. Most frequent were bla OXA-244 (n = 230) and bla OXA-48 (n = 224), detected in 14 and 12 countries, respectively. Isolates carrying bla OXA-244 have increased rapidly since 2021. The increasing detection of carbapenemase genes in the E. coli high-risk lineage ST131 is a public health concern.
| S-EPMC11583312 | biostudies-literature