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116 results for “Enterococcus”
mGEMS Enterococcus faecalis reference dataset
<p>This dataset contains the <em>E. faecalis</em> sequences (all available assemblies from the NCBI as of 2 February 2020 which could be assigned to a multilocus sequence type), their multilocus sequence types inferred with the mlst software (v2.18.1) using the MLST scheme described in <a href="https://doi.org/10.1128/JCM.02596-05">10.1128/JCM.02596-05</a>, and accession numbers used in the mGEMS publication as the reference dataset.</p>
Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteremia.
<p>Insertion sequences (ISs) and other transposable elements are associated with the mobilization of antibiotic resistance determinants and the modulation of pathogenic characteristics. In this work, we aimed to investigate the association between ISs and antibiotic resistance genes, and their role in dissemination and modification of the antibiotic resistant phenotype. To that end, we leveraged fully resolved <em>Enterococcus faecium</em> and <em>Enterococcus faecalis</em> genomes of isolates collected over five days from an inpatient with prolonged bacteremia. Isolates from both species harbored similar IS family content but showed significant species-dependent differences in copy number and arrangements of ISs throughout their replicons. Here, we describe two inter-specific IS-mediated recombination events and IS-mediated excision events in plasmids of <em>E. faecium</em> isolates. We also characterize a novel arrangement of the ISs in a Tn1546-like transposon in <em>E. faecalis</em> isolates likely implicated in a vancomycin genotype-phenotype discrepancy. Furthermore, an extended analysis revealed a novel association between daptomycin resistance mutations in <em>liaSR</em> genes and a putative composite transposon in<em> E. faecium</em>, offering a new paradigm for the study of daptomycin resistance and novel insights into the dissemination of daptomycin resistance. In conclusion, our study highlights the role ISs and other transposable elements play in the rapid adaptation and response to clinically relevant stresses such as aggressive antibiotic treatment in enterococci.</p>
Diet-induced changes in the jejunal microbiota of developing broilers reduce the abundance of Enterococcus hirae and Enterococcus faecium
<p>This ready to load <strong>phyloseq </strong>R S4 object contains the OTU table, taxonomy table and sample metadata. This data was build using kraken v2.1.2, kraken-biom v1.0.1 and phyloseq version 1.4. Sequencing data is deposited at NCBI-SRA under BioProject: PRJNA952340. </p><p> </p><p><strong>Study abstract</strong></p><p>Paul B. Stege, Dirkjan Schokker, Frank Harders, Soumya K. Kar, Norbert Stockhofe, Vera Perricone, Johanna M. J. Rebel, Ingrid C. de Jong, Alex Bossers </p><p> </p><p>Modern broiler breeds allow for high feed efficiency and rapid growth, which come at a cost of increased susceptibility to pathogens and disease. Broiler growth rate, feed efficiency, and health are affected by the composition of the gut microbiota, which in turn is influenced by diet. In this study, we therefore assessed how diet composition can affect the broiler jejunal gut microbiota. A total of 96 broiler chickens were divided into four diet groups: control, coated butyrate supplementation, medium-chain fatty acid supplementation, or a high-fibre low-protein content. Diet groups were sub-divided into age groups (4, 12 and 33 days of age) resulting in groups of 8 broilers per diet per age. The jejunum content was used for metagenomic shotgun sequencing to determine the microbiota taxonomic composition at species level. The composed diets resulted in a total of 104 differentially abundant bacterial species. Most notably were the butyrate-induced changes in the jejunal microbiota of broilers 4 days post-hatch, resulting in the reduced relative abundance of mainly <i>Enterococcus</i> <i>faecium</i> and the opportunistic pathogen <i>Enterococcus</i> <i>hirae</i>, when compared to the control diet. This effect takes place during early broiler development, which is critical for broiler health, thus exemplifying the importance of how diet can influence the microbiota composition and its relation to broiler health. Future studies should therefore elucidate how diet can be used to promote a beneficial microbiota in the early stages of broiler development.</p>
Data from: Antimicrobial resistance of Staphylococcus and Enterococcus bacteria in rural dogs in Hungary - a preliminary report
<p><span>Antimicrobial resistance (AMR) is one of the most relevant health challenges globally. Since resistant bacteria and their resistance genes circulate through the ecosystem, AMR is among the main focuses of One Health. Dogs are the best friends of humans, therefore their relationships with the owners are mostly very close. This connection can make the dogs vehicles of AMR between the environment and humans. Based on this hypothesis, we investigated faecal samples from 37 dogs in Inner Somogy, Hungary. We isolated and investigated for antibiotic susceptibility 21 and 6 strains of <em>Staphylococcus</em> and <em>Enterococcus</em> genera, respectively. Among staphylococci and enterococci, 12 and 3 strains proved to be resistant to at least one antibiotic. Multidrug resistant strains were detected only among coagulase negative staphylococci, mainly in <em>S. sciuri</em> species. The antibiotics that proved to be inefficient against the most strains were benzylpenicillin (8 strains), moxifloxacin (6 strains), clindamycin (5 <em>S. sciuri</em> strains), and fusidic acid (12 strains). In the case of moxifloxacin and fusidic acid, the MIC excessed the EUCAST clinical breakpoint. Analysing the epidemiological background of the animals, outdoors keeping and higher income level of the owners seemed risk factors of AMR carrying, though the sample size of this study could not confirm statistically the apparent interdependence.</span></p>
Genomic surveillance of Enterococcus faecalis in South Africa
<p>efaecalis_raw_reads.tar.gz <br>- Tar of Illumina raw reads from E. faecalis isolates S92, S101, S109, S111, S116, S119, S121, S131, S134.</p> <p>public_efaecalis_genomes.txt<br>- A list of genome ncbi accessions used in the study.</p>
Draft Genome Sequences of Two Bacteriocin-Producing Enterococcus faecium Strains Isolated from Nonfermented Animal Foods in Spain
<p>Raw sequences of two bacteriocin-producing Enterococcus faecium.</p> <p> </p>
Figure 6: Theoretical Prediction of Ampicillin Resistance in Enterococcus faecium (2020-2030)
<p><strong>Figure 6: Theoretical Prediction of Ampicillin Resistance in Enterococcus faecium (2020-2030)</strong></p> <p> </p>
Antibiotic interactions shape short-term evolution of resistance in Enterococcus faecalis
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Core SNP multiple alignments composed by L. garvieae, L. lactis, Streptococcus and Enterococcus strains.
<p>Core SNP multiple alignments composed by L. garvieae, L. lactis, Streptococcus and Enterococcus strains.</p>
Oral cholestyramine prevents the enrichment of diverse daptomycin-resistance mutations in intestinal Enterococcus faecium populations
<p><em><strong>Background and Objectives</strong></em>: Previously, we showed proof-of-concept in a mouse model that oral administration of cholestyramine prevented enrichment of daptomycin-resistant <em>Enterococcus faecium</em> in the gastrointestinal (GI) tract during daptomycin therapy. Cholestyramine binds daptomycin in the gut, which removes daptomycin selection pressure and so prevents the enrichment of resistant clones. Here, we investigated two open questions related to this approach: 1) can cholestyramine prevent the enrichment of diverse daptomycin mutations emerging <em>de novo</em> in the gut? 2) how does the timing of cholestyramine administration impact its ability to suppress resistance?</p> <p><em><strong>Methodology</strong></em>: Mice with GI <em>E. faecium</em> were treated with daptomycin with or without cholestyramine, and <em>E. faecium</em> was cultured from feces to measure changes in daptomycin susceptibility. A subset of clones was sequenced to investigate the genomic basis of daptomycin resistance.</p> <p><em><strong>Results</strong></em>: Cholestyramine prevented the enrichment of diverse resistance mutations that emerged de novo in daptomycin-treated mice. Whole-genome sequencing revealed that resistance emerged through multiple genetic pathways, with most candidate resistance mutations observed in the clsA gene. Additionally, we observed that cholestyramine was most effective when administration started prior to the first dose of daptomycin. However, beginning cholestyramine after the first daptomycin dose reduced the frequency of resistant <em>E. faecium</em> compared to not using cholestyramine at all.</p> <p><em><strong>Conclusions and Implications</strong></em>: Cholestyramine prevented the enrichment of diverse daptomycin-resistance mutations in intestinal <em>E. faecium</em> populations during daptomycin treatment, and it is a promising tool for managing transmission of daptomycin-resistant <em>E. faecium</em>.</p>
Figure 4: Antibiotic sensitivity and resistance pattern of Enterococcus faecium
<p><strong>Figure 4: Antibiotic sensitivity and resistance pattern of Enterococcus faecium</strong></p>
Figure 5: Theoretical Prediction of Vancomycin Resistance in Enterococcus faecium(2020-2030)
<p><strong>Figure 5: Theoretical Prediction of Vancomycin Resistance in Enterococcus faecium(2020-2030)</strong></p> <p> </p>
Characterization of Enterococcus Faecalis Endocarditis and Impact of Amoxicillin MIC Elevation on Patient Outcome
ClinicalTrials.gov study NCT05530837. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Carbapenemase-Producing Organism and Vancomycin-Resistant Enterococcus Management
ClinicalTrials.gov study NCT05200546. IPD Sharing: NO. Countries: 1. Publications: 6.
Combination Treatment for Enterococcus Faecalis Bacteriemia Multicenter, Observational Study"
ClinicalTrials.gov study NCT04070820. IPD Sharing: NO. Countries: 1. Publications: 21.
Impact of Probiotic Regimen on Vancomycin Resistant Enterococcus Intestinal Carriage
ClinicalTrials.gov study NCT00437580. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Phenotypic and Genotypic Variations of Enterococcus Spp
ClinicalTrials.gov study NCT05751317. IPD Sharing: NO. Countries: 1. Publications: 1.
Effect of Live Combined Bifidobacterium,Lactobacillus and Enterococcus Capsules on Oral Mucositis in Nasopharyngeal Carcinoma Patients Receiving Radiotherapy.
ClinicalTrials.gov study NCT03112837. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
The Influence of Probiotics on Vancomycin-Resistant Enterococcus
ClinicalTrials.gov study NCT00591474. IPD Sharing: Not stated. Countries: 1. Publications: 40.
Data from: Prevalence of vancomycin-variable Enterococcus faecium (VVE) among vanA-positive sterile site isolates and patient factors associated with VVE bacteremia
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.