Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
781
datasets available to search
ShareScore release 0.7.1
Dataset results
781 results for “Staphylococcus”
Genomics polymorphisms of Staphylococcus aureus strain NCTC 8325 in the lab stock maintained at TUM (WT), after 30 passes in BHI media (D) and after 30 passes detecting 4 -fold MIC increase to isocyanide -code I16- 3 biological replicates (A,B,C), and 3 independent colonies sequenced per replicate at the end of the experiment.
<p>Genomics polymorphisms of Staphylococcus aureus strain NCTC 8325 in the lab stock maintained at TUM (WT), after 30 passes in BHI media (D) and after 30 passes detecting 4 -fold MIC increase to isocyanide -code I16- 3 biological replicates (A,B,C), and 3 independent colonies sequenced per replicate at the end of the experiment. Determined from Illumina shotgun genomic sequencing datasets, mapping and analyses vs the reference genome of the strain https://www.ncbi.nlm.nih.gov/nuccore/NC_007795.1/</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>
Meta-Analysis on the Effect of Biopreservatives on Staphylococcus aureus in Cheese
<p>Recording of the talk “Meta-analysis on the effect of biopreservatives on <em>Staphylococcus aureus</em> in cheese” presented by Ursula Gonzales-Barron at the 71<sup>st</sup> Annual Meeting of the European Federation of Animal Science, EAAP, Online virtual meeting (1-4 Dec 2020).</p>
Meta-regression Models Describing the Effects of Essential Oils and Added Lactic Acid Bacteria on Staphylococcus aureus Inactivation in Cheese
<p>Recording of the talk “Meta-regression models describing the effects of essential oils and added lactic acid bacteria on <em>Staphylococcus aureus</em> inactivation in cheese”, presented by Beatriz Nunes Silva at the 2020 International Association for Food Protection Annual Meeting, IAFP, Online virtual meeting (26-28 Oct 2020).</p>
Figure 1 in Metal nanoparticles produced by plants with antibacterial properties against Staphylococcus aureus
Figure 1. Synthesis of metal nanoparticles using plant extracts.
Supervised Molecular Dynamics Movies from: Deciphering the molecular recognition mechanism of multidrug resistance Staphylococcus aureus NorA efflux pump using a Supervised Molecular Dynamics approach
<p>Molecular Recognition pathway of Supervised molecular dynamic simulations of MdfA-CLM NorA-CPX and NorA-CPX.</p>
Deciphering the molecular recognition mechanism of multidrug resistance Staphylococcus aureus NorA efflux pump using a Supervised Molecular Dynamics approach.
<p><strong>Legend of Movie-S1</strong></p> <p>The Movie is composed by four synchronized and animated panels that show different aspects of the SuMD simulation. The time evolution is reported in nanosecond. In the first panel (upper left), the molecular representation of the system is shown. The MdfA backbone is represented by the new cartoon style (cyan). The CLM is shown in yellow and by a transparent surface. The protein residues within 3 Å from the ligand are made explicit by a stick representation.</p> <p>In the second panel (upper-right), the CM-distance between the protein and the ligand centers of mass is reported.</p> <p>In the third panel (lower left), the MMGBSA energy profile is reported.</p> <p>In the fourth panel (lower-right) cumulative electrostatic interactions are reported for the 15 MdfA residues most contacted by CLM during the whole simulation.</p> <p> </p> <p><strong>Legend of Video-S2</strong></p> <p>The Movie shows the SuMD trajectory of CLM on MdfA compared to the CLM crystallographic pose. MdfA is represented in cyan new cartoon transparency. The crystallographic pose is showed in yellow while the experimental one in light green. At 16.69 ns a RMSD value of 1.77 Å is highlighted.</p> <p> </p> <p><strong>Legend of Video-S3</strong></p> <p>The Movie is composed by four synchronized and animated panels that show different aspects of the SuMD simulation. The time evolution is reported in nanosecond. In the first panel (upper left), the system is shown. The NorA backbone is represented by the new cartoon style (red) and the protein residues within 3 Å of CPX are showed in stick. CPX is rendered by a green stick.</p> <p>In the second panel (upper-right), the distance between the centre of mass of the ligand and the protein during the trajectory is reported.</p> <p>In the third panel (lower left), the MMGBSA energy profile is reported. In the fourth panel (lower-right) cumulative electrostatic interactions are reported for the 15 NorA residues most contacted by CPX during the whole SuMD trajectory.</p> <p>It is important to note that the following video has a duration that is half of the simulation of SuMD. However, this straid does not alter the description of the trajectory performed by the ligand.</p> <p> </p> <p><strong>Legend of Video-S4</strong></p> <p>The Movie depicts the clustering analysis of CPX during the whole SuMD simulation. The NorA protein is shown in red new cartoon transparency. CPX is rendered by a light-green stick and by a transparent surface. The spheres are shown in 7 different colours, according to the different clusters. Each sphere dimension is in according to the cluster dimensions. After a first recognition site, the ligand conformations are clustered in different sites of the NorA channel. It is important to note that the following video has a duration that is half of the simulation of SuMD. However, this straid does not alter the description of the trajectory performed by the ligand.</p>
A core genome MLST (cgMLST) scheme for Staphylococcus pseudintermedius
<p>A core-genome MLST scheme for <em>Staphylococcus pseudintermedius </em>was developed using chewBBACA version 2.8.5 (Silva et al, 2018) with default settings (https://github.com/B-UMMI/chewBBACA_tutorial). A training file was generated using Prodigal version 2.6.3 (Hyatt et al, 2010). The scheme was generated using 74 complete genomes and is comprised of 1,356 genes present in 99% of the genomes. cgMLST types were designated relative to conventional MLST sequence types. Phylogenetic trees from the chewBBACA allele calls were constructed using GrapeTree version 1.5.0 and the RapidNJ algorithm (Zhou et al, 2018).</p> <p>Due to format updates, two versions of the scheme are included: one usable with chewBBACA version 2.8.5, one updated for the most recent version in September 2024, version 3.3.10.</p> <p><strong>References:</strong></p> <p>- Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification. BMC Bioinformatics 2010;11:119. https://doi.org/10.1186/1471-2105-11-119. </p> <p><span>- Silva M, Machado MP, Silva DN, Rossi M, Moran-Gilad J, Santos S, et al. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. <em>Microb Genom</em> 2018;4:</span><span> </span>e000166<span> 10.1099/mgen.0.000166.</span></p> <p>- Zhou Z, Alikhan NF, Sergeant MJ, Luhmann N, Vaz C, Francisco AP, et al. GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens. <em>Genome Res</em> 2018;28(9):1395-404 10.1101/gr.232397.117.</p> <p> </p>
Genome assemblies of Staphylococcus pseudintermedius
<p>Supplementary Dataset to the manuscript "Global phylogenomic analysis of Staphylococcus pseudintermedius reveals genomic and prophage diversity in multi-drug resistant lineages", by Lucy F. Grist, Alice Brown, Noel Fitzpatrick, Giuseppina Mariano, Roberto M. La Ragione, Arnoud H. M. van Vliet and Jai W. Mehat.</p> <p>The dataset contains 2,276 genome assemblies of Staphylococcus pseudintermedius, combining three different types of data, made available here for open research purposes:</p> <ul> <li>Genome assemblies of 110 new UK isolates not previously available. These have also been uploaded into NCBI genome, and have a SCpseud_UoSXXX filename and the SRR code for NCBI SRA.</li> <li>Genome assemblies (1,144) obtained from the NCBI Genome repository, recognisable by the StaphpseudXXXX_GCA filenames</li> <li>Genome assemblies (1,022) generated from sequencing reads obtained from NCBI SRA and the ENA repositories, recognisable by the StaphpseudXXXX_SRR and StaphpseudXXXX_ERR filenames.</li> </ul> <p>Genomes were assembled using Shovill version 1.1.0 (https://github.com/tseemann/shovill) using the default settings and the Spades assembler. Only genomes with N50>50 kb, L50<20, and a number of contigs <200 were included in this study. </p>
Disturbing the spatial structure of biofilms affects the expression of agr regulated virulence factors in Staphylococcus aureus
<p><em>Staphylococcus aureus</em> uses quorum sensing and nutrient availability to control the expression of <em>agr</em>-regulated virulence factors. Quorum sensing is mediated by autoinducing peptide (AIP), which at high concentration, reduces expression of surface attachment proteins (<em>coa</em>, <em>fnbpA</em>), and increases expression of exotoxins (<em>lukS</em>) and proteases (<em>splA</em>). Nutrient availability can be sensed through the <em>saeS</em>/<em>saeR</em> system. Low nutrients increase expression of <em>saeR</em>, which augments expression of <em>coa</em> and <em>fnbpA</em> distinct from AIP. The formation of spatial structure, such as biofilms, can alter quorum sensing and nutrient acquisition. In natural environments, biofilms encounter forces that may alter their spatial structure. This may impact quorum sensing and/or nutrient acquisition, and thus affect the expression of <em>agr</em>-regulated virulence factors. However, this has not been studied. We show that periodically disturbing biofilms composed of <em>S. aureus</em> using a physical force affects the expression of <em>agr</em>-regulated virulence factors. In nutrient-poor environments, disturbance increased the expression of <em>coa</em>, <em>fnbpA</em>, <em>lukS</em>, and <em>splA</em>. Disturbance into a nutrient-rich environment at low or high disturbance amplitudes moderately reduced expression of <em>coa</em> and <em>fnbpA</em> but increased expression of <em>lukS</em> and <em>splA</em>. Interestingly, at an intermediate amplitude, the overall expression of <em>agr-</em>regulated virulence factors was the lowest; expression of <em>lukS</em> and <em>splA</em> remained unchanged relative to an undisturbed biofilm while expression of <em>coa</em> and <em>fnbpA</em> significantly decreased. We hypothesize that these changes are a result of disturbance-driven changes in access to AIP and nutrients. Our results may allow the identification of environments where virulence is enhanced, or reduced, owing to disturbance.</p>
Data for: Copper ions inhibit pentose phosphate pathway function in Staphylococcus aureus
<p>To gain a better insight of how Cu ions toxify cells, metabolomic analyses were performed in <em>S. aureus</em> strains that lack the described Cu ion detoxification systems (ΔcopBL <em>ΔcopAZ</em>; <em>cop<sup>-</sup></em>). Exposure of the <em>cop<sup>-</sup></em> strain to Cu(II) resulted in an increase in the concentrations of metabolites utilized to synthesize phosphoribosyl diphosphate (PRPP). PRPP is created using the enzyme phosphoribosylpyrophosphate synthetase (Prs) which catalyzes the interconversion of ATP and ribose 5-phosphate to PRPP and AMP. Supplementing growth medium with metabolites requiring PRPP for synthesis improved growth in the presence of Cu(II). A suppressor screen revealed that a strain with a lesion in the gene coding adenine phosphoribosyltransferase (<em>apt</em>) was more resistant to Cu. Apt catalyzes the conversion of adenine with PRPP to AMP. The <em>apt</em> mutant had an increased pool of adenine suggesting that the PRPP pool was being redirected. Over-production of <em>apt</em>, or alternate enzymes that utilize PRPP, increased sensitivity to Cu(II). Increasing or decreasing expression of <em>prs</em> resulted in decreased and increased sensitivity to growth in the presence of Cu(II), respectively. We demonstrate that Prs is inhibited by Cu ions <em>in</em> <em>vivo</em> and <em>in vitro</em> and that treatment of cells with Cu(II) results in decreased PRPP levels. Lastly, we establish that <em>S. aureus</em> that lacks the ability to remove Cu ions from the cytosol is defective in colonizing the airway in a murine model of acute pneumonia, as well as the skin. The data presented are consistent with a model wherein Cu ions inhibits pentose phosphate pathway function and are used by the immune system to prevent<em> S. aureus</em> infections.</p>
Figure 8: Theoretical Prediction of Oxacillin Resistance in Staphylococcus Aureus 2020-2030
<p><strong>Figure 8: Theoretical Prediction of Oxacillin Resistance in Staphylococcus Aureus 2020-2030 </strong></p> <p> </p>
Cystic fibrosis autoantibody signatures associate with Staphylococcus aureus lung infection or cystic fibrosis-related diabetes
<p>While cystic fibrosis (CF) lung disease is characterized by persistent inflammation and infections, and chronic inflammatory diseases are often accompanied by autoimmunity, autooimmune reactivity in CF has not been studied in depth. In this work, we undertook an unbiased approach to explore the systemic autoantibody repertoire in CF. Our results show higher levels of several new autoantibodies in the blood of people with CF (PwCF) compared to control subjects. Some of these are IgA autoantibodies targeting neutrophil components or autoantigens linked to neutrophil-mediated tissue damage in CF. We also found that PwCF with higher systemic IgM autoantibody levels have lower prevalence of <em>S. aureus</em> infection. On the other hand, IgM autoantibody levels in <em>S. aureus</em>-infected PwCF correlate with lung disease severity. Diabetic PwCF have significantly higher levels of IgA autoantibodies in their circulation compared to nondiabetic PwCF, and several of their IgM autoantibodies are associated with worse lung disease. In contrast, in nondiabetic PwCF blood levels of IgA autoantibodies correlate with lung disease. We have also identified other autoantibodies in CF that are associated with <em>P. aeruginosa</em> airway infection. In summary, we have identified several new autoantibodies and associations of autoantibody signatures with specific clinical features in CF.</p>
Data for A Far-Red Fluorescent Probe to Visualize Staphylococcus aureus in Patient Samples
<p>Raw and processed data supporting the manuscript "A Far-Red Fluorescent Probe to Visualize <em>Staphylococcus aureus</em> in Patient Samples"</p>
Airway environment drives the selection of quorum sensing mutants and promote Staphylococcus aureus chronic lifestyle
<p>Sequence data linked to the manuscript "Airway environment drives the selection of quorum sensing mutants and promote <em>Staph</em><em>ylococcus</em><em> aureus</em> chronic lifestyle"</p> <p>- Shotgun metagenomic from sputa of Patients A B C H J</p> <p>- 10 hemolytic and 10 non-hemolytic isolates from competition assays at day 5</p>
Adjunctive Fosfomycin for Treatment of Staphylococcus Aureus Bacteraemia
ClinicalTrials.gov study NCT06695832. IPD Sharing: YES. Countries: 3. Publications: 21.
Persistent Methicillin Resistant Staphylococcus Aureus Eradication Protocol (PMEP)
ClinicalTrials.gov study NCT01594827. IPD Sharing: NO. Countries: 1. Publications: 4.
Methicillin-resistant Staphylococcus Aureus (MRSA) Skin and Soft Tissue Infection (SSTI) Prevention in Military Trainees
ClinicalTrials.gov study NCT01105767. IPD Sharing: Not stated. Countries: 1. Publications: 8.
Comparison of Telavancin and Vancomycin for Hospital-acquired Pneumonia Due to Methicillin-resistant Staphylococcus Aureus
ClinicalTrials.gov study NCT00124020. IPD Sharing: Not stated. Countries: 1. Publications: 3.
The Impact of Treating Staphylococcus Aureus Infection and Colonization on the Clinical Severity of Atopic Dermatitis
ClinicalTrials.gov study NCT00179959. IPD Sharing: Not stated. Countries: 1. Publications: 1.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.