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33 results for “beta lactamase”
Beta-lactamase Trajectory Data
<p>Processed Beta-lactamase trajectories from Gromacs. PBC corrected, alpha carbon only. Matrix produced from JEDi software. Used in related work. </p>
Imipenem hydrolysis by the L1 and the NDM-1 metallo-beta-lactamases: QM/MM structures of the stationary points
<p>Stationary points (transition states and minima) for the hydrolysis reactions of the imipenem in the active sites of the L1 and NDM-1 metallo-beta-lactamases. The reactions occure in three elementary steps each. For the NDM-1 there are two compeeting pathways leading to the different products. Enamine and imine forms of the hydrolyzed imipenem may form and those are marked with "N" and "C", respectively, according to the atom being protonated at the last step. Structures are calculated at the QM(PBE0-D3/6-31G**)/MM(AMBER) level.</p>
Beta-Lactamase X-ray diffraction data recorded at Diamond Light Source I04 as part of commissioning & development
<p>X-ray diffraction data from crystals of beta-lactamase recorded during commissioning. The data were recorded in two omega scans of 3600 images @ 0.1 degrees / frame with different kappa and phi settings on a mini kappa device, with a Dectris PILATUS2 6M detector, at a wavelength of 1.239850A (10keV) for remote-SAD on the native Zn site.</p> <p> </p> <p>Data uploaded for education and tutorial purposes as a good quality example set using multi-axis geometry. </p> <p> </p> <p>For convenience the data are compressed with gzip and combined into one tar file for each sweep.</p>
Data Source file for manuscript: Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients
<p>ABSTRACT</p><p>Infections caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-PE) are associated with excess morbidity and mortality. Despite recognition of this immediate impact on human health, essential aspects of their molecular epidemiology remain under-investigated. This includes knowledge on the potential of a particular strain to persist in a host, mutational events during colonization, and the genetic diversity in individual patients over time. To investigate long-term genetic diversity of colonizing and infecting ESBL-producing <i>Klebsiella pneumoniae </i>species complex and ESBL-<i>Escherichia coli</i> in individual patients over time, we conducted performed a ten-year longitudinal retrospective study and extracted clinical and microbiological data from electronic health records. In this investigation, 76 ESBL-<i>K. pneumoniae</i> species complex and 284 ESBL-<i>E. coli</i> isolates were recovered from 19 and 61 patients. Strain persistence was detected in all patients colonized with ESBL-<i>K. pneumoniae </i>species complex, and 83.6% of patients colonized with ES BL-<i>E. coli</i>. Antimicrobial resistance genes, plasmid replicons, and whole ESBL-plasmids were shared between isolates regardless of chromosomal relatedness. Our study suggests that patients colonized with ESBL-producers may act as durable reservoirs for ongoing transmission of ESBLs, and that they are at a prolonged risk of recurrent infection with colonizing strains.</p><p>DATA SOURCE FILE</p><p>In this Data Source file, you will find access to the raw data, metadata and results obtained during the study: "Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients". Data is organized following the structure of Figures/Tables of the manuscript and Supplementary Material. Additional figures not included in the main manuscript nor in the Supplementary Material are also available.</p><p>All sequencing and sample data from this study can be accessed at the NCBI database under the BioProject number PRJNA910977: <a href="http://dataview.ncbi.nlm.nih.gov/object/PRJNA910977">http://dataview.ncbi.nlm.nih.gov/object/PRJNA910977. </a>No new software was developed during this study. Standard bioinformatics software was used and the commands used can be accessed at the Supplementary Information file.</p>
Computer-Aided Drug Design (CADD): To Screen Potential Antibiotics Against Klebsiella Pneumoniae Beta-Lactamase Enzyme
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Data for "Functional Dynamics of Substrate Recognition in TEM Beta-Lactamase"
<p>Molecular dynamics data associated with the publication: "Functional Dynamics of Substrate Recognition in TEM Beta-Lactamase"</p> <p>Trajectores were generated in GROMACS, and the carbon alpha coordinates were extracted and aligned with the JEDi analysis software. Details of the simulations and analysis are given in the publication.</p> <p>Data in apo.zip contains trajectories for 32 total trajectories of TEM-1, TEM-2, TEM-10, and TEM-52 beta-lactamase, each starting form different 8 crystal structures</p> <p>Data in holo.zip contains 16 trajectories of TEM-1, TEM-2, TEM-10, and TEM-52 beta-lactamase in complex with ampicillin, amoxicillin, cefotaxime, and ceftazidime each.</p> <p>Trajectories files are in comma delimited format, with rows representing degrees for freedom (789 total), and columns representing samples (10000 per trajectory file).</p> <p>Supervised Projective Learning for Orthogonal Completeness (SPLOC) software for analysis as performed in the publication can be found at: https://github.com/BioMolecularPhysicsGroup-UNCC/MachineLearning/tree/master/SPLOC </p>
Reprocessed / rebinned to 0.5 degree images: Beta-Lactamase X-ray diffraction data recorded at Diamond Light Source I04 as part of commissioning & development
<p>Derived from https://zenodo.org/record/841060; made more compact (though no longer "raw" data) for use in tutorials</p>
Pathogenic potential and the role of clones and plasmids in beta-lactamase-producing E. coli from chicken faeces in Vietnam
<p>Raw data used to present figures and tables in the manuscript.</p>
Supplementary data for "The fitness of beta-lactamase mutants depends nonlinearly on resistance level at sublethal antibiotic concentrations."
<p>Supplementary data files and scripts, notes and figures accompanying the manuscript with working title "The fitness of beta-lactamase mutants depends nonlinearly on resistance level at sublethal antibiotic concentrations". The figures and tables this dataset underpins is indicated in the name of each file of the dataset, or in the section "Code and data accessibility" of the manuscript.</p>
Urinary Tract Infection Due to Beta-lactamase-producing Enterobacteriaceae in Children
ClinicalTrials.gov study NCT02832258. IPD Sharing: NO. Countries: 1. Publications: 7.
Extended Tricyle Project Indonesia for Extended-spectrum Beta-lactamase Positive Klebsiella Pneumoniae and Escherichia Coli
ClinicalTrials.gov study NCT07106944. IPD Sharing: UNDECIDED. Countries: 0. Publications: 1.
International Travel and the Spread of Extended-spectrum Beta-lactamase-producing Escherichia Coli
ClinicalTrials.gov study NCT01296165. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Ceftolozane/Tazobactam Versus Meropenem for Febrile Neutropenia on Patients Colonized With or at Risk for Infection With Extended Spectrum Beta Lactamase - Producing Pathogens
ClinicalTrials.gov study NCT06342115. IPD Sharing: NO. Countries: 1. Publications: 16.
Impact of Specific Antimicrobials and MIC Values on the Outcome of Bloodstream Infections Due to Extended-spectrum Beta-lactamase (ESBL) or Carbapenemase-producing Enterobacteriaceae: an Observational
ClinicalTrials.gov study NCT01764490. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Quantifying antibiotic impact on within-patient dynamics of extended-spectrum beta-lactamase resistance
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A dataset for establishing a machine learning-based QSAR model to screen beta-lactamase inhibitors using the FARM -BIOMOL chemical library
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Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes
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Enzyme-inhibitor complexes of unithiol with metallo-beta-lactamases and a NDM1-meropenem enzyme-substrate complex
<p>Gemetry configurations obtained at the QM(PBE0-D3/(6-31G**+LANL2DZ(Zn)))/MM(CHARMM) level of theory.</p> <p> </p>
Piperacillin-tazobactam and Temocillin as Carbapenem-alternatives for the Treatment of Severe Infections Due to Extended-spectrum Beta-lactamase-Producing Gram-negative Enterobacteriaceae in the Inten
ClinicalTrials.gov study NCT05565222. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Urinary Tract Infections Caused by Extended-spectrum Beta-lactamase-producing Enterobacteria
ClinicalTrials.gov study NCT06910878. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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