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174
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ShareScore release 0.9.0
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174 results for “Klebsiella”
RNA_Seq of recipients mice with Klebsiella and Lactobacillus
GEO Series GSE185601. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Causality of gut bacteria Klebsiella pneumoniae to hypertension development
GEO Series GSE184584. Mus musculus. 13 samples. Type: Expression profiling by high throughput sequencing.
Subinhibitory Concentrations of Antibiotics Alter the Response of Klebsiella pneumoniae to Components of Innate Host Defense
GEO Series GSE201383. Klebsiella pneumoniae. 18 samples. Type: Expression profiling by high throughput sequencing.
Dataset related to article "The Long Pentraxin PTX3 Controls Klebsiella Pneumoniae Severe Infection "
<p>This record contains raw data related to article “The Long Pentraxin PTX3 Controls <em>Klebsiella Pneumoniae</em> Severe Infection"</p> <p><em>Klebsiella pneumoniae</em> is a common pathogen in human sepsis. The emergence of multidrug-resistant <em>K. pneumoniae</em> strains represents a major clinical challenge in nosocomial and community acquired infections. The long pentraxin PTX3, a key component of humoral innate immunity, is involved in resistance to selected pathogens by promoting opsonophagocytosis. We investigated the relevance of PTX3 in innate immunity against <em>K. pneumoniae</em> infections using <em>Ptx3</em> <sup>-/-</sup> mice and mouse models of severe <em>K. pneumoniae</em> infections. Local and systemic PTX3 expression was induced following <em>K. pneumoniae</em> pulmonary infection, in association with the up-regulation of TNF-α and IL-1β. PTX3 deficiency in mice was associated with higher bacterial burden and mortality, release of pro-inflammatory cytokines as well as IL-10 in the lung and systemically. The analysis of the mechanisms responsible of PTX3-dependent control of <em>K. pneumoniae</em> infection revealed that PTX3 did not interact with <em>K. pneumoniae</em>, or promote opsonophagocytosis. The comparison of susceptibility of wild-type, <em>Ptx3<sup>-/-</sup>, C3<sup>-/-</sup></em> and <em>Ptx3<sup>-/-</sup></em> /<em>C3<sup>-/-</sup></em> mice to the infection showed that PTX3 acted in a complement-independent manner. Lung histopathological analysis showed more severe lesions in <em>Ptx3</em> <sup>-/-</sup> mice with fibrinosuppurative, necrotizing and haemorrhagic bronchopneumonia, associated with increased fibrin deposition in the lung and circulating fibrinogen consumption. These findings indicate that PTX3 contributes to the control of <em>K. pneumoniae</em> infection by modulating inflammatory responses and tissue damage. Thus, this study emphasizes the relevance of the role of PTX3 as regulator of inflammation and orchestrator of tissue repair in innate responses to infections</p>
Wzi regulates host innate immunity to promote Klebsiella pneumoniae survival in a CPS-dependent and -independent manner
GEO Series GSE286873. Mus musculus. 13 samples. Type: Expression profiling by high throughput sequencing.
Whole transcriptomic analysis of mechanisms of tolerance and resistance to chlorhexidine in carbapenemase-producing Klebsiella pneumoniae clinical strains
GEO Series GSE147316. Klebsiella pneumoniae. 16 samples. Type: Expression profiling by high throughput sequencing.
Understanding resistance to polymyxin and amikacin in Klebsiella pneumoniae
GEO Series GSE264574. Klebsiella pneumoniae. 6 samples. Type: Expression profiling by high throughput sequencing.
Bdellovibrio RNA seqence (Klebsiella pneumoniae)
GEO Series GSE112863. Bdellovibrio bacteriovorus HD100. 21 samples. Type: Expression profiling by high throughput sequencing.
RmpA as a Global Regulator Modulates Switching Between Hypermucoviscosity and Biofilm in Hypervirulent Klebsiella pneumoniae [RNA-seq]
GEO Series GSE286114. Escherichia coli; Klebsiella pneumoniae. 12 samples. Type: Expression profiling by high throughput sequencing.
Causality of gut bacteria Klebsiella pneumoniae to hypertension development II
GEO Series GSE209720. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
Neutrophil Extracellular Trap-borne C3-Driven Endothelial Dysfunction in Klebsiella pneumoniae Liver Abscess
GEO Series GSE288691. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Human umbilical cord MSCs prime monocytes to recruit and activate eosinophils for enhanced host defence against Klebsiella pneumoniae
GEO Series GSE298453. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
RmpA as a Global Regulator Modulates Switching Between Hypermucoviscosity and Biofilm in Hypervirulent Klebsiella pneumoniae [ChIP-seq]
GEO Series GSE286111. Klebsiella pneumoniae. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Development of cgMLST schemes for Klebsiella oxytoca and Klebsiella planticola species complexes
<p>Core genome multi-locus sequence typing (cgMLST) provides a high level of resolution typing among bacterial populations. Two novel cgMLST schemes have been implemented for <em>Klebsiella oxytoca</em> and <em>Klebsiella </em>(<em>Raoultella</em>) <em>planticola</em> species complexes (KoSC and KplaSC), ubiquitous bacteria broadly responsible for clinical and community-acquired infections, to investigate on population structure with enhanced resolution over conventional MLST analysis.</p> <p><strong>Dataset screening</strong></p> <p>Public genomes have been downloaded from the NCBI genome repository representing the overall population of KoSC (<em>K. oxytoca</em>, <em>K. michiganensis</em>, <em>K. grimontii </em>and <em>K. pasteurii</em>) and KplaSC (<em>K. planticola </em>and <em>K. ornithynolitica</em>) isolated worldwide. Eight strains from the Collection of Institut Pasteur (CIP, Paris, France) (n=1 <em>K. planticola</em>, n=2 <em>K. ornithynolitica </em>for KplaSC; n=1 <em>K. oxytoca</em>, n=1 <em>K. michiganensis</em>, n=2 <em>K. grimontii </em>and n=1 <em>K. pasteurii </em>for KoSC), and six <em>K. oxytoca </em>reference strains (ATCC<sup>®</sup> 700324<sup>™</sup>, ATCC<sup>®</sup> 13182<sup>™</sup>, ATCC<sup>®</sup> 49131<sup>™</sup>, ATCC<sup>®</sup> 51983<sup>™</sup>, ATCC<sup>®</sup> 13030<sup>™</sup> and ATCC<sup>®</sup> BAA-3059<sup>™</sup>; retrieved at https://www.atcc.org/) were further included in the public dataset. A first screening of public genomes was carried out based on assemblies’ quality metrics, by filtering out sequences with more than 500 contigs, total genome size outside the typical length of <em>Klebsiella</em> spp. (<4.5 Mb and >6.5 Mb) and N50 lower than 30000. Strains with mixed species as calculated by the ribosomal MLST based species identification tool (https://pubmlst.org/species-id) were also excluded. The remaining assemblies were then clustered together with KoSC and KplaSC genomes isolated from artisanal food productions (dataset available at <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB56668">https://www.ebi.ac.uk/ena/browser/view/PRJEB56668</a>) based on pairwise MASH-based distance (https://gitlab.pasteur.fr/GIPhy/JolyTree), to carefully select reference genomes for the scheme construction. Representative genomes for each cluster were selected based on best contiguity metrics, and the diversity of available metadata (location and collection date) and of sequence types (classical MLST or rMLST where MLST was not available). A total of 104 and 51 genomes for KoSC and KplaSC (directories “KoSC/Genomes” and “KplaSC/Genomes”) were used to build a cgMLST scheme for each species complex.</p> <p><strong>cgMLST schemes creation</strong></p> <p>The chewBBACA suite v2.8.5 (<a href="https://github.com/B-UMMI/chewBBACA">https://github.com/B-UMMI/chewBBACA</a>) was implemented to build cgMLST schemes by following recommendations and steps available at https://github.com/B-UMMI/chewBBACA#i-whole-genome-multilocus-sequence-typing-wgmlst-schema-creation. Paralogous loci were removed from the wgMLST schemes (directories “KoSC/Schema/wgMLST_17686_schema.tar.gz” and “KplaSC/Schema/wgMLST_13051_schema.tar.gz”) and the loci present in at least 99% of samples were extracted. The quality of core loci was estimated with the chewBBACA <em>Schema Evaluation</em> module and the reported loci with high allele variability were excluded from the scheme.</p> <p>The cgMLST schemes were finally composed of 3,272 loci for KoSC (file “KoSC/Schema/cgMLST_3272_Genes_list.txt”) and 2,957 loci for KplaSC (file “KplaSC/Schema/cgMLST_2957_Genes_list.txt”).</p> <p>wgMLST and cgMLST allele profiles have been included for KoSC (files “KoSC/Allele_profiles/wgMLST_allele_profiles.tsv” and “KoSC/Allele_profiles/cgMLST_allele_profiles.tsv”) and KplaSC (files “KplaSC/Allele_profiles/wgMLST_allele_profiles.tsv” and “KplaSC/Allele_profiles/cgMLST_allele_profiles.tsv”).</p>
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International Brain Laboratory public data
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OpenNeuro
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