Ontology highlight
ABSTRACT:
PROVIDER: PRJNA701635 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13699940_1.fastq.gz | Fastqsanger.gz | |||
| SRR13699940_2.fastq.gz | Fastqsanger.gz | |||
| SRR13699941_1.fastq.gz | Fastqsanger.gz | |||
| SRR13699941_2.fastq.gz | Fastqsanger.gz | |||
| SRR13699942_1.fastq.gz | Fastqsanger.gz |
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Project description:Observation of Increase in NDM-1 positive K.pneumoniae in Germany with link to previouse exposure to Ukraine
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Project description:Adult mesenchymal stem cells exert immunomodulatory effects that might improve the host response during sepsis. Knowledge on the effect of adipocyte-derived mesenchymal stem cells (ASCs) in sepsis is limited. Klebsiella (K.) pneumoniae is a common cause of gram-negative pneumonia and sepsis. The aim of this study was to determine the effect of human ASCs on the host response during pneumosepsis in mice. For this mice were infected with K. pneumoniae via the airways to induce a gradually evolving infection in the lung cumulating in pneumosepsis. One or 6 hours (h) after infection, mice were infused intravenously with ASCs or vehicle, and euthanized after 16h or 48h respectively. The effects of freshly cultured and cryopreserved ASCs were compared, the latter formulation being more clinically relevant. Intravenously administered ASCs were visualized in lung tissue by immunostaining at 1 and 3h, but not at 15h after infusion. While early after infection ASCs did not or only modestly influence bacterial loads, they reduced bacterial burdens in lungs and distant organs at 48h. ASCs reduced the lung levels of pro-inflammatory cytokines and attenuated lung pathology, but did not influence distant organ injury. ASCs strongly modified the lung transcriptome in both uninfected mice and mice with pneumosepsis, especially affecting. Cryopreserved and cultured ASCs induced largely similar effects. These data indicate that human ASCs induce profound immune modulatory effects in the lungs, resulting in reduced bacterial burdens and lung inflammation during pneumosepsis caused by a common human pathogen, suggesting that ASCs may be an adjunctive therapeutic in this condition. Experimental groups were defined as follows: (1) plac_cryo, placebo treated and K.pneumoniae infected control mice for cryopreserved MSCs; (2) plac_cult, placebo treated and K.pneumoniae infected control mice for cultured MSCs; (3) cryo, K.pneumoniae infected mice treated with cryopreserved MSCs; (4) cult, K.pneumoniae infected mice treated with cultured MSCs; (5) n_cult, non-infected control mice for cultured MSCs; (6) n_cryo, non-infected control mice for cryopreserved MSCs; (7) n, normal mouse lung baseline. In a separate experiment, mice were treated with a selective prekallikrein (PKK) directed antisense oligonucleotide (ASO) or a scrambled control ASO for 3 weeks prior to infection. Host response readouts were determined at 12 or 36 hours postinfection, including genome-wide messenger RNA profiling of lungs, or mice were followed for survival Pre-processing and quality control of the scans were performed by using the oligo method (version 1.44) and probes were annotated using the platform design info for Affymetrix Clariom_S_Mouse_HT available through Bioconductor. Array data were background corrected by Robust Multi-array Average (RMA) and quantiles-normalized. Microarray quality control was performed by means of the array quality metrics method (version 3.36.0). The occurrence of non-experimental chip effects was evaluated by the surrogate variable analysis method (version 3.28.0) and corrected using the combat method.
2018-10-31 | GSE121970 | GEO
Project description:We performed RNA-seq experiments to compare the gene expression profiles of cells expressing single-codon substitutions in the antibiotic resistance genes NDM-1, CAT-I, or aadB in the absence of antibiotics. Mutations with deleterious fitness effects in the absense of antibiotics also caused significant changes in gene expression in a number of genes related to stress-response pathways including the regulator of colanic acid capsule synthesis (Rcs) response, the phage shock protein response (Psp), and the oxidative stress response. Fold differences in gene expression were mutation- and gene-dependent.
2022-12-31 | GSE199248 | GEO
Project description:Antibiotic resistance associated with the expression of the clinically significant carbapenemases, IMP, KPC, and NDM and OXA-48 in Enterobacteriaceae is emerging as a worldwide calamity to health care. In Australia, IMP-producing Enterobacteriaceae is the most prevalent carbapenemase-producing Enterobacteriaceae (CPE). Genomic characteristics of such carbapenemase-producing Enterobacteriaceae (CPE) are well described, but the corresponding proteome is poorly characterised. We have thus developed a method to analyse dynamic changes in the proteome of CPE under antibiotic pressure. Specifically, we have investigated the effect of meropenem at sub-lethal concentrations to develop a better understanding of how antibiotic pressure leads to resistance. Escherichia coli, producing either NDM, IMP or KPC type carbapenemase were included in this study, and their proteomes were analysed in growth conditions with or without meropenem.
2018-07-11 | PXD008019 | Pride
Project description:The spread of carbapenemase-producing Enterobacterales (CPE) is emerging as a significant clinical concern in tertiary hospitals and in particular, long-term care facilities with deficiencies in infection control. This study aims to evaluate an advanced matrix-assisted laser desorption/ionization mass spectrometry (A-MALDI) method for the identification of carbapenemases and further discrimination of their subtypes in clinical isolates. The A-MALDI method was employed to detect CPE target proteins. Enhancements were made to improve detectability and mass accuracy through the optimization of MALDI-TOF settings and internal mass calibration. A total of 581 clinical isolates were analyzed, including 469 CPE isolates (388 KPC, 51 NDM, 40 OXA, and 2 GES) and 112 carbapenemase-negative isolates. Clinical evaluation of the A-MALDI demonstrated 100% accuracy and precision in identifying all the collected CPE isolates. Additionally, A-MALDI successfully discriminated individual carbapenemase subtypes (KPC-2 or KPC-3/4; OXA-48 or OXA-181 or OXA-232; GES-5 or GES-24) and also differentiated co-producing carbapenemase strains (KPC & NDM; KPC & OXA; KPC & GES; NDM & OXA), attributed to its high mass accuracy and simultaneous detection capability. A-MALDI is considered a valuable diagnostic tool for accurately identifying CPE and carbapenemase’s subtypes in clinical isolates. It may also aid in selecting appropriate antibiotics for each carbapenemase subtype. Ultimately, we expect that the A-MALDI method will contribute to preventing the spread of antibiotic resistance and improving human public health.
2024-11-26 | PXD058284 | Pride
Project description:The spread of carbapenemase-producing Enterobacterales (CPE) is emerging as a significant clinical concern in tertiary hospitals and in particular, long-term care facilities with deficiencies in infection control. This study aims to evaluate an advanced matrix-assisted laser desorption/ionization mass spectrometry (A-MALDI) method for the identification of carbapenemases and further discrimination of their subtypes in clinical isolates. The A-MALDI method was employed to detect CPE target proteins. Enhancements were made to improve detectability and mass accuracy through the optimization of MALDI-TOF settings and internal mass calibration. A total of 581 clinical isolates were analyzed, including 469 CPE isolates (388 KPC, 51 NDM, 40 OXA, and 2 GES) and 112 carbapenemase-negative isolates. Clinical evaluation of the A-MALDI demonstrated 100% accuracy and precision in identifying all the collected CPE isolates. Additionally, A-MALDI successfully discriminated individual carbapenemase subtypes (KPC-2 or KPC-3/4; OXA-48 or OXA-181 or OXA-232; GES-5 or GES-24) and also differentiated co-producing carbapenemase strains (KPC & NDM; KPC & OXA; KPC & GES; NDM & OXA), attributed to its high mass accuracy and simultaneous detection capability. A-MALDI is considered a valuable diagnostic tool for accurately identifying CPE and carbapenemase’s subtypes in clinical isolates. It may also aid in selecting appropriate antibiotics for each carbapenemase subtype. Ultimately, we expect that the A-MALDI method will contribute to preventing the spread of antibiotic resistance and improving human public health.
2024-11-25 | PXD046179 | Pride