Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1225923 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32466100_1.fastq.gz | Fastqsanger.gz | |||
| SRR32466100_2.fastq.gz | Fastqsanger.gz | |||
| SRR32466200_1.fastq.gz | Fastqsanger.gz | |||
| SRR32466200_2.fastq.gz | Fastqsanger.gz | |||
| SRR32466300_1.fastq.gz | Fastqsanger.gz |
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Project description:Carbapenemases Producing Enterobacteriaceae
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Project description:Infections caused by carbapenem-resistant Acinetobacter baumannii (CRAb) are associated with high patient morbidity and mortality. The serious threat for human health imposed by CRAb was recently underscored by identification of close-to-untouchable carbapenem- and tetracycline-resistant isolates. Since outer membrane vesicles (OMVs) of Gram-negative bacteria may contribute to antimicrobial resistance, our present study was aimed at investigating OMVs produced by the first two carbapenem- and tetracycline-resistant CRAb isolates in Europe. These isolates, denoted CRAb1 and CRAb2 contain large, nearly identical plasmids that specify multiple resistances. Both isolates produce OMVs that were analyzed by differential light scattering, transmission electron microscopy and proteomics. By comparison with OMVs from the plasmid-free non-carbapenem-resistant A. baumannii isolate Ab1, which is an isogenic ancestor of the CRAb1 isolate, we show that plasmid carriage by the CRAb1 and CRAb2 isolates leads to an increased OMV size that is accompanied by increased diversity of the OMV proteome. Our analyses show that OMVs from CRAb1 and CRAb2 are major reservoirs of proteins involved in antimicrobial resistance, including the plasmid-encoded carbapenemases BlaNDM-1, and BlaOXA-97. We also show that these OMV-borne carbapenemases hydrolyze imipenem and protect otherwise carbapenem-sensitive A. baumannii and Escherichia coli isolates against this antibiotic. Altogether, our observations show that OMVs from highly drug-resistant CRAb confer tolerance against last-resort antibiotics to non-resistant bacterial pathogens.
2025-04-14 | PXD051698 | Pride
Project description:The emergence and spread of carbapenem-resistant Klebsiella pneumoniae (CR-KPN) infections have worsened the current situation worldwide. Clinically, cotrimoxazole (CTX) and amikacin (AMI) are considered to be the preferred drugs in the treatment of (CR-KPN). But for now, the extensive use of cotrimoxazole (CTX) and amikacin (AMI) During the course of treatment leads to the emergence of cotrimoxazole- and amikacin-resistant infections, which is of great clinical concern. Previous evidence has shown that bacteria with reduced metabolism tend to be resistant to antibiotics, however, the mechanism remains unclear. In the present study, proteomics was performed on the sensitive, cotrimoxazole-resistant, amikacin-resistant and cotrimoxazole/amikacin-both-resistant KPN clinical isolates, and 2266 proteins were identified in total by liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) analysis. Further bioinformatic analysis showed down-regulation of tricarboxylic acid cycle pathway and up-regulation of alcohol metabolic or glutathione metabolism processes, which may contribute to ROS clearance and cell survival, in drug-resistant isolates. Finally, combined with minimum inhibitory concentration (MIC) of Amikacin and Cotrimoxazole on different KPN isolates, we identified nine proteins contributed mostly to such an alteration and the survival of bacteria under drug pressure, which could reveal novel mechanisms or pathways involved in drug resistance. These proteins and their pathways might be used as targets for the development of novel therapeutics against antimicrobial-resistant (AMR) infections.
2021-11-25 | PXD028544 | Pride
Project description:Munschauer M, Nguyen CT, Sirokman K, Hartigan CR, Hogstrom L, Engreitz JM, Ulirsch JC, Fulco CP, Subramanian V, Chen J, Schenone M, Guttman M, Carr SA, Lander ES. Nature 2108.
2018-06-30 | MSV000082561 | MassIVE
Project description:Inhibition of fungal growth by Congo Red (CR) has been known for a long time and claimed to be associated to a specific binding to fibrillar chains of β-1,3-glucans which blocks cell wall polysaccharide synthesis. It has also been suggested that the effect of CR could be pleiotropic, especially because of its oxido-reductive properties. One way to elucidate the mechanism of action of CR is to identify transcription factors (TF) which regulate the response to CR and interrogate their regulon. The analysis of TF mutants with differential sensitivity to CR would be also a way to identify new regulatory pathways involved in cell wall biosynthesis. During the investigation of the sensitivity to CR of a TF mutant library, several mutants either sensitive or resistant to CR were analysed . The morphology of the conidial germination was affected differently by CR in the parental strain and TF mutants. Abnormal distorted swollen conidia called Quasimodo cells were seen in presence of the CR. The size of the Quasimodo cells in the resistant mutants are bigger and adsorb more CR than the germinating conidia of the sensitive or parental strain. This is associated to a difference in permeability of the mutants. The clearing of the drug from the medium by the resistant strain was mainly responsible for the survival and later growth of some of resting conidia of these mutants which did not adsorb intracellularly the drug whereas in the sensitive mutants all conidia adsorbed the drug and were consequently killed. Although there are some modifications of the composition of the cell wall, a transcriptomic analysis of the mutant showed that CR affected many different pathways, including iron and calcium metabolism. Accordingly, the susceptibility to other cell wall drugs of the sensitive and the resistant TF mutants varied with the mutants and not always in connexion with their sensitivity to CR. Interestingly, a new paradoxical effect of the CR was discovered in the resistant mutant since the growth of one of them could be stimulated after recovering from the CR stress.
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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:HCC827 cells were grown in gradually increasing concentrations of cetuximab beginning at 0.1 ug/ml. Drug concentrations were slowly increased until the resistant cells were able to proliferate in 100 ug/ml of cetuximab. Individual clones of cetuximab resistant (CR; CR1 to CR4) cells were isolated and confirmed to be drug resistant.
2011-11-23 | GSE30255 | GEO
Project description:This study researched the combined effects of hexavalent chromium (Cr(VI)) concentration and antibiotics on the ARGs of Bacillus cereus SH-1. As the Cr(VI) concentration increased, it triggered Reactive Oxygen Species (ROS) oxidative stress in SH-1, increased antioxidant enzyme activity, enhanced plasmid conjugative transfer and reduced the removal efficiency of Cr(VI) by SH-1. Meanwhile, antibiotic resistance varied with TET (Tetracycline) and AMC (Amoxicillin) MICs (minimum inhibitory concentration) rising and AZM (Azithromycin) and CL (Chloramphenicol) MICs decreasing with Cr(VI) induction. Overexpression of eight genes of the HAE-1 family efflux pumps was detected through metagenomics and proteomics. Co-contamination of Cr(VI) and antibiotics led to the emergence and spread of antibiotics resistant bacteria (ARBs).
2024-07-01 | PXD053553 |
Project description:Purpose: Resistance to androgen deprivation therapies is a major driver of mortality in advanced prostate cancer. Therefore, there is a need to develop new pre-clinical models that allow the investigation of resistance mechanisms and the assessment of drugs for the treatment of castration resistant prostate cancer. Methods: We generated two novel cell line models (LAPC4-CR and VCaP-CR) which were derived by passaging LAPC4 and VCaP cells in vivo and in vitro under castrate conditions. We performed detailed transcriptomic (RNA-seq) to delineate expression differences between castration-sensitive and castration-resistant cell lines. LAPC4-CR and VCaP-CR cell lines maintained AR expression, but exhibited distinct expression changes on the mRNA and protein level. Integrated analyses including data from LNCaP and the previously described castration resistant LNCaP-abl cells revealed an expression signature of castration resistance. Results: Integrated analyses including data from LNCaP and the previously described castration resistant LNCaP-abl cells revealed an expression signature of castration resistance.
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Project description:Ewing's Sarcoma cell lines were made resistant to different IGF-1R drugs to investigate mechanisms and pathways modulated by the resistance. EWS TC-71 cell line was exposed to increasing concentration to three different anti-IGF-1R drugs (HAb AVE1642, TKI NVP-AEW541, HAb CP-751,871, cell lines named respectively as TC/AVE, TC/AEW or TC/CP) for at least six months. Expression profile of resistant cell variants was compared either singularly for each resistance or commonly vs. parental cell line. Two technical replicates for resistant variants and three biological replicated for parental cell were present.
2012-10-03 | E-GEOD-34027 | biostudies-arrayexpress