Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1097307 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR30684700_1.fastq.gz | Fastqsanger.gz | |||
| SRR30684700_2.fastq.gz | Fastqsanger.gz | |||
| SRR30684601_1.fastq.gz | Fastqsanger.gz | |||
| SRR30684601_2.fastq.gz | Fastqsanger.gz |
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Project description:Exposure pattern of triclosan and tetracycline change their impacts on methanogenic digestion microbiomes
| PRJNA1131089 | ENA
Project description:The present project investigates transcriptomics changes in laboratory mutants of Salmonella typhimurium SL1344 obtained by pre-exposure to biocides, including triclosan (TRI), benzalkonium chloride (BZC), and chlorexidine (CHX), and antibiotics including Ampicillin (AP) and ciprofloxacin (Cip), as well as in natural isolates selected for their resistance to these same biocides. Changes in gene expression were investigated using a 12k combimatrix customarray, design-based on the genome of SL1344 as well as a variety of genes of plasmid origins.
2016-06-30 | E-MTAB-2554 | biostudies-arrayexpress
Project description:Antimicrobial resistance (AMR) is a global health crisis that is predicted to worsen. While improper antibiotic usage is an established driver, less is known on the impacts of metal supplements. Here, we probe the impact of zinc (Zn) on AMR. In conflict settings where diarrhea disease cases are high, Zn, which is associated with weapons of war, is given as a supplement for diarrhea treatment prior to antibiotics such as ciprofloxacin. In this study, we find that E. coli’s exposure order to zinc impacts resistance development, with increasing pre-exposure leading to accelerated ciprofloxacin resistance, while combined exposure of zinc with ciprofloxacin delays ciprofloxacin resistance. We did not find evidence that zinc pre-exposure leads to genetic changes or changes in antibiotic tolerance, though the lag phase and doubling time of E. coli was increased, suggesting gene expression may be changed. While the zinc phenotype was no longer observed if ciprofloxacin exposure did not occur right after zinc pre-exposure, the resulting elevated MIC was more stable. These results are important as they highlight the need to reexamine the clinical role of zinc in treating diarrheal diseases and assess if changes in resistance development observed in vitro are also observed in vivo.
2023-06-13 | GSE234536 | GEO
Project description:Commercial probiotic bacteria must be tested for acquired antibiotic resistance elements to avoid potential transfer to pathogens. The European Food Safety Authority recommends testing resistance using microdilution culture techniques previously used to establish inhibitory thresholds for the Bifidobacterium genus. Many Bifidobacterium animalis subsp. lactis strains exhibit increased resistance to tetracycline, historically attributed to the ribosomal protection gene tet(W). However, some strains that harbor genetically identical tet(W) genes show various inhibition levels suggesting that other genetic elements also contribute to observed differences. Here, we adapted several molecular assays to confirm the inhibition of B. animalis subsp. lactis strains Bl-04 and HN019, and employed RNA-seq to assess the transcriptional differences related to genomic polymorphisms. We detected specific stress responses to the antibiotic by correlating ATP concentration to viable genome copies from droplet digital PCR, and found that the bacteria were still metabolically active in high drug concentrations. Transcriptional analyses revealed that several polymorphic regions, particularly a novel multi-drug efflux transporter, were differentially expressed between the strains in each experimental condition, likely having phenotypic effects. We also found that the tet(W) gene was up-regulated only during sub-inhibitory tetracycline concentrations, while two novel tetracycline resistance genes were up-regulated at high concentrations. Furthermore, many genes involved in amino acid metabolism and transporter function were up-regulated while genes for complex carbohydrate utilization, protein metabolism, and CRISPR-Cas systems were down-regulated. These results provide high-throughput means for assessing antibiotic resistance and determine the genetic network that contributes to the global tetracycline response between two highly related probiotic strains.
2018-09-27 | GSE117878 | GEO
Project description:A triclosan-ciprofloxacin cross-resistant mutant strain of Staphylococcus aureus displays an alteration in the expression of several cell membrane structural and functional genes. Triclosan is an antimicrobial agent found in many consumer products. Several studies have demonstrated that triclosan inhibits the bacterial fatty acid biosynthetic enzyme, enoyl-ACP reductase (FabI). Studies have also demonstrated that decreased susceptibility to triclosan correlates with ciprofloxacin resistance in several bacteria. In these bacteria, resistance to both drugs maps to genes encoding multi-drug efflux pumps. The focus of this study was to determine whether triclosan resistance contributes to ciprofloxacin resistance in Staphylococcus aureus. Gene expression profiling was performed to compare the gene expression profiles of unexposed and triclosan-exposed wild-type and JJ5 determined that an alteration in global gene expression possibly resulting in a change in cell membrane structure and function is likely responsible for triclosan and ciprofloxacin resistance in JJ5. Keywords: Treatment response WT and triclosan resistant mutant were treated with triclosan and their gene expression was compared to their untreated conterparts.
2010-05-26 | E-GEOD-5799 | biostudies-arrayexpress
Project description:A triclosan-ciprofloxacin cross-resistant mutant strain of Staphylococcus aureus displays an alteration in the expression of several cell membrane structural and functional genes. Triclosan is an antimicrobial agent found in many consumer products. Several studies have demonstrated that triclosan inhibits the bacterial fatty acid biosynthetic enzyme, enoyl-ACP reductase (FabI). Studies have also demonstrated that decreased susceptibility to triclosan correlates with ciprofloxacin resistance in several bacteria. In these bacteria, resistance to both drugs maps to genes encoding multi-drug efflux pumps. The focus of this study was to determine whether triclosan resistance contributes to ciprofloxacin resistance in Staphylococcus aureus. Gene expression profiling was performed to compare the gene expression profiles of unexposed and triclosan-exposed wild-type and JJ5 determined that an alteration in global gene expression possibly resulting in a change in cell membrane structure and function is likely responsible for triclosan and ciprofloxacin resistance in JJ5. Keywords: Treatment response
2008-01-11 | GSE5799 | GEO
Project description:Trans-acting regulatory RNAs have the capacity to base pair with more mRNAs than experimentally detected under given conditions. This raises the question whether the sRNA target specificity can change upon metabolic or environmental changes. In Sinorhizobium meliloti, the sRNA rnTrpL is derived from a tryptophan (Trp) transcription attenuator, which is located upstream of the Trp biosynthesis gene trpE(G) and harbors the small ORF trpL. When Trp is available, efficient trpL translation causes transcription termination and liberation of rnTrpL, which then downregulates the trpDC operon. On the other hand, the trpL-encoded leader peptide peTrpL has a Trp-independent role in posttranscriptional regulation of antibiotic resistance. Here, we show that upon tetracycline (Tc) exposure, rnTrpL accumulates independently of Trp availability. Further, we provide evidence that both rnTrpL and peTrpL act together in the Tc-dependent destabilization of rplUrpmA mRNA encoding ribosomal proteins L21 and L27. rnTrpL, peTrpL and rplUrpmA mRNA were copurified in an antibiotic- dependent ribonucleoprotein complex (ARNP). In vitro ARNP reconstitution with competing trpD and rplU transcripts revealed that peTrpL and Tc reprogram the rnTrpL specificity in favor of rplU. In vivo, this probably supports bacterial adaptation to antibiotics. Our findings provide evidence for sRNA reprograming in response to antibiotic exposure.
2021-08-10 | PXD019516 | Pride
Project description:Antimicrobial exposure can potentially lead to increased antimicrobial resistance plasmid transfer. RNA sequencing data was collected from conjugal pairs of Salmonella enterica and Escherichia coli exposed or not exposed to tetracycline over a time course to determine differences in transcript numbers associated with conjugation and tetracycline exposure. The samples were sequenced on the Illumina HiSeq X10 platform with the 150-bp paired-end kit. Among the most highly up-regulated genes in the tetracycline exposed samples were also tetracycline efflux pump genes across the timepoints. In addition, some conjugal transfer-associated genes (e.g. traJ and traA) were upregulated in the tetracycline exposed samples.
2024-03-25 | GSE261094 | GEO
Project description:WblC, also known as WhiB7, is a widely conserved WhiB-like transcription factor in actinomycetes that activates transcription of many targets upon antibiotic challenge to bring about intrinsic resistance to a wide range of translation-targeting antibiotics. As we found that WblC controls many genes involved in translation and that WblC promotes translation rate upon antibiotic stress in the model actinomycetes Streptomyces coelicolor, we speculated that WblC might alter the protein composition of ribosome during antibiotic stress. To test this, we prepared 70S ribosome fraction from wild-type S. coelicolor cells untreated or treated with tetracycline and ΔwblC mutant treated with tetracycline, and then compared the protein compositions of each 70S samples by mass spectrometric quantification.
2020-05-27 | PXD015538 | Pride
Project description:Given the risk of environmental pollution by pharmaceutical compounds and the effects of these compounds on exposed ecosystems, ecologically relevant and realistic assessments are required. However, many studies have been mostly focused on individual responses in a single generation exposed to one-effect concentration. Here, transcriptional responses of the crustacean Daphnia magna to the antibiotic tetracycline across multiple generations and effect concentrations were investigated. The results demonstrated that tetracycline induced different transcriptional responses of daphnids that were dependent on dose and generation. For example, reproduction-related expressed sequence tags (ESTs), including vitellogenin, were distinctly related to the dose-dependent tetracycline exposure, whereas multigenerational exposure induced significant change of molting-related ESTs such as cuticle protein. Sixty-five ESTs were shared in all contrasts, suggesting a conserved mechanism of tetracycline toxicity regardless of exposure concentration or time. Most of them were associated with general stress responses including translation, protein and carbohydrate metabolism, and oxidative phosphorylation. In addition, effects across the dose-response curve showed higher correlative connections among transcriptional, physiological, and individual responses than multigenerational effects. In the multigenerational exposure, the connectivity between adjacent generations decreased with increasing generation number. The results clearly highlight that exposure concentration and time trigger different mechanisms and functions, providing further evidence that multigenerational and dose-response effects cannot be neglected in environmental risk assessment.
2017-10-16 | GSE94439 | GEO