Pseudomonas aeruginosa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA135391 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Bacteria in biofilms have higher antibiotic tolerance than their planktonic counterparts. A major outstanding question is the degree to which the biofilm-specific cellular state and its constituent genetic determinants contribute to this hyper-tolerant phenotype. Here, using genome-wide functional profiling of a complex, heterogeneous mutant population of Pseudomonas aeruginosa MPAO1, we identified large sets of mutations that contribute to antibiotic tolerance predominantly in the biofilm or planktonic setting only. Our mixed population-based experimental design recapitulated the complexity of natural biofilms and, unlike previous studies, revealed clinically observed behaviors including the emergence of quorum sensing-deficient mutants. Our study revealed a substantial contribution of the cellular state to the antibiotic tolerance of biofilms, providing a rational foundation for the development of novel therapeutics against P. aeruginosa biofilm-associated infections. This dataset compares the expression of SAH108, a strain with enhanced antibiotic tolerance in the biofilm state, to expression in wild-type strains.
2011-11-21 | GSE26142 | GEO
Project description:Bacteria in biofilms have higher antibiotic tolerance than their planktonic counterparts. A major outstanding question is the degree to which the biofilm-specific cellular state and its constituent genetic determinants contribute to this hyper-tolerant phenotype. Here, using genome-wide functional profiling of a complex, heterogeneous mutant population of Pseudomonas aeruginosa MPAO1, we identified large sets of mutations that contribute to antibiotic tolerance predominantly in the biofilm or planktonic setting only. Our mixed population-based experimental design recapitulated the complexity of natural biofilms and, unlike previous studies, revealed clinically observed behaviors including the emergence of quorum sensing-deficient mutants. Our study revealed a substantial contribution of the cellular state to the antibiotic tolerance of biofilms, providing a rational foundation for the development of novel therapeutics against P. aeruginosa biofilm-associated infections. This dataset compares the expression of SAH108, a strain with enhanced antibiotic tolerance in the biofilm state, to expression in wild-type strains. We compared the expression of two biological replicates from strain SAH108 to samples from three wild-type, reference strains. All samples were collected from exponentially-growing planktonic cultures.
2011-11-21 | E-GEOD-26142 | biostudies-arrayexpress
Project description:ndvB is a gene expressed preferrentialy in biofilms of Pseudomonas aeruginosa and has been implicated in antibiotic resistance. This gene also has a role in signaling in some plant pathogens. A knockout ndvB strain was used to determine if it controlled any other gene expression related to antibiotic resistance We used microarrays of wildtype and ndvB knockout P. aeruginosa grown in biofilms to identify the role of ndvB in gene expression
2012-04-26 | GSE32032 | GEO
Project description:Transcriptomic, metabolomic, physiological, and computational modeling approaches were integrated to gain insight into the mechanisms of antibiotic tolerance in an in vitro biofilm system. Pseudomonas aeruginosa biofilms were grown in drip-flow reactors on a medium composed to mimic the exudate from a chronic wound (CWE). After 72 hours, the biofilms were treated with CWE (control biofilms) or CWE containing ciprofloxacin (treated biofilms) for an additional 24 hours. Planktonic samples were cultivated to early logarithmic phase in CWE. The biofilm specific growth rate was estimated via elemental balances to be approximately 0.37 h-1, or one-third of the planktonic maximum specific growth rate. Global analysis of gene expression indicated decreased anabolic activity in biofilms compared to planktonic cells. A focused transcriptomic analysis revealed the induction of multiple stress responses in biofilm cells, including those associated with growth arrest, zinc limitation, hypoxia, and acyl-homoserine lactone quorum sensing.
2018-10-03 | GSE120760 | GEO
Project description:ndvB is a gene expressed preferrentialy in biofilms of Pseudomonas aeruginosa and has been implicated in antibiotic resistance. This gene also has a role in signaling in some plant pathogens. A knockout ndvB strain was used to determine if it controlled any other gene expression related to antibiotic resistance We used microarrays of wildtype and ndvB knockout P. aeruginosa grown in biofilms to identify the role of ndvB in gene expression Wildtype and ndvB knockout PA14 biofilms were grown for 48 hours followed by RNA extraction. RNA was pooled from 2 wells for each condition to obtain a single biological replicate. Affymetrix microarray processing was performed on PA01 genechips and data analysis was carried out using R statistical framework with bio-conductor packages using RMA and MAS5.0 normalization procedures
2012-04-25 | E-GEOD-32032 | biostudies-arrayexpress
Project description:Chronic infections with Pseudomonas aeruginosa are a leading cause of morbidity and mortality in persons with cystic fibrosis (pwCF). P. aeruginosa persists in the CF lung by utilizing adaptation strategies to cause infection, including altering the expression of metabolic genes to acquire nutrients that are abundant in the CF airway. Glycerol in the airway is imported and metabolized by the glp regulon, which is under the control of the GlpR repressor. It has been shown that the loss of GlpR results in increased biofilm development in P. aeruginosa CF isolate compared to a wound isolate. Based on the increased biofilm phenotype observed and because biofilms are associated with increased antibiotic tolerance, we questioned whether GlpR plays a role in mediating antibiotic resistance of P. aeruginosa. We measured tobramycin tolerance in wild-type and glpR-defective P. aeruginosa isolates from the CF airway (FRD1) and a wound (PAO1). Cultures were grown in lysogeny broth or synthetic cystic fibrosis sputum consisting of the base formula of primarily amino acids (SCFM1) or supplemented with mucins and DNA (SCFM2), with dose-dependent concentrations of tobramycin. We tested the impact of a glpR mutation on P. aeruginosa adherence on bronchial epithelial cells from pwCF (CFBE) in the presence of tobramycin. CFBE cells were inoculated at an MOI of ~1:20 for 1 hour, given fresh apical media for 5 more hours, then apical and basal media was replaced with media containing 20 µg/ml tobramycin. We measured colony forming units (CFUs) and lactate dehydrogenase (LDH) release for cytotoxicity. Loss of glpR increased tolerance to tobramycin in both the PAO1 and FRD1 backgrounds in vitro at a concentration of 0.625 µg/mL in lysogeny broth and SCFM1. On both CFBE’s and 16HBE’s, the antibiotic resistance phenotype was more prominent in FRD1 glpR with a 2-log increase in viable bacteria when grown on cells and treated with 20 ug/ml tobramycin. However, changes in cytotoxicity where not observed between wildtype and GlpR mutants as LDH measurements were not significantly different. Our results indicate that GlpR may regulate antibiotic tolerance, in addition to biofilm development and glycerol metabolism. Additional studies are necessary to determine the mechanism of how GlpR modulates biofilm development and antibiotic tolerance.
2025-09-05 | GSE280261 | GEO
Project description:We grew Pseudomonas aeruginosa biofilms on CFBE41o- human airway cells in culture, and we treated these biofilms with tobramycin. Microarray analysis was performed to gain an understanding of the global transcriptional changes that occur during antibiotic treatment. Keywords: Antibiotic Response
2008-06-10 | GSE9989 | GEO
Project description:Pseudomonas aeruginosa is a critical priority pathogen, whose proclivity to establish chronic infections and to resist antibiotic treatment is intimately linked to its ability to form biofilms at the infection site. Recent developments in our understanding of these biofilms has pointed to the fact that the surface-bound biofilms recapitulated by in vitro models do not sufficiently capture the type of biofilms that occur in infection sites, such as the CF lung. This study aimed to develop a straightforward and medium throughput model for free floating biofilms, alongside a protocol that permits fractionating of the biofilm into its constituent parts. The RNA-seq investigation takes the cells fraction at three timepoints in biofilm development (and one point in a planktonic culture for comparison), to ask what genes are driving the development of these free floating aggregate biofilms.
2025-06-27 | GSE301018 | GEO
Project description:Transcriptome analysis was applied to characterize the physiological activities of Psuedomonas aeruginosa cells grown for three days in drip flow biofilm reactors when compared to the activities of P. aeruginosa grown planktonically to exponential phase in the same media. Here, rather than examining the effect of an individual gene on biofilm antibiotic tolerance, we used a transcriptomics approach to identify regulons and groups of related genes that are induced during biofilm growth of Pseudomonas aeruginosa. We then tested for statistically significant overlap between the biofilm-induced genes and independently compiled gene lists corresponding to stress responses and other putative antibiotic protective mechanisms. This data was evaluated and used to select strains that carry transposon mutations in genes that might play a role in antibiotic tolerance of biofilms. The strains were evaluated for defects in biofilm tolerance.
2015-05-11 | GSE65869 | GEO
Project description:Pseudomonas aeruginosa is known to tolerate antibiotic therapy during infection. This prevents clearance of infection and negatively impacts patient outcomes. Here, we report the transcriptome sequence of antibiotic-treated and untreated P. aeruginosa cultures and the differential gene expression observed when treated cells are compared to untreated cells.
2018-10-31 | GSE120602 | GEO