Ontology highlight
ABSTRACT:
PROVIDER: PRJNA526444 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:RNA sequencing was performed on E. coli K12 MG1655 on three media (M9, CA-MHB, R10LB) treated with four antibiotics (Ciprofloxacin, Trimethoprim-sulfamethoxazole, Ceftriaxone, Meropenem) at their media-specific MIC90s
2021-08-05 | GSE159494 | GEO
Project description:Array-CGH analysis and Burkholderia pseudomallei isolates pre and post ceftazidime relapse.
2011-10-07 | GSE25832 | GEO
Project description:The response of antibiotic adapted resistant mutants of B. cenocepacia J2315 to antibiotic stress was investigated using expression profiling of three biological replicates and comparing the profiles to the J2315 parent control grown without antibiotics.<br>A reference design was used with Cy3 labeled genomic DNA of B. cenocepacia J2315 as common reference. Three test conditions with three biological replicates each were compared to three replicates of the control condition.<br>Test conditions: J2315-A grown in the presence of 250 ug per ml amikacin, J2315-M grown in the presence of 8 ug per ml meropenem and J2315-T grown in the presence of 60 ug per ml trimethoprim and 300 ug per ml sulfamethoxazole.<br>Control condition: J2315 parent strain grown without antibiotics.
2010-08-12 | E-MEXP-2708 | biostudies-arrayexpress
Project description:To use whole genome microarrays to compare the differences in genome contents of 5 B. pseudomallei isolated from clinical specimens and environmental sample with B. pseudomallei K96243 reference strain and reveals variable patterns of Genomic Islands (GIs) Keywords: Comparative genomic hybridization DNA microarrays were used to compare genome of clinical and environmental B. pseudomallei isolates with B. pseudomallei K96243 reference strain (B. pseudomallei K96243 vs. B. pseudmallei isolates). Each hybridization was used for comparison between B. pseudomallei K96243 as a reference strain with environmental isolate BP45s, environmental isolate BP28L, clinical isolate H307, clinical isolate P54, clinical isolate P82. Two replicate per array. Multiple hits with 90-99.99 % identity correspond to other locus are replicate of their genes were averaged and analyzed.
2012-07-30 | E-GEOD-19558 | biostudies-arrayexpress
Project description:Burkholderia mallei and Burkholderia pseudomallei are both potential biological threats agents. Melioidosis caused by B. pseudomallei is endemic in Southeast Asia and Northern Australia, while glanders caused by B. mallei infections are rare. Here we studied the proteomes of different B. mallei and B. pseudomallei isolates to determine species specific characteristics. Analyzing the expressed proteomes of B. mallei and B. pseudomallei revealed differences between B. mallei and B. pseudomallei but also between isolates from the same species. Expression of multiple virulence factors and proteins of several PKS/NRPS clusters was demonstrated. Proteome analysis can be used not only to identify bacteria but also to characterize the expression of important factors that putatively contribute to pathogenesis of B. mallei and B. pseudomallei.
2022-12-15 | PXD028126 | Pride
Project description:Array-CGH analysis and Burkholderia pseudomallei isolates pre and post ceftazidime relapse. Genomic DNA from both the parental strains and variant strains were labeled with Cy3 or Cy5 fluorescent dyes and hybridized onto a customized microarray with probes designed from the reference Bp K96243 genome. Log2 signal ratios of parental strain over the variant strains were then computed after normalization to find genomic loss or gain in the variant strains.
2011-10-06 | E-GEOD-25832 | biostudies-arrayexpress
Project description:With the global increase in the use of carbapenems, several gram-negative bacteria have acquired carbapenem resistance, thereby limiting treatment options. Klebsiella pneumoniae is one of such notorious pathogen that is being widely studied to find novel resistance mechanisms and drug targets. These antibiotic-resistant clinical isolates generally harbor many genetic alterations, and identification of causal mutations will provide insights into the molecular mechanisms of antibiotic resistance. We propose a method to prioritize mutated genes responsible for antibiotic resistance, in which mutated genes that also show significant expression changes among their functionally coupled genes become more likely candidates. For network-based analyses, we developed a genome-scale co-functional network of K. pneumoniae genes, KlebNet (www.inetbio.org/klebnet). Using KlebNet, we could reconstruct functional modules for antibiotic-resistance, and virulence, and retrieved functional association between them. With complementation assays with top candidate genes, we could validate a gene for negative regulation of meropenem resistance and four genes for positive regulation of virulence in Galleria mellonella larvae. Therefore, our study demonstrated the feasibility of network-based identification of genes required for antimicrobial resistance and virulence of human pathogenic bacteria with genomic and transcriptomic profiles from antibiotic-resistant clinical isolates.
2018-06-10 | GSE115539 | GEO
Project description:An important, but rarely performed, test of Koch’s molecular postulates involves evaluating the capacity of candidate virulence genes to confer pathogenicity in otherwise non-virulent species. Unbiased genomic surveys of avirulent natural isolates might reveal rare variants possessing specific virulence features, which might prove useful in testing their functional sufficiency. Using a custom pan-genome array, we analyzed a panel of avirulent Burkholderia thailandensis (Bt) isolates related to Burkholderia pseudomallei (Bp), the causative agent of the often fatal human and animal disease melioidosis. We report the discovery of variant Bt isolates exhibiting isolated acquisition of a capsular polysaccharide biosynthesis gene cluster (BpCPS), long regarded as an critical species-specific virulence factor essential for Bp mammalian virulence. BpCPS-expressing Bt strains exhibited certain pathogen-related phenotypes including resistance to human complement binding, but did not exhibit enhanced virulence when assessed in two different in vivo animal infection models. Phylogenetic analysis revealed that the BpCPS-expressing Bt strains likely reside within an evolutionary subgroup distinct from the majority of previously-described Bt strains. Our findings suggest that BpCPS acquisition alone is unlikely to fully explain the ability of Bp to colonize humans and animals, highlighting the importance of other collaborating factors in the pathogenesis of mammalian melioidosis. Genomic DNA of several Bt strains were hybridized against a common reference strain (Bt E264), to see gain/loss
2010-08-14 | E-GEOD-18766 | biostudies-arrayexpress