Clinical strains
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB32677 | ENA |
REPOSITORIES: ENA
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Project description:In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90000 probes covering six sequenced Helicobacter pylori(H. pylori) genomes was designed and utilized for comparative genomic profiling of eight unsequenced strains isolated from patients with different gastroduodenal diseases in Heilongjiang province of China. Since significant genomic variation were found among these strains, an additional 76 H. pylori stains with different clinical outcomes isolated from various provinces of China were further tested by PCR to demonstrate this distinction. We observed several highly variable regions among strains of gastritis, gastric ulceration and gastric cancer. They are involved in genes associated with bacterial type I, type II and type III R-M system as well as in a virB gene neighboring the well studied cag pathogenic island. Previous studies have reported the diverse genetic characterization of this pathogenic island, but it is conserved in the strains tested by microarray in this study. Moreover, a number of genes involved in the type IV secretion system related to DNA horizontal transfer between H. pylori strains were identified based on the comparative analysis of the strain specific genes. These findings may provide new insights for discovering biomarkers for prediction of gastric diseases.
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Project description:We worked with microarrys analysis in presence of 3-oxo-C12-HSL molecule to analyze the profile of the genes implicated in the Quorum Quenching network in A.baumannii clinical strains. Interestingly, only 13 genes were overexpressed under 3-oxo-C12-HSL molecule being the most level a gene which encodes an Alpha/beta hydrolase enzyme (5.01). The 46.15% of the genes overexpressed were implicated in the synthesis of the acyl-homoserine lactones (AHLs).
2017-06-12 | GSE87009 | GEO
Project description:Staphylococcus aureus can cause a broad spectrum of diseases that vary widely in clinical presentation and disease severity[121]. Methicillin-Resistant S. aureus (MRSA) strains first described in the 1960’s[122] were hospital acquired (HA MRSA), however in the 1990’s, community-associated MRSA strains (CA MRSA) were identified and are considered to be more virulent[16]. Therapeutics and management of MRSA focuses on novel antibacterials and vaccines targeting virulence factors. To date no clinical trials for vaccines have succeeded[123] due to the poor understanding of the pathogenic mechanisms exhibited by S.aureus.We investigated the differential gene expression of four clinical MRSA strains in vitro, belonging to HA and CA MRSA, at the stationary and exponential growth phases, using RNA-seq on the Ion torrent next generation sequencing platform. This study reveals the high diversity of virulence trait expression among MRSA strains within strains as well as between different growth phases, and also suggests potential factors other than PVL that contributes to enhanced virulence in CA MRSA
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Project description:Background. The bacterial foodborne pathogen Campylobacter jejuni is a common cause of acute gastroenteritis and is also associated with the postinfectious neuropathies, Guillain-Barré and Miller Fisher syndromes. This study described the use of multilocus sequence typing and DNA microarrays to examine the genetic content of a collection of South African C. jejuni strains, recovered from patients with enteritis, Guillain-Barré or Miller Fisher syndromes. Methodology/Principal Findings. The comparative genomic analysis by using multilocus sequence typing and DNA microarrays demonstrated that the South African strains with Penner heat-stable (HS) serotype HS:41 were clearly distinct from the other South African strains. Further analysis of the DNA microarray data demonstrated that the serotype HS:41 strains from South African GBS and enteritis patients are highly similar in gene content. Interestingly, the South African HS:41 strains were distinct in gene content when compared to serotype HS:41 strains from other geographical locations due to the presence of genomic islands, referred to as Campylobacter jejuni integrated elements. Only the genomic integrated element CJIE1, a Campylobacter Mu-like prophage, was present in the South African HS:41 strains whereas absent in the closely-related HS:41 strains from Mexico. A more distantly-related HS:41 strain from Canada possessed both genomic integrated elements CJIE1 and CJIE2. Conclusion/Significance. These findings demonstrated that these C. jejuni integrated elements may contribute to the differentiation of closely-related C. jejuni strains. In addition, the presence of bacteriophage-related genes in CJIE1 may probably contribute to increasing the genomic diversity of these C. jejuni strains. This comparative genomic analysis of the foodborne pathogen C. jejuni provides fundamental information that potentially could lead to improved methods for analyzing the epidemiology of disease outbreaks and their sources. Keywords: comparative genomic indexing analysis
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Project description:Microarray hybridization analysis was conducted to identify genes that may affect biofilm formation. Isolates from the 50 clinical isolates, two from LSG (strain number 2 and 7) and two from HSG donors (strain number 10 and 33) were selected. We monitored relative mRNA abundance in the four clinical S. aureus isolates using the Genechip S. aureus Genome Array (GeneChip Expression, Affymetrix, Inc., USA) to study the patterns of gene expression. The arrays contain probe sets corresponding to more than 3,300 S. aureus ORFs. Additionally, they contain probes to detect RNA of either forward or reverse orientation from more than 4,800 intergenic regions. In total, 107 were used as a control to verify the test results. A total of 432 probes on the microarrays overlapped between ORFs and intergenic regions. Two samples from each strains were used for the microarray and two independent experiments were performed.
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Project description:GAS strains were grown in THY broth to early exponential phase and RNA extracted. cDNA was generated and the expression profiles were determined using the RMLgenechip. Comparisons between the sample groups allow the identification of genes differentially expressed between strains. This experiment compared pre- and post- mouse passaged GAS strains. Keywords: GAS comparison
2006-02-01 | GSE3899 | GEO