Ontology highlight
ABSTRACT:
PROVIDER: PRJNA634613 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:25 blaNDM-positive strains collected from bovine farms in China
| PRJNA1207204 | ENA
Project description:blaNDM-positive live poultry market sample
| PRJNA877800 | ENA
Project description:Genomic content of Vaccine strains were probed against the known sequence of the virulent strain Rlow of M. gallisepticum to identify divergent or absent genes in the attenuated strains.
2009-12-24 | GSE19629 | GEO
Project description:Inactivation of blaNDM-1-positive and blaNDM-1-negative Escherichia coli strains and their differential gene expression upon solar irradiation
| PRJEB13897 | ENA
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
2007-12-19 | GSE9862 | GEO
Project description:Genotyping studies suggest that there is genetic variability among P. gingivalis strains, however the extent of variability remains unclear, and the regions of variability have only partially been identified. We previously used heteroduplex analysis of the ribosomal operon intergenic spacer region (ISR) to type P. gingivalis strains in several diverse populations, identifying 6 predominant heteroduplex types and many minor ones. In addition we used ISR sequence analysis to determine the relatedness of P. gingivalis strains to one another, and demonstrated a link between ISR sequence phylogeny and the disease-associated phenotype of P. gingivalis strains. The availability of whole genome microarrays based on the genomic sequence of strain W83 has allowed a more comprehensive analysis of P. gingivalis strain variability, using the entire genome. The objectives of this study were to define the phylogeny of P. gingivalis strains using the entire genome, to compare the phylogeny based on genome content to the phylogeny based on a single locus (ISR), and to identify genes that are associated with the strongly disease-associated strain W83 that could be important for virulence. Keywords: Comparative genomic hybridization
2008-10-09 | GSE13128 | GEO
Project description:Background: Efflux pumps are important cofactors for carbapenem resistance in Enterobacter cloacae. The regulatory mechanism by which asmA influences efflux pump function in this species remains unclear. This study explored the regulatory role of asmA on efflux pumps in carbapenem-resistant Enterobacter cloacae. Results: Sixteen carbapenem-resistant Enterobacter cloacae were collected. All strains carried blaNDM, 87.5% of which were blaNDM-1 and 12.5% were blaNDM-5. PAβN had weak inhibition on carbapenem resistance in ST78 and strong inhibition in ST2260. ST2260(CY-8) was still resistant to carbapenems after elimination of blaNDM and could be inhibited by PAβN. However, ST78(CY-9) lost its resistance to carbapenems. Knockout of asmA reduced the MIC of ST2260 by 16-fold. ST78 showed no such changes. Growth curves revealed impaired growth only in ST2260ΔasmA. Transcriptomics/qRT-PCR revealed no significantly altered acrAB-tolC or marA expression in either strain. Membrane proteomics detected AcrB loss specifically in ST2260ΔasmA. The loss of asmA affected a wide range of membrane proteins, especially OmpW. Molecular docking predicted that AsmA could bind to AcrB, with stronger binding energy in ST78. The buried area of the CY-8 model involved 110 contact residues, while the number of contacts of the CY-9 model increased to 144. The AsmA chain of the two models had 46 common contact residues, and the AcrB chain had 60 common contact residues. AcrB of ST78 generally carries the I277V mutation. Conclusion: asmA is highly conserved in Enterobacter cloacae. It has functional heterogeneity in different ST types. In ST2260, asmA can affect efflux pump-mediated carbapenem resistance. AsmA can regulate AcrAB-TolC not by affecting marA. It is predicted that AsmA can maintain the carbapenem resistance of Enterobacter cloacae ST2260 by helping AcrB anchor to the inner membrane. The difference in carbapenem resistance mediated by efflux pumps between ST78 and ST2260 suggests that ST78 commonly carries the AcrB I277V mutation, which is a key site for efflux of β-lactams.
2025-08-08 | GSE304310 | GEO