Escherichia coli
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ABSTRACT:
PROVIDER: PRJDB13852 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome sequence analysis of antimicrobial-resistant bacteria
| PRJDB8858 | ENA
Project description:Collateral sensitivity of antibiotic resistant bacteria to antimicrobial peptides
| PRJNA379428 | ENA
Project description:Large plasmid sequencing, antimicrobial resistant Escherichia coli strains
| PRJDB9410 | ENA
Project description:The rise of antimicrobial resistant pathogens calls for new antibacterial treatments, but potent new compounds are scarce. Development of new antibiotics is difficult, especially against Gram-negative bacteria, as here uptake is strongly hindered by the additional outer membrane. Most antimicrobial agents against Gram-negatives use the porin mediated pathway to cross the outer membrane, which limits the choice of an antibiotic, as it has to fit by size, charge and hydrophilicity. In E. coli, the major porins OmpF and OmpC are associated with antibiotic translocation and therefore also with unspecific antibiotic cross-resistance. In this regard, alternative uptake routes are of interest. We were interested in the uptake opportunities of the small, natural product antibiotic negamycin and thereby found new uptake pathways across the outer membrane of E. coli. Besides OmpF and OmpC, we investigated the role of the minor porins OmpN and ChiP in negamycin translocation. We detected an effect of OmpN and ChiP on negamycin susceptibility and confirmed passage by electrophysiological assays. The structure of OmpN was resolved in order to analyze the negamycin translocation mechanism by computational simulations. As abundancy of these minor porins was low in E. coli, their transcript levels were analyzed by RNA-Seq. Increased transcripts levels of ompN and chiP were observed upon negamycin treatment, hinting at a role in antibiotic uptake. These new, additional uptake pathways across the outer membrane of E. coli highlight the antibiotic potential of negamycin, especially as resistance development is low due to availability of multiple uptake routes at both the outer and inner membranes
2023-10-01 | GSE183363 | GEO
Project description:PhoP is considered a regulator of virulence despite being conserved in both pathogenic and non-pathogenic Enterobacteriaceae. While Escherichia coli strains represent both non-pathogenic commensal isolates and numerous virulent pathotypes, the PhoP virulence regulator has only been studied in commensal E. coli. To better understand how conserved transcription factors contribute to virulence, we characterized PhoP in pathogenic E. coli. Loss of phoP significantly attenuated E. coli during extraintestinal infection. This was not surprising since we demonstrated that PhoP differentially regulated the transcription of >600 genes. In addition to survival at acidic pH and resistance to polymyxin B, PhoP was required for repression of motility and oxygen-independent changes in the expression of primary dehydrogenase and terminal reductase respiratory chain components. All phenotypes have in common a reliance on an energized membrane. Thus, we hypothesized that PhoP mediated these effects by regulating genes that generate a proton motive force. Indeed, bacteria lacking PhoP exhibited a hyper-polarized membrane, and dissipation of the transmembrane electrochemical gradient increased the susceptibility of the phoP mutant to acidic pH, while inhibiting respiratory generation of the proton gradient restored resistance to antimicrobial peptides independent of lipopolysaccharide modification. These findings demonstrate a connection between PhoP, virulence, and the energized state of the membrane.
2011-07-29 | GSE31029 | GEO
Project description:Diverse antimicrobial-resistant E. coli strains to evaluate AMR genotyping algorithms
| PRJNA779173 | ENA
Project description:Comparative Transcriptomic Profiling of Antimicrobial Resistant and Virulent Escherichia coli of Poultry Origin
| PRJNA375003 | ENA
Project description:Escherichia coli intestinal infection pathotypes are characterized by distinct adhesion patterns including the recently described clumpy adhesion phenotype. Here we identify and characterize genetic factors contributing to clumpy adhesion of E. coli strain 4972. In this strain, the transcriptome and proteome of adhered bacteria were found distinct from planktonic bacteria in supernatant. A total of 622 genes in the transcriptome were differentially expressed in bacteria present in clumps relative to the planktonic bacteria. Seven genes targeted for disruption had variable distribution in different pathotypes and nonpathogenic E. coli with pilV and spnT genes being the least frequent or absent from most groups. Deletion (Δ) of five differentially expressed genes, flgH, ffp, pilV, spnT and yggT affected motility, adhesion or antibiotic stress. ΔflgH exhibited 80 % decrease and ΔyggT depicted 145.5 % increase in adhesion, and upon complementation, adhesion significantly reduced to 13 %. ΔflgH lost motility and was regenerated when complemented whereas Δffp had significantly increased motility and reintroduction of the same gene reduced it to the wild-type level. The clumps produced by of Δffp and ΔspnT were more resistant and protected the bacteria with ΔspnT showing the best clump formation in terms of ampicillin stress protection. ΔyggT had the lowest tolerance to gentamicin where the antibiotic stress completely eliminated the bacteria. Overall, we were able to investigate the influence of clump formation on the cell surface adhesion and antimicrobial tolerance with the contribution of several factors crucial to clump formation on susceptibility to the selected antibiotics.
2024-04-09 | PXD042731 | Pride
Project description:PhoP is considered a regulator of virulence despite being conserved in both pathogenic and non-pathogenic Enterobacteriaceae. While Escherichia coli strains represent both non-pathogenic commensal isolates and numerous virulent pathotypes, the PhoP virulence regulator has only been studied in commensal E. coli. To better understand how conserved transcription factors contribute to virulence, we characterized PhoP in pathogenic E. coli. Loss of phoP significantly attenuated E. coli during extraintestinal infection. This was not surprising since we demonstrated that PhoP differentially regulated the transcription of >600 genes. In addition to survival at acidic pH and resistance to polymyxin B, PhoP was required for repression of motility and oxygen-independent changes in the expression of primary dehydrogenase and terminal reductase respiratory chain components. All phenotypes have in common a reliance on an energized membrane. Thus, we hypothesized that PhoP mediated these effects by regulating genes that generate a proton motive force. Indeed, bacteria lacking PhoP exhibited a hyper-polarized membrane, and dissipation of the transmembrane electrochemical gradient increased the susceptibility of the phoP mutant to acidic pH, while inhibiting respiratory generation of the proton gradient restored resistance to antimicrobial peptides independent of lipopolysaccharide modification. These findings demonstrate a connection between PhoP, virulence, and the energized state of the membrane. Comparison of gene expression between wild-type CFT073 and a CFT073 phoP deletion mutant during logarithmic phase growth in LB medium. Three biological replicates were compared from each strain.
2011-07-28 | E-GEOD-31029 | biostudies-arrayexpress
Project description:Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water
| PRJDB4884 | ENA