Ontology highlight
ABSTRACT:
PROVIDER: PRJNA494290 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Whole genome sequences of Escherichia coli from blood stream infections
| PRJNA514215 | ENA
Project description:Escherichia coli is a major cause of blood stream and urinary tract infections. Owing to the spread of antimicrobial resistance, it is often treated with an inadequate antibiotic. With the aim to accelerate the diagnostics of this key pathogen, we used the flycode technology to generate nanobodies against the conserved and highly abundant outer membrane protein OmpA. Two nanobodies each recognizing a different isoform of OmpA were shown by flow cytometry to recognize > 91% of 85,680 E. coli OmpA sequences deposited in a large bacterial genome database. Crystal structures of these nanobodies in complex with the respective OmpA isoform revealed interactions with all four surface accessible loops of OmpA. Steric hindrance caused by dense O-antigen layers initially impeded reliable capture of clinical E. coli strains. By generating nanobody constructs with long linkers and by thinning the O-antigen layer through alterations to growth medium and buffers, we achieved to capture <50 CFU/mL. Our work provides a framework to generate nanobodies for the specific and sensitive detection and capture of clinically relevant pathogenic bacteria.
2025-06-11 | PXD054264 | Pride
Project description:Treatment failures of antibiotic therapy are of major concern and can be caused by a misalignment of the antibiotic susceptibility determined in vitro with the behaviour of the pathogen in the patient. The aim of this study was to investigate the transcriptomic response of the uropathogenic strain E. coli CFT073 to antibiotic treatment in blood stream infection (BSI) models in order to understand and avoid antibiotic therapy failures in urosepsis treatments. Blood stream infection models were established by growing E. coli CFT073 in pooled human blood with and without ciprofloxacin. The antibiotic challenge was introduced at mid-logarithmic phase of growth of the organism to depict a clinical scenario. The responses were quantified by comparing to the responses at a given time point without the challenge. Global gene expression profiling of these conditions was examined using commercial DNA microarrays. The organismâ??s metabolic genes appeared to be regulated differently in each medium, this indicated that the bacterial growth regulation were different between the models. Bacterial growth in human serum mainly involved regulations of amino acid synthesis/utilisation such as glycine, arginine, thiamine, regulations of fimbrial proteins and bacteriophage genes. When comparing the responses to antibiotic challenge, bacteria grown in the respective medium displayed specific responses to the antibiotic challenge which were not seen in the other media. The common functions of genes that responded to the ciprofloxacin challenge were SOS response, DNA repair, DNA replication, fimbrial genes and bacteriophage initiation. A subset of the bacteriophage genes showed similar responses between the three models. From genes that were differentially regulated, responses observed in the serum model appeared to have the highest fold changes. In this study we established new models to investigate blood stream infections. They have been used to identify previously unknown differences in the molecular response to antibiotic treatment by the uropathogenic E. coli CFT073 depending on the media. These unique responses will help to unravel the complexity of bloodstream infection and can help to improve the antibiotic therapy that is used. A 10 array study using total RNA recovered from bacteria that were grown in human whole blood, with and without ciprofloxacin challenge. Arrays were performed in 5 biological replicates from each condition.
2016-04-01 | E-GEOD-68106 | biostudies-arrayexpress
Project description:Clinical blood stream infections Escerichia coli isolates and HR strains. Genome sequencing and assembly
| PRJNA1083935 | ENA