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Title: Study of the molecular response of uropathogenic E. coli to ciprofloxacin in human bloodstream infection models to enhance the understanding of antibiotic therapy in urosepsis
Author: Gandi, Senthil Kumar
ISNI:       0000 0004 5990 9817
Awarding Body: University of Edinburgh
Current Institution: University of Edinburgh
Date of Award: 2014
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Urinary tract infection (UTI) is a major burden for healthcare due to high prevalence and increasing multi-drug resistance, and advance to urosepsis which accounts up to 20-30% of sepsis cases. Therapy failures due to inappropriate antibiotic treatment are a serious issue. We are studying the transcriptomic response of the uropathogenic strain E. coli CFT073 to antibiotic treatment during bloodstream infection (BSI) models in order to understand and avoid antibiotic therapy failures in bloodstream infection/urosepsis treatments which are caused by in vivo and in vitro differences of bacterial response to antibiotic challenge which cannot be explained by antibiotic resistance mechanisms. Bloodstream infection models and controls were established by growing E. coli CFT073 in Iso-Sensitest medium, pooled human serum, and pooled human whole blood with and without ciprofloxacin. The minimum inhibitory concentration (MIC) values for E. coli CFT073 in these models were identified and used to set the antibiotic challenge in the serum/blood cultures. The antibiotic challenge was introduced at mid logarithmic phase of growth of the organism to depict a clinical scenario. Global gene expression profiling of these conditions was examined using E. coli Genechip 2.0 from Affymetrix. Data analysis was performed using the Partek Genomics Suite. The difference in the growth medium was well reflected in the growth pattern. In contrast to the growth in IST, the growth in whole blood was double the duration and growth in human serum was 6 fold longer. This difference was also reflected in the transcriptomic study where metabolic genes were regulated differently in each medium as expected. 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; this could be an inverse proportion to the nutrient availability in the medium. In this study we have established new models to investigate bloodstream infections based on human serum and whole blood. 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. In ongoing and future studies we will exploit these differences in gene expression as biomarkers of bacterial response to antibiotics for the development of diagnostic tools for antibiotic therapy monitoring and as well as tools for diagnostics and stratification in drug development.
Supervisor: Bachmann, Till ; Amyes, Sebastian Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: blood stream infection ; ciprofloxacin ; gene expression ; biomarkers