PhD defence D.E. (Dimard) Foudraine

Dissertation in short:

Within the INSPECTION project, several targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays were developed and validated for the rapid detection of antimicrobial resistance mechanisms in E. coli and K. pneumoniae, two bacterial species which cause significant morbidity and mortality. The main project goal was to demonstrate the potential of LC-MS/MS as a diagnostic tool for the detection of antimicrobial resistance. This is important, as new rapid and accurate tests are required for the detection of resistant bacteria to shorten the time to appropriate treatment for patients with bacterial infections. The project focused on resistance to beta-lactam, aminoglycoside and fluoroquinolone antibiotics as these are frequently used to treat infections caused by E. coli and K. pneumoniae. Within the project, beta-lactam, aminoglycoside and fluoroquinolone resistance was studied using a combination of discovery-based proteomics and whole genome sequencing (WGS). Furthermore, targeted LC-MS/MS assays were developed for the detection of the most prevalent bacterial mechanisms that confer resistance to carbapenem and aminoglycoside antibiotics. In addition, E. coli strains carrying certain beta-lactamase genes were studied after prolonged meropenem exposure. In the final part of the project, a multiplex targeted LC-MS/MS assay was developed for the rapid detection of 27 beta-lactam, aminoglycoside and fluoroquinolone resistance mechanisms in positive blood cultures. In the future, we aim to expand our panel for the detection of other resistance mechanisms and we aim to automate the developed method to make it more suitable for routine diagnostics.