Klinisk validering av helgenombaserade analyser som verktyg mot antibiotikaresistens

Tidsperiod: 2019-12-01 till 2021-12-31

Projektledare: Susanne Sütterlin

Finansiär: Vetenskapsrådet

Bidragstyp: Bidrag för anställning eller stipendier

Budget: 2 000 000 SEK

Whole genome sequencing of bacteria has developed rapidly and the availability of comprehensible bioinformatic analysis tools has increased exponentially. While being routinely used for public health purposes, there is still no application of bioinformatics in clinical daily routine work. This work investigates strategies to identify useful applications of bioinformatics for urinary tract infections, and aims to validate DNA extraction protocols as well as bioinformatic processing according to clinical laboratory standards.Clinically well-defined Escherichia coli serve as model population, and for each isolate, clinical patient data, phenotypic bacterial properties of the isolates and bioinformatical analysis results are pooled. Certain focus is on a thorough validation of extraction protocols and quality assessments of sequence data with regard to the purpose of the intended analysis. From literature and public sequence database information, a custom database of virulence factors for colonization and invasiveness in the urinary tract is built. This database is then used to characterize and compare a collection of non-invasive isolates (cystitis) with another collection of invasive (blood stream) isolates.This project is an effort to implement WGS-based techniques into clinical practice that may serve as a tool for treatment decision making. Thus, WGS may help save unnecessary use of antibiotics, and thus slow down the development of antibiotic resistance.