Rapid identification of bacterial and fungal pathogens and resistance determinants directly from positive blood culture bottles using whole genome sequencing: a path to point-of-care diagnostics

Funding period: 2023–2025
Lead: Laura Mataseje
Total GRDI funding: $422,300

The gold standard for diagnosing blood stream infections is blood culture followed by phenotypic methods for identifying organism and antimicrobial susceptibility testing, which can take up to 5 days. Whole genome sequencing directly from blood culture bottle specimens is an attractive candidate for rapid diagnostics.

This project aims to improve methodologies for isolating high-quality DNA from blood culture samples and to validate and optimize newer rapid sequencing kits and equipment as well as bioinformatic tools to achieve the highest accuracy while maintaining short turnaround times.

Data from sequencing will be used to develop new informatic pipelines specific to organism identification and detection of antimicrobial resistance with outputs that are formatted for reporting to clinicians and infectious disease specialists. These objectives will contribute to an overall goal of reducing the turnaround time from receipt of sample to data generation and reporting from days to hours. By developing methodologies for rapid sequencing and informatic analysis, the team aims to unlock the potential for rapid diagnosis of blood stream infections in the clinical lab, which will improve infection control and antimicrobial stewardship initiatives. These methodologies could also be expanded to the bedside in the future.