| dc.description.abstract | Urinary Tract Infection (UTI) is a prevalent global health concern that accounts for 1-3% of primary healthcare visits and approximately 13.7% of community-based antibiotic prescriptions. The urinary tract is the most common source of E. coli bacteremia and urosepsis (when UTI spreads to the bloodstream) accounts for a quarter of all sepsis cases. The current methods for UTI diagnosis are time-consuming, taking 3-5 days before the prescription of the right antibiotics, resulting in empirical treatment. Rapid diagnosis has become increasingly important with the growing burden of antimicrobial resistance (AMR). Real-time whole genome sequencing combined with rapid bioinformatics analysis enables the timely detection of pathogens and their AMR profile.
In this proof-of-concept study, nanopore sequencing using the MinION device was directly applied to urine samples spiked with six WHO-priority pathogens most associated with UTI, including: Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa, Enterococcus faecalis, and Staphylococcus aureus. Two clinically significant UTI concentrations (10^3 and 10^5 CFU/ml) of pathogens were sequenced for each species. Importantly, the detection method did not require urine culture and DNA amplification. As sequencing is costly, PCR was performed solely for the verification of pathogen detection before sequencing. Identification of pathogens at concentrations 105 CFU/ml was possible within 10 minutes, and all predefined AMR genes were detected within 3 hours using raw nanopore sequencing data. Moreover, we were able to identify E. coli, K. pneumoniae, and P. mirabilis at 10^3 CFU/ml, which demonstrates the potential for the detection of pathogens using nanopore sequencing at lower concentrations with further research and optimization. The result of this study holds great promise for future applications in clinical microbiology for rapid diagnosis of UTI, prevention of AMR, and for health care surveillance. | |