AFFECTING an estimated 405 million people globally each year, UTIs are typically diagnosed using culture-based methods that can take between two and four days, delays that often force clinicians to prescribe antibiotics empirically, contributing to rising antimicrobial resistance.
In a new study, researchers evaluated eleven culture-independent sample-preparation methods using specimens from 78 patients with complicated UTIs. The goal was to find the fastest, most accurate way to prepare samples for real-time nanopore sequencing, a technology that can read microbial DNA directly without requiring a culture step. Once sequenced, the samples underwent metagenomic analysis to identify pathogens and determine antimicrobial susceptibility.
Low-Cost Sequencing Shows High Accuracy in Complicated UTI Cases
The results were significant. The optimised approach reached a 99% accuracy rate for identifying the infection-causing pathogen, correctly detecting 100 out of 101 cases. It also achieved 90% accuracy in profiling antimicrobial susceptibility, with a specificity of 95%, making it highly reliable for guiding treatment decisions. The method detected pathogens even in extremely low concentrations, as few as 32 bacterial cells per microlitre, and performed well even when host cells vastly outnumbered bacteria.
Importantly, the sequencing approach revealed 13 infections that standard clinical diagnostics had missed. These additional pathogens were later confirmed using independent methods such as PCR and the Vivalytic system, underscoring the enhanced sensitivity of metagenomic sequencing.
Beyond performance, cost and practicality were central considerations. The study found that the optimised method is up to 30% cheaper than comparable published techniques and commercial kits. Researchers also demonstrated that simple measurements, DNA yield and flow cytometry, can be used to pre-screen samples, ensuring that only viable candidates undergo sequencing. This strategy helps reduce unnecessary expenses, a key factor for adoption in clinical settings.
Sequencing for Better Antibiotic Decisions
The entire workflow, from sample collection to actionable results, takes about four hours, offering a dramatic improvement over the standard multiday process. The authors argue that this rapid, scalable approach could play a major role in improving diagnostic and antimicrobial stewardship by reducing guesswork and enabling more targeted antibiotic prescribing.
If widely implemented, the method could significantly enhance UTI management and curb the growing threat of antimicrobial resistance.
Reference
Bellankimath AB et al. Metagenomic sequencing enables accurate pathogen and antimicrobial susceptibility profiling in complicated UTIs in approximately four hours. Nat Commun. 2025. Doi: 10.1038/s41467-025-66865-8
