Rapid bacterial pathogen identification with nanopore sequencing in clinical urinary tract infection setting
Abstract
Urinary tract infections (UTIs) affect approximately two-thirds of women worldwide, posing a significant healthcare burden. Uncomplicated UTIs can escalate if not treated promptly. Inappropriate antibiotic use, driven by slow conventional diagnostics, contributes to the escalating crisis of antimicrobial resistance (AMR). A rapid, accurate, and affordable pathogen identification with integrated AMR profiling is essential for effective treatment and responsible antibiotic stewardship.Traditional UTI diagnosis relies on urine culture and antimicrobial susceptibility testing (AST), often requiring up to 96 hours and thus necessitating the empiric use of broad-spectrum antibiotics as a first-line of treatment. While faster options like dipsticks and Polymerase Chain Reaction (PCR) exist, they offer limited pathogen coverage and lack AMR information. Next-generation sequencing (NGS) and mass spectrometry (MS) enable comprehensive profiling but are hindered by cost, complexity, and turnaround times exceeding 24 hours.MinION, a third-generation nanopore sequencing device, is known for its real-time sequencing and portability, making it a potential point-of-care device for UTI diagnostics. This study investigates the clinical utility of nanopore sequencing through a secondary analysis of anonymized clinical records and leftover urine samples from 401 patients (50 percent Thai, 50 percent international) treated at Bumrungrad International Hospital, Bangkok, Thailand. The cohort…
How strong is the evidence?
Evidence Hub reads this as a cohort study, done in people. Its evidence level is 3 of 5 (Moderate · trial / cohort / secondary analysis). Trials without a large randomized design, cohorts and secondary analyses give moderate evidence. Reported size: 401 participants or records.
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