Analytical validation of a highly accurate and reliable next-generation sequencing-based urine assay

Area of Science:

• Microbiology
• Genomics
• Infectious Diseases

Background:

• Urinary tract infections (UTIs) are common, but current urine culture diagnostics have limitations, potentially leading to misdiagnosis and inappropriate antimicrobial use.
• Next-generation sequencing (NGS)-based metagenomics presents a more precise alternative for pathogen detection in clinical settings.

Purpose of the Study:

• To develop and validate BIOTIA-ID, a clinical-grade NGS pipeline for accurate pathogen identification and antimicrobial resistance profiling in urine samples.
• To demonstrate the superiority of BIOTIA-ID over conventional culture-based methods for UTI diagnosis.

Main Methods:

• Development and validation of the BIOTIA-ID NGS pipeline using clinical and spiked urine samples.
• Application of a machine learning-based bioinformatic pipeline for pathogen and resistance marker identification.
• Validation on 1,470 urine specimens, with discordant results reconciled using qPCR or Sanger sequencing.

Main Results:

• BIOTIA-ID achieved high sensitivity (97.2%) and specificity (99.6%) with low limits of detection for bacterial and fungal species.
• The assay identified common antimicrobial resistance genes, such as sul, blaSHV, and cfxA, in specific bacterial species.
• 87% concordance with comparator methods, demonstrating robust performance.

Conclusions:

• BIOTIA-ID is a comprehensive, accurate, and clinical-grade NGS diagnostic assay for urine specimens.
• The assay offers significant advantages over traditional urine culture, improving UTI diagnostics and guiding targeted antimicrobial therapy.
• Implementation of BIOTIA-ID can enhance patient management for recurrent and complicated UTIs and support antimicrobial stewardship.