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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Published on: August 20, 2021
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Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based,
Victoria A Janes1, Sébastien Matamoros1, Patrick Munk2
1Department of Medical Microbiology, University of Amsterdam, Amsterdam UMC, Amsterdam, Netherlands.
The Lancet. Microbe
|June 10, 2022
Summary
Metagenomics shows promise for faster urinary tract infection diagnosis by detecting pathogens and resistance genes directly from urine. This approach could improve patient care by complementing traditional culture methods.
Area of Science:
- Microbiology
- Genomics
- Clinical Diagnostics
Background:
- Urinary tract infection (UTI) diagnosis relies on semi-quantitative bacterial culture, a slow and potentially unreliable method, especially with antibiotic use.
- Metagenomics offers a potential alternative for rapid and accurate UTI diagnosis by directly sequencing urine microbiota and resistome.
- Current diagnostic methods face limitations in speed and reliability, necessitating advanced approaches.
Purpose of the Study:
- To compare the diagnostic accuracy of metagenomics against traditional semi-quantitative bacterial culture for UTI diagnosis.
- To evaluate metagenomics for semi-quantitative detection of bacterial pathogens and antimicrobial resistance genes in urine samples.
- To assess the potential of metagenomics to improve diagnostic speed and reliability in UTI cases.
Main Methods:
- Prospective study of consecutive urine samples from a clinical laboratory.
- Screening of samples by DNA concentration, followed by PCR-free metagenomic sequencing of selected high-DNA samples.
- Calculation of a diagnostic index (DNA concentration x pathogen read fraction) and comparison with culture using AUROC analysis.
- Resistance gene detection using ResFinder and PointFinder, compared with phenotypic antimicrobial susceptibility testing.
Main Results:
- Metagenomic DNA concentration screening achieved an AUROC of 0.85, effectively ruling out culture positivity in 91% of cases at a specific cutoff.
- The diagnostic index demonstrated an AUROC of 0.87, with high positive predictive value (93%) at a defined cutoff.
- Agreement between genotypic and phenotypic antimicrobial resistance testing varied by antibiotic, ranging from 71% to 100%.
Conclusions:
- This study provides proof-of-concept for using metagenomics in semi-quantitative pathogen and resistome detection for UTI diagnosis.
- Metagenomics shows potential to enhance diagnostic accuracy and speed compared to conventional culture methods.
- Further prospective clinical validation is warranted to confirm the value of metagenomics in patient management for UTIs.
