ArticleFrontiers in microbiology2022
Rapid Detection of Bacterial Pathogens and Antimicrobial Resistance Genes in Clinical Urine Samples With Urinary Tract Infection by Metagenomic Nanopore Sequencing.
Article in Frontiers in microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it, 45 citations in OpenAlex.
- Exploring the clinical and diagnostic value of metagenomic next-generation sequencing for urinary tract infection: a systematic review and meta-analysis.BMC infectious diseases · 2024Pooled it
- 1,2,3-Triazole-linked DNA biosensors: molecular design to real-time applications.RSC advances · 2026Review
- Oxford Nanopore Sequencing, a Promising Technology for Precision Diagnostics in Intensive Care Units: A Narrative Review.Biomedicines · 2026Review
- A rapid ionic liquid-based DNA extraction method for molecular diagnostics of urinary tract infections.Microbiology spectrum · 2026Article
- A Proof-of-Concept of a 2-Hours Direct Antimicrobial Susceptibility Test from Inoculated Urine Samples.Microorganisms · 2026Article
- Current status and prospects of nanopore sequencing technology in the detection of pathogenic microorganisms.Frontiers in microbiology · 2026Review
- Laboratory tests for bovine respiratory bacteria and antimicrobial resistance in commercial feedlot cattle: comparing culture, long-read metagenomics, and recombinase polymerase amplification.Frontiers in microbiology · 2026Article
- Metagenomic sequencing enables accurate pathogen and antimicrobial susceptibility profiling in complicated UTIs in approximately four hours.Nature communications · 2025Article
- Application and evaluation of HB&L system in the rapid diagnosis of urinary tract infection.Translational andrology and urology · 2025Article
- Article
- Rapid detection of β-lactamase activity using the rapid Amp NP test.Microbiology spectrum · 2025Article
- Optimizing sample preparation for culture-free nanopore sequencing to enable rapid pathogen and antimicrobial resistance profiling in bovine mastitis.Frontiers in microbiology · 2025Article
- A simple, low-cost, and highly efficient protocol for rapid isolation of pathogenic bacteria from human blood.Frontiers in microbiology · 2025Article
- Applying nanopore sequencing in the etiological diagnosis of bloodstream infection.Frontiers in microbiology · 2025Review
- Culture and amplification-free nanopore sequencing for rapid detection of pathogens and antimicrobial resistance genes from urine.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2024Article
- Innovative Biosensor Technologies in the Diagnosis of Urinary Tract Infections: A Comprehensive Literature Review.Indian journal of microbiology · 2024Review
- Impact of cell lysis treatment before saliva metagenomic DNA extraction on the oral microbiome and the associated resistome.Clinical and experimental dental research · 2024Article
- Unveiling microbial diversity: harnessing long-read sequencing technology.Nature methods · 2024Review
- Predictive phage therapy forProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Bacterial enrichment prior to third-generation metagenomic sequencing improves detection of BRD pathogens and genetic determinants of antimicrobial resistance in feedlot cattle.Frontiers in microbiology · 2024Article
Corrections and comments
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Authors and funding
14 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Urinary tract infections (UTIs) are among the most common acquired bacterial infections in humans. The current gold standard method for identification of uropathogens in clinical laboratories is cultivation. However, culture-based assays have substantial drawbacks, including long turnaround time and limited culturability of many potential pathogens. Nanopore sequencing technology can overcome these limitations and detect pathogens while also providing reliable predictions of drug susceptibility in clinical samples. Here, we optimized a metagenomic nanopore sequencing (mNPS) test for pathogen detection and identification in urine samples of 76 patients with acute uncomplicated UTIs. We first used twenty of these samples to show that library preparation by the PCR Barcoding Kit (PBK) led to the highest agreement of positive results with gold standard clinical culture tests, and enabled antibiotic resistance detection in downstream analyses. We then compared the detection results of mNPS with those of culture-based diagnostics and found that mNPS sensitivity and specificity of detection were 86.7% [95% confidence interval (CI), 73.5-94.1%] and 96.8% (95% CI, 82.4-99.9%), respectively, indicating that the mNPS method is a valid approach for rapid and specific detection of UTI pathogens. The mNPS results also performed well at predicting antibiotic susceptibility phenotypes. These results demonstrate that our workflow can accurately diagnose UTI-causative pathogens and enable successful prediction of drug-resistant phenotypes within 6 h of sample receipt. Rapid mNPS testing is thus a promising clinical diagnostic tool for infectious diseases, based on clinical urine samples from UTI patients, and shows considerable potential for application in other clinical infections.
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