ArticleEBioMedicine2025
Yield of clinical metagenomics: insights from real-world practice for tissue infections.
Article in EBioMedicine, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Metagenomic next-generation sequencing for pathology-suspected fungal infections at rare anatomical sites: a case series.Future science OA · 2026Article
- Review
- Diagnostic and Therapeutic Options in Myocarditis and Inflammatory Cardiomyopathy.Biomedicines · 2026Review
- Integrating metagenomics and metatranscriptomics intoThe Journal of general virology · 2026Review
- Real-life impact of clinical metagenomics in the intensive care unit: a multicenter retrospective study in greater paris area hospitals.Critical care (London, England) · 2026Article
- Metagenomic next-generation sequencing: new horizons in microbiology.Frontiers in cellular and infection microbiology · 2026Review
- Transforming tuberculosis diagnosis with clinical metagenomics: progress and roadblocks.Journal of clinical microbiology · 2025Review
- Metagenomic fingerprints in bronchoalveolar lavage differentiate pulmonary diseases.NPJ digital medicine · 2025Article
- The Role of microRNAs and Cell-Free DNAs in Fungal Infections: Systematic Review and Meta-Analysis of the Literature.Journal of fungi (Basel, Switzerland) · 2025Review
Corrections and comments
- Erratum issued
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWhile metagenomic next-generation sequencing (mNGS) has been acknowledged as a valuable diagnostic tool for infections, its clinical validity and impact on patient management when using fresh tissue samples remains uncertain.
methodsWe conducted a retrospective cross-sectional study involving patients who underwent tissue mNGS at a tertiary hospital in China from February 2021 to February 2024, aiming to assess its ability to detect plausible pathogens and its clinical validity and impact.
findingsA total of 520 mNGS results from 508 patients were analysed, detecting plausible pathogens in 302 (58.1%) tests, including 260 single-pathogen and 42 (13.9%) multi-pathogen results. Rare pathogens, such as Balamuthia mandrillaris, Bartonella henselae, and Sporothrix globosa, were identified. Of the multi-pathogen results, 22 were with predominance of anaerobes. mNGS showed higher positivity in cases with high initial suspicion of infection than those used for ruling out infection (PR 1.961, 95% CI: 1.604-2.394) and in patients living with HIV (PR 1.312, 95% CI: 1.047-1.643) or solid organ transplant recipients (PR 1.346, 95% CI: 1.103-1.643) compared to immunocompetent individuals. Sensitivity and specificity for diagnosing confirmed/probable infections were 85.0% (95% CI: 76.7%-93.3%) and 93.7% (95% CI: 86.8%-100.0%), respectively. mNGS influenced clinical management in 258 (49.6%) cases by identifying new infections and in 112 (21.5%) by excluding infections. It prompted initiation (20.2%), modification (23.1%), or discontinuation (6.3%) of antimicrobial therapy.
interpretationmNGS demonstrates high diagnostic accuracy for tissue infections. Its impact on clinical management highlights the need to integrate it into current diagnostic practices.
fundingNational Natural Science Foundation of China (No. 82472371), "Leading Geese" Research and Development Plan of Zhejiang Province (No. 2024C03218), and Pudong New Area Joint Project (PW2021D-09).
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