Experience of implementing metagenomic next-generation sequencing in patients with suspected pulmonary infection in clinical practice
Abstract Pulmonary infections remain a leading cause of infectious disease-related hospitalizations. Metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic tool for identifying pathogens responsible for pulmonary infections. However, implementing mNGS in clinical practic...
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Nature Portfolio
2025-03-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-025-94840-2 |
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| author | Yuting Lai Binqi Chen Sida Chen Yan Shen |
| author_facet | Yuting Lai Binqi Chen Sida Chen Yan Shen |
| author_sort | Yuting Lai |
| collection | DOAJ |
| description | Abstract Pulmonary infections remain a leading cause of infectious disease-related hospitalizations. Metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic tool for identifying pathogens responsible for pulmonary infections. However, implementing mNGS in clinical practice presents several challenges. We conducted a retrospective analysis of 97 patients with suspected pulmonary infections who were admitted to our hospital and underwent mNGS alongside conventional microbiologic tests (CMT) over the past three years. We compared the diagnostic efficacy of mNGS versus CMT and assessed the clinical applications and challenges associated with mNGS in managing pulmonary infections. mNGS detected pathogens in 63.9% of cases, outperforming CMT (27.8%) and showing notable improvements in identifying Mycobacterium, fungal species, and rare pathogens. Antibiotic regimens were adjusted for 77.4% of patients with positive mNGS results, with clinical improvement observed in 93.5%. Of the 138 microbial strains initially identified by mNGS as possible pathogens, 65 (47.1%) were reclassified as colonizing organisms upon further clinical evaluation, including bacteria and fungi commonly associated with pulmonary infections. Notably, one patient was diagnosed with aspiration pneumonia due to oral anaerobes, which mNGS had categorized as normal microbial flora. In conclusion, mNGS serves as a valuable diagnostic approach for pulmonary infections, enhancing etiologic precision and informing patient management. Nevertheless, a comprehensive clinical interpretation of mNGS-identified microorganisms is essential to achieve accurate diagnosis. |
| format | Article |
| id | doaj-art-06c660dafb3640dfbb23bbbaf613d842 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Nature Portfolio |
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| spelling | doaj-art-06c660dafb3640dfbb23bbbaf613d8422025-08-20T03:41:49ZengNature PortfolioScientific Reports2045-23222025-03-011511910.1038/s41598-025-94840-2Experience of implementing metagenomic next-generation sequencing in patients with suspected pulmonary infection in clinical practiceYuting Lai0Binqi Chen1Sida Chen2Yan Shen3Department of Respiratory, Longgang Central HospitalGuangzhou University of Chinese MedicineDepartment of Respiratory, Longgang Central HospitalDepartment of Respiratory, Longgang Central HospitalAbstract Pulmonary infections remain a leading cause of infectious disease-related hospitalizations. Metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic tool for identifying pathogens responsible for pulmonary infections. However, implementing mNGS in clinical practice presents several challenges. We conducted a retrospective analysis of 97 patients with suspected pulmonary infections who were admitted to our hospital and underwent mNGS alongside conventional microbiologic tests (CMT) over the past three years. We compared the diagnostic efficacy of mNGS versus CMT and assessed the clinical applications and challenges associated with mNGS in managing pulmonary infections. mNGS detected pathogens in 63.9% of cases, outperforming CMT (27.8%) and showing notable improvements in identifying Mycobacterium, fungal species, and rare pathogens. Antibiotic regimens were adjusted for 77.4% of patients with positive mNGS results, with clinical improvement observed in 93.5%. Of the 138 microbial strains initially identified by mNGS as possible pathogens, 65 (47.1%) were reclassified as colonizing organisms upon further clinical evaluation, including bacteria and fungi commonly associated with pulmonary infections. Notably, one patient was diagnosed with aspiration pneumonia due to oral anaerobes, which mNGS had categorized as normal microbial flora. In conclusion, mNGS serves as a valuable diagnostic approach for pulmonary infections, enhancing etiologic precision and informing patient management. Nevertheless, a comprehensive clinical interpretation of mNGS-identified microorganisms is essential to achieve accurate diagnosis.https://doi.org/10.1038/s41598-025-94840-2Metagenomic next-generation sequencingEtiological diagnosisClinical utilityResult interpretationTreatment impact |
| spellingShingle | Yuting Lai Binqi Chen Sida Chen Yan Shen Experience of implementing metagenomic next-generation sequencing in patients with suspected pulmonary infection in clinical practice Scientific Reports Metagenomic next-generation sequencing Etiological diagnosis Clinical utility Result interpretation Treatment impact |
| title | Experience of implementing metagenomic next-generation sequencing in patients with suspected pulmonary infection in clinical practice |
| title_full | Experience of implementing metagenomic next-generation sequencing in patients with suspected pulmonary infection in clinical practice |
| title_fullStr | Experience of implementing metagenomic next-generation sequencing in patients with suspected pulmonary infection in clinical practice |
| title_full_unstemmed | Experience of implementing metagenomic next-generation sequencing in patients with suspected pulmonary infection in clinical practice |
| title_short | Experience of implementing metagenomic next-generation sequencing in patients with suspected pulmonary infection in clinical practice |
| title_sort | experience of implementing metagenomic next generation sequencing in patients with suspected pulmonary infection in clinical practice |
| topic | Metagenomic next-generation sequencing Etiological diagnosis Clinical utility Result interpretation Treatment impact |
| url | https://doi.org/10.1038/s41598-025-94840-2 |
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