ArticleAnnals of translational medicine2020
Application of next generation sequencing-based rapid detection platform for microbiological diagnosis and drug resistance prediction in acute lower respiratory infection.
Article in Annals of translational medicine, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 35 citations in OpenAlex.
- Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pneumonia in Patients With Cancer.Cancer medicine · 2026Article
- Spinal Tuberculosis Diagnosed by Metagenomics Capture (MetaCAP) in a Patient Undergoing Maintenance Hemodialysis: A Case Report.The American journal of case reports · 2026Article
- Toxoplasma gondii infection diagnosed by tNGS in a patient with acute lymphoblastic leukemia: a case report.BMC infectious diseases · 2025Article
- Clinical evaluation of two pathogen enrichment approaches for next-generation sequencing in the diagnosis of lower respiratory tract infections.Microbiology spectrum · 2025Article
- Host DNA depletion assisted metagenomic sequencing of bronchoalveolar lavage fluids for diagnosis of pulmonary tuberculosis.Annals of clinical microbiology and antimicrobials · 2025Article
- Targeted next-generation sequencing for respiratory infections in patients with haematological malignancies.Frontiers in cellular and infection microbiology · 2025Article
- Application of targeted next-generation sequencing for pathogens diagnosis and drug resistance prediction in bronchoalveolar lavage fluid of pulmonary infections.Frontiers in cellular and infection microbiology · 2025Article
- Comparing the diagnostic value of targeted with metagenomic next-generation sequencing in immunocompromised patients with lower respiratory tract infection.Annals of clinical microbiology and antimicrobials · 2024Article
- Clinical application of nanopore-targeted sequencing technology in bronchoalveolar lavage fluid from patients with pulmonary infections.Microbiology spectrum · 2024Article
- Article
- Comparative analysis of metagenomic and targeted next-generation sequencing for pathogens diagnosis in bronchoalveolar lavage fluid specimens.Frontiers in cellular and infection microbiology · 2024Article
- Application of metagenomic next-generation sequencing in the diagnosis of infectious diseases.Frontiers in cellular and infection microbiology · 2024Review
- Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples.Veterinary sciences · 2023Review
- Clinical application value of metagenomic second-generation sequencing technology in hematologic diseases with and without transplantation.Frontiers in cellular and infection microbiology · 2023Article
- Ultra-multiplex PCR technique to guide treatment ofOpen life sciences · 2023Article
- Multiplex PCR-based next generation sequencing as a novel, targeted and accurate molecular approach for periprosthetic joint infection diagnosis.Frontiers in microbiology · 2023Article
- Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections.Genome medicine · 2022Article
- Applying the pathogen-targeted next-generation sequencing method to pathogen identification in cerebrospinal fluid.Annals of translational medicine · 2021Article
- A Microbial World: Could Metagenomic Next-Generation Sequencing Be Involved in Acute Respiratory Failure?Frontiers in cellular and infection microbiology · 2021Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAcute lower respiratory infections (ALRIs) have a high mortality rate. We aimed to apply a platform that rapidly detects 36 microorganisms and 49 antibiotic resistance markers in the clinical diagnosis of ALRI and drug resistance prediction.
methodsMulticenter collection of clinical samples from patients with ALRIs was carried out from 2017 to 2018. Sputum culture (SC) was performed, which provided two outcomes: the detected pathogens and the resistance to different antibiotics. Additionally, each sputum sample was used to extract deoxyribonucleic acids (DNAs) followed by high-throughput sequencing.
resultsEleven commonly observed pathogens were surveyed, and for all samples with positive SC results (137 cases), the overall coverage was 95.62% according to the sequencing results. The receiver operating characteristic (ROC) curve was drawn, and cutoff reads of the most frequently detected pathogens were acquired. Overall, sequencing exhibited significantly higher sensitivity in the detection of pathogens compared with the traditional SC method, with a generally satisfactory specificity. Furthermore, we investigated the correlation between antibiotic resistance gene phenotypes and the actual outcomes of the drug sensitivity test, and some significant correlations were found, especially for the resistance to Amikacin in the presence of
conclusionsSequencing-based sputum metagenomics can reveal a profile of the lung pathogen microbiome. The sequencing method offers both sufficient accuracy and significantly higher sensitivity in the detection of pathogens, and can be at least a complementary approach to traditional SC reporting. The sequencing technique also revealed some novel potential correlations between the presence of different pathogens, as well as new antimicrobial-resistant genes.
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