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      Metagenomic Next-Generation Sequencing versus Traditional Pathogen Detection in the Diagnosis of Peripheral Pulmonary Infectious Lesions

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          Abstract

          Purpose

          The aim of this study was to evaluate the value of metagenomic next-generation sequencing (mNGS) in peripheral pulmonary infection management by comparing the diagnostic yield of mNGS and traditional pathogen detection methods on interventional specimens obtained by bronchoscopy.

          Patients and Methods

          This study enrolled patients suspected with pulmonary infection who were admitted to Tianjin Medical University General Hospital from June 2018 to August 2019. Specimens were obtained from bronchoscopy for mNGS analysis and traditional pathogen detection (including bronchoalveolar lavage fluid microbial culture, smear microscopy, and lung biopsy histopathology), and the diagnostic yields were compared between mNGS and traditional methods to evaluate the diagnostic value of mNGS in peripheral pulmonary infection diagnosis.

          Results

          In this study, by comparing mNGS with traditional pathogen detection, the results indicated that, first, mNGS identified at least one microbial species in almost 89% of the patients with pulmonary infection; second, mNGS detected microbes related to human diseases in 94.49% of samples from pulmonary infection patients who had received negative results from traditional pathogen detection; third, the accuracy and sensitivity of mNGS are higher than those of traditional pathogen detection; and, finally, mNGS could simultaneously detect and identify a large variety of pathogens.

          Conclusion

          Metagenomic NGS analysis provided fast and precise pathogen detection and identification, contributing to prompt and accurate treatment of peripheral pulmonary infection.

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          Most cited references36

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          The impact of next-generation sequencing technology on genetics.

          If one accepts that the fundamental pursuit of genetics is to determine the genotypes that explain phenotypes, the meteoric increase of DNA sequence information applied toward that pursuit has nowhere to go but up. The recent introduction of instruments capable of producing millions of DNA sequence reads in a single run is rapidly changing the landscape of genetics, providing the ability to answer questions with heretofore unimaginable speed. These technologies will provide an inexpensive, genome-wide sequence readout as an endpoint to applications ranging from chromatin immunoprecipitation, mutation mapping and polymorphism discovery to noncoding RNA discovery. Here I survey next-generation sequencing technologies and consider how they can provide a more complete picture of how the genome shapes the organism.
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            Microbiological Diagnostic Performance of Metagenomic Next-generation Sequencing When Applied to Clinical Practice

            Metagenomic next-generation sequencing (mNGS) was suggested to potentially replace traditional microbiological methodology because of its comprehensiveness. However, clinical experience with application of the test is relatively limited.
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              Transforming clinical microbiology with bacterial genome sequencing.

              Whole-genome sequencing of bacteria has recently emerged as a cost-effective and convenient approach for addressing many microbiological questions. Here, we review the current status of clinical microbiology and how it has already begun to be transformed by using next-generation sequencing. We focus on three essential tasks: identifying the species of an isolate, testing its properties, such as resistance to antibiotics and virulence, and monitoring the emergence and spread of bacterial pathogens. We predict that the application of next-generation sequencing will soon be sufficiently fast, accurate and cheap to be used in routine clinical microbiology practice, where it could replace many complex current techniques with a single, more efficient workflow.
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                Author and article information

                Journal
                Infect Drug Resist
                Infect Drug Resist
                IDR
                idr
                Infection and Drug Resistance
                Dove
                1178-6973
                19 February 2020
                2020
                : 13
                : 567-576
                Affiliations
                [1 ]Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital , Tianjin, People’s Republic of China
                [2 ]Graduate School, Tianjin Medical University , Tianjin, People’s Republic of China
                [3 ]Hematopoietic Stem Cell Transplantation Center, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College , Tianjin, People’s Republic of China
                [4 ]Department of Hematology, Tianjin First Central Hospital , Tianjin, People’s Republic of China
                Author notes
                Correspondence: Jing Feng; Jie Cao Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital , Anshan Road No. 154, Heping District, Tianjin300052, People’s Republic of ChinaTel +86 22 6036 2255 Email TMUHUJI@163.com; wanbo412@163.com
                Author information
                http://orcid.org/0000-0002-8567-894X
                Article
                235182
                10.2147/IDR.S235182
                7036976
                32110067
                04db9798-6cfc-4be2-bfab-72722d560b37
                © 2020 Huang et al.

                This work is published and licensed by Dove Medical Press Limited. The full terms of this license are available at https://www.dovepress.com/terms.php and incorporate the Creative Commons Attribution – Non Commercial (unported, v3.0) License ( http://creativecommons.org/licenses/by-nc/3.0/). By accessing the work you hereby accept the Terms. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. For permission for commercial use of this work, please see paragraphs 4.2 and 5 of our Terms ( https://www.dovepress.com/terms.php).

                History
                : 18 October 2019
                : 24 January 2020
                Page count
                Figures: 2, Tables: 4, References: 44, Pages: 10
                Funding
                This research was supported by grants from National Science and Technology Major Project of China (No.2018ZX10305409-001-001), National Natural Science Foundation of China (81970083, 81270144, 81570084 and 30800507 to J.F), and the National Key Technology R&D Program, China (2015BAI12B00 to J.F).
                Categories
                Original Research

                Infectious disease & Microbiology
                pulmonary infection,metagenomic next-generation sequencing,bronchoscopy,bronchoalveolar lavage,smear microscopy,transbronchial lung biopsy

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