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

Abstract

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.

Optimal specimen type for accurate diagnosis of infectious peripheral pulmonary lesions by mNGS

“…TBLB specimens and sterile saline soaked with protective needle tip were sent to a commercial laboratory for mNGS. In addition to culture, other traditional pathogen detection methods based on invasive respiratory specimens obtained through bronchoscopy were described in detail in a previously published study in our center [ 27 ]. Gram staining, acid-fast staining, hexamine silver staining, the galactomannan antigen detection test (GM test) with BALF samples, and Mycobacterium tuberculosis / rifampicin resistance test (X-pert) with BALF samples were performed to identify bacteria including M. tuberculosis and fungi including Pneumocystis carinii .…”

High‐Throughput Metagenomics for Identification of Pathogens in the Clinical Settings

“…However, frequent and inappropriate use of antibiotics in respiratory tract infections limits the sensitivity and reliability of culture-based testing, which often occurs in clinical settings. mNGS provides relatively fast and precise detection and identification of a large variety of pathogens, contributing to the prompt and accurate treatment of pulmonary infection, [147][148][149] particularly for critically ill patients and those with mixed-infection. [150,151] The most common pathogens causing lower respiratory pulmonary infectious have been identified as bacteria, such as Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii.…”

“…As the cell walls of fungi and intracellular bacteria are thick, cell wall disrupting methods are used to extract DNA, which may affect the detection of RNA viruses. [ 148 ] Therefore, it is important to consider the use of a variety of cell wall disrupting techniques to improve the efficiency of cell breakage and the detection rate for RNA viruses.…”

“…Current limitations suggest that mNGS can be a complementary, and perhaps an essential test in certain clinical settings, rather than being an “one‐in‐all” test. [ 148 ]…”

Diagnosis of complication in lung transplantation by TBLB + ROSE + mNGS

“…The detection of pathogens is a prerequisite to exclude infections. mNGS also called high-throughput sequencing, allows for unbiased detection of virtually any pathogen present in a given sample [ 7 , 8 , 9 , 10 ]. In thisstudy, we report several cases and reviewed our institutional experience for diagnosing infection and rejection based on clinical, radiologic, cytologic, pathological, or microbiological findings.…”