Metagenomic next-generation sequencing indicates more precise pathogens in patients with pulmonary infection: A retrospective study

Abstract

BackgroundTimely identification of causative pathogens is important for the diagnosis and treatment of pulmonary infections. Metagenomic next-generation sequencing (mNGS), a novel approach to pathogen detection, can directly sequence nucleic acids of specimens, providing a wide range of microbial profile. The purpose of this study was to evaluate the diagnostic performance of mNGS in the bronchoalveolar lavage fluid (BALF) of patients with suspected pulmonary infection.MethodsFrom April 2019 to September 2021, 502 patients with suspected pneumonia, who underwent both mNGS of BALF and conventional microbiological tests (CMTs), were classified into different groups based on comorbidities. The diagnostic performances of mNGS and CMTs were compared. Comprehensive clinical analysis was used as the reference standard.ResultsThe diagnostic accuracy and sensitivity of mNGS were 74.9% (95% confidence interval [CI], 71.7-78.7%) and 72.5% (95% CI, 68.2-76.8%) respectively, outperformed those of CMTs (36.9% diagnostic accuracy, 25.4% sensitivity). For most pathogens, the detection rate of mNGS was higher than that of CMTs. Polymicrobial infections most often occurred in immunocompromised patients (22.1%). Only 2.3% patients without underlying diseases developed polymicrobial infections. Additionally, the spectrums of pathogens also varied among the different groups. We found the positive predictive values (PPV) to be dependent upon both the pathogen of interest as well as the immunologic status of the patient (e.g., the PPV of Mycobacterium tuberculosis was 94.9% while the PPV of Pneumocystis jirovecii in immunocompetent individuals was 12.8%). This information can help physicians interpret mNGS results.ConclusionmNGS of BALF can greatly enhance the accuracy and detection rate of pathogens in patients with pulmonary infections. Moreover, the comorbidities and types of pathogens should be taken consideration when interpreting the results of mNGS.

Experience of implementing metagenomic next-generation sequencing in patients with suspected pulmonary infection in clinical practice

“…As the reported incidence of pulmonary tuberculosis has been declining consistently for more than 10 years, China is still one of the high tuberculosis burden countries, accounting for 7.1% of all estimated incident cases worldwide [9]. In this study, Mycobacterium tuberculosis complex was the most common identi ed pathogen, with a detection rate of 16.5%, similar to several previous studies using mNGS analysis [10][11]. The sensitivity of mNGS for tuberculosis diagnosis has been proven to be similar to Xpert MTB/RIF assay and culture [12].…”

Case report: Cutaneous anthrax diagnosed using mNGS of a formalin-fixed paraffin-embedded tissue sample

“…So, we successfully diagnosed cutaneous anthrax through mNGS on FFPE tissues, promptly treated the patient with penicillin and achieved a good prognosis. The application of mNGS technology in medicine also has certain limitations, such as complex operations, high costs, and the detection process has not yet been standardized, and in the absence of a unified standard for the mNGS biochemical analysis process, users choose biochemical analysis software based on personal experience and simplicity, which will affect the repeatability of experiments and the reliability of results ( Han et al., 2019 ; Wu et al., 2022 ). However, there is potential for cost reductions due to increased demand and technological development.…”

Infective Endocarditis during Pregnancy—Keep It Safe and Simple!

“…Cell-free DNA sequencing and other state-of-the-art molecular methods are showing their usefulness in the etiological diagnosis of IE, especially in those with negative bacterial cultures [ 92 , 93 ]. A representative example is metagenomic next-generation sequencing, which according to clinical studies published to date has a higher sensitivity than classical diagnostic methods [ 94 , 95 ]. Duan et al [ 96 ] analyzed a group of 109 patients, both with and without different infectious pathologies, and demonstrated that although the sensitivity of the method is superior, no statistically significant differences were reported in specificity compared to cultures ( p = 0.41).…”