Metagenomic next-generation sequencing of bronchoalveolar lavage fluid in non-severe and severe pneumonia patients

Zhao, Hongqin; Zhao, Yanhong; Yan, Nana; Wang, Yu; Li, Wushuang; Zhao, Jiangman; Xu, Yue; Tang, Hui; Liu, Xunchao

doi:10.1016/j.mimet.2023.106848

Cited by 2 publications

(4 citation statements)

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“…In addition, a greater proportion of our hospitalized patients presented with severe pneumonia. Although there was also an increase in mNGS detection of mixed conditions in cases of severe pneumonia, which is consistent with the findings of Zhao et al [31], our difference was not statistically significant. This may be due to different sample sizes and standardized protocols for mNGS detection.…”

Section: Discussionsupporting

confidence: 91%

“…This may be due to different sample sizes and standardized protocols for mNGS detection. It was also demonstrated by Zhao et al [31].…”

Section: Discussionsupporting

confidence: 55%

“…It was also demonstrated by Zhao et al . [31]. The validity of mNGS for pathogen detection in both common and severe pneumonia cases was consistent regardless of the severity of the disease.…”

Section: Discussionmentioning

confidence: 85%

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Improving pulmonary infection diagnosis with metagenomic next-generation sequencing of bronchoalveolar lavage fluid

Long,

Xia,

Feng

et al. 2024

Journal of Medical Microbiology

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Introduction. Inappropriate use of antibiotics and inadequate therapeutic regimens for early-stage pulmonary infections are major contributors to increased prevalence of complications and mortality. Moreover, due to the limitations in sensitivity of conventional testing, there is an urgent need for more diagnostically efficient methods for the detection and characterization of pathogens in pulmonary infections. Hypothesis/Gap Statement. Metagenomic next-generation sequencing (mNGS) can contribute to the diagnosis and management of pulmonary infections. Aim. This study aimed to evaluate the clinical application and value of mNGS in the diagnosis of clinically suspected pulmonary infections by comparing with conventional testing. Methodology. In this study, the diagnosis performance of mNGS was evaluated using bronchoalveolar lavage fluid (BALF) samples from 143 patients with suspected lung infections. First, we conducted a prospective study on 31 patients admitted to Yuebei People’s Hospital Affiliated to Shantou University Medical College to investigate the clinical value. Then a retrospective analysis was performed by including more patients (n=112) to reduce the random error. Pathogens were detected by mNGS and conventional methods (culture and PCR). Then, the types and cases of detected pathogens, as well as the specificity and sensitivity, were compared between the two methods. We evaluated the performance of mNGS in detecting bacterial, fungal, viral and mixed infections in BALF. The effect of disease severity in pulmonary infections on the integrity of mNGS pathogen detection was also explored. Results. The mNGS provided an earlier and more comprehensive pathogen profile than conventional testing, which in turn prompted a change in clinical medication, which led to improvement in eight patients (8/31=25.81 %) in the presence of other serious comorbidities. In a retrospective analysis, mNGS was much more sensitive than conventional testing in the diagnosis of pulmonary infections (95.33 % vs. 55.56 %; P<0.001), with a 39.77 % increase in sensitivity. The detection rate of mNGS for mixed infections was significantly higher than that of conventional testing methods for both common and severe pneumonia (48/67=71.64 % vs. 12/52=23.08 %, P<0.001; 44/59=74.58 % vs. 11/59=18.64 %, P<0.0001). Conclusion. The sensitivity of mNGS in the diagnosis of pathogenic microorganisms in pulmonary infections far exceeds that of conventional culture tests. As a complementary method to conventional methods, mNGS can help improve the diagnosis of pulmonary infections. In addition, mNGS pathogen integrity detection rate was similar in common and severe pneumonia. We recommend the prompt use of mNGS when mixed or rare pathogen infections are suspected, especially in immunocompromised individuals and/or critically ill individuals.

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Section: Discussionsupporting

confidence: 91%

“…This may be due to different sample sizes and standardized protocols for mNGS detection. It was also demonstrated by Zhao et al [31].…”

Section: Discussionsupporting

confidence: 55%

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Improving pulmonary infection diagnosis with metagenomic next-generation sequencing of bronchoalveolar lavage fluid

Long,

Xia,

Feng

et al. 2024

Journal of Medical Microbiology

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“…Yan et al 12 showed that the use of mNGS was associated with lower rates of antibiotic escalation and may facilitate the cessation of antivirals in patients with LRTIs. Zhao et al 13 demonstrated that the pathogen-positive rate of mNGS in BALF samples was higher than that of culture in patients despite prior antibiotic use, and the results also showed that mNGS of BALF was a potentially useful tool for testing mixed pathogens in severe pneumonia.…”

Section: Introductionmentioning

confidence: 99%

Clinical Application and Evaluation of Metagenomic Next-Generation Sequencing for Lower Respiratory Tract Infections and Human Tumor Screening

Huang,

Weng,

et al. 2023

IJGM

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Background To evaluate the clinical value of metagenomic next-generation sequencing (mNGS) in screening of lower respiratory tract infections (LRTIs) and human tumors. Methods Human samples included bronchoalveolar lavage fluid (BALF), sputum, lung biopsy tissue, and peripheral blood from 188 patients who were admitted to our hospital between January 2020 and September 2022 were analyzed using mNGS for simultaneous pathogen and chromosome copy number variation (CNV) detection. Traditional microbial culture and comprehensive microbial test (CMT) were also conducted. The diagnostic efficiencies of the three methods (mNGS, traditional culture, and CMT groups) were compared. Results Among the 188 patients, 149 (79.3%) were in the LRTIs group and 39 (20.7%) were in the non-LRTIs group. The diagnostic sensitivity and accuracy of the mNGS group were higher than those of the traditional culture and CMT groups ( P < 0.001; P < 0.001; P < 0.001; P < 0.001), and the specificity was higher than that of the CMT group ( P = 0.039) but lower than that of the traditional culture group ( P = 0.006). The positive predictive values of the mNGS and traditional culture groups were higher than that of the CMT group ( P = 0.004; P = 0.011). The negative predictive value of the mNGS group was higher than that of the CMT group ( P = 0.003). In addition, all samples were subjected to simultaneous chromosome CNV detection, and 8% (15/188) were positive for CNV. Of the 15 patients, 10 were initially misdiagnosed as non-neoplastic diseases, with a misdiagnosis rate of 66.7% (10/15). The BALF CNV test was performed on 13 patients diagnosed with primary or metastatic lung cancer, with a positivity rate of 38.5%. Conclusion The sensitivity and accuracy of pathogen diagnosis using mNGS were better than those of traditional culture and CMT. CNV detection is an important auxiliary diagnostic tool for cancer, particularly for screening occult tumors.

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Metagenomic next-generation sequencing of bronchoalveolar lavage fluid in non-severe and severe pneumonia patients

Cited by 2 publications

References 58 publications

Improving pulmonary infection diagnosis with metagenomic next-generation sequencing of bronchoalveolar lavage fluid

Improving pulmonary infection diagnosis with metagenomic next-generation sequencing of bronchoalveolar lavage fluid

Clinical Application and Evaluation of Metagenomic Next-Generation Sequencing for Lower Respiratory Tract Infections and Human Tumor Screening

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