Improving Suspected Pulmonary Infection Diagnosis by Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing: a Multicenter Retrospective Study

Jin, Xiao; Li, Juan; Shao, Mingyue; Lv, Xuedong; Ji, Ningfei; Zhu, Yehan; Huang, Mao; Yu, Feichao; Zhang, Chang-wen; Xie, Lixu; Huang, Jianling; Chen, Sixi; Zhu, Changjun; Lv, Minjie; Feng, Ganzhu

doi:10.1128/spectrum.02473-21

Cited by 40 publications

(22 citation statements)

References 40 publications

(51 reference statements)

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“…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].…”

Section: Discussionsupporting

confidence: 85%

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

Lai,

Chen,

Chen

et al. 2024

Preprint

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Background Pulmonary infection remains one of the leading infectious diseases of hospitalization. Metagenomic next-generation sequencing (mNGS) has been proven to be a promising diagnostic technology in etiological identification for pulmonary infection. But when applying mNGS to clinical practice, physicians still face many challenges. Methods We retrospectively analyzed the data of 97 patients admitted to our hospital with suspected pulmonary infection prescribed to mNGS during the past 3 years. The clinical application of mNGS in the diagnosis and management of pulmonary infection and also challenges were investigated. Results Causative or possibly causative pathogens were detected in 63.9% of patients by mNGS, performing consistently well for Mycobacterium tuberculosis, non-tuberculous mycobacteria, fungus and rare pathogens. In 43.3% of patients, 65 microbes reported as causative or possibly causative pathogens by laboratory were reclassified as colonization after fully interpretation by physicians. Antibiotics were adjusted for 34.0% of patients mainly based on positive mNGS results and not adjusted for 41.2% with pathogens identified already covered by empirical therapy or negative mNGS results. Conclusions mNGS is a promising tool in etiological diagnosis of pulmonary infection. However, physicians should go beyond the reported pathogens by laboratory and investigate fully in clinical practice. The effect on clincal treatment deserves further investigation from aspect of cost effectiveness and also application scenarios should be illustrated.

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Section: Discussionsupporting

confidence: 85%

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

Lai,

Chen,

Chen

et al. 2024

Preprint

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“…At present, there is no uniform standard for the interpretation of mNGS results. The criteria for mNGS positivity have been established according to the literature (Fang et al, 2020;Jin et al, 2022), as follows: 1) >30% relative abundance of bacteria (excluding M. tuberculosis) and fungi at the genus level; 2) one or more unique reads of M. tuberculosis either at the species or the genus level; 3) a stringent map read number (SMRN) of ≥3 for viruses; and 4) positive culture and/or histopathological examination and at least 50 unique reads from a single species of bacteria or fungi. The final etiology confirmation of all cases was decided by a group of clinical microbiologists and physicians.…”

Section: Criteria For Positive Mngs Resultsmentioning

confidence: 99%

The clinical significance of in-house metagenomic next-generation sequencing for bronchoalveolar lavage fluid diagnostics in patients with lower respiratory tract infections

Qin

Zhou

Peng

et al. 2022

Front. Cell. Infect. Microbiol.

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ObjectiveMetagenomic next-generation sequencing (mNGS) technology has the potential to detect a wide range of pathogenic microorganisms. However, reports on the diagnostic value and clinical significance of different platforms of mNGS for patients with lower respiratory tract infections (LRTIs) remain scarce.MethodsA total of 306 patients with suspected LRTIs were enrolled from January 2019 to December 2021. The diagnostic performance of conventional methods and mNGS on bronchoalveolar lavage fluid (BALF) were compared. BALF mNGS was performed using a commercial and an in-house laboratory. The diagnostic value and the clinical implications of mNGS for LRTIs were analyzed for the different platforms.ResultsThe positive rate of mNGS in the in-house group was higher than that in the commercial group (85.26% vs. 70.67%, p < 0.001). mNGS significantly increased the pathogen detection rate compared with conventional methods [from 70.67% vs. 22.67% (p < 0.001) to 85.26% vs. 30.77% (p < 0.001)]. The pathogens detected using mNGS included bacteria, fungi, viruses, and atypical pathogens. The in-house platform performed well on a wider spectrum of microbial distribution. Furthermore, it showed an advantage in detecting mixed pathogens in immunocompromised patients. Among the mNGS positive cases, 34 (32.0%) cases had their antibiotics adjusted in the commercial group, while 51 (38.3%) cases had a change of treatment in the in-house group. Moreover, the turnaround time of mNGS and the time from mNGS to discharge in the in-house group were significantly shorter than those in the commercial group.ConclusionIn-house mNGS had a higher detection rate and can show a wider spectrum of pathogens, with potential benefits for the clinic by shortening the turnaround time and hospitalization, and it may be more suitable for clinical microbiology laboratories.

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“…This poses a challenge to spine surgeons: how to identify pathogens early and quickly, enabling rapid and precise treatment. Macrogenomic sequencing (mNGS), as an emerging non-culture-based technology with high sensitivity and speci city, fast detection and less affected by pre-sampling antibiotics [20,21]., has shown higher sensitivity than traditional culture-based methods in the detection of pathogens in bloodstream infections, lung infections, and other diseases in terms of con rming infections and their causative organisms [22][23][24].In this paper, the positive detection rate of mNGS (61.2%) was signi cantly higher than that of routine microbiological culture (30.8%) and calcitoninogen assay (28%), in line with the ndings of a previous study [25]. Notably, 17 culture-negative patients presented positive results by mNGS.…”

Section: Discussionmentioning

confidence: 99%

Spinal infections? mNGS combined with microculture and pathology for answers

Chen,

Liu,

Huang

et al. 2024

Preprint

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Background This study focuses on the efficacy of genome sequencing technology (mNGS) in diagnosing infections of the spine and the development of therapeutic regimens combining mNGS, microbiological cultures, and pathological investigations to provide new perspectives for the treatment of spinal infections. Methods Data were collected on 108 patients with suspected spinal infections between January 2022 and December 2023. Lesion tissues were obtained through C-arm assisted puncture or open surgery for mNGS, conventional microbiological culture, or pathological analysis. Treatment plans involving personalized antimicrobial therapy were tailored based on mNGS findings, microbial cultures, and pathological analysis, with a follow-up evaluation 7 days postoperatively. The sensitivity and specificity of mNGS for detecting spinal infection pathogens, as well as its impact on treatment and prognosis, were assessed based on the final clinical outcomes. Results In the diagnosis of spinal infections, the positive detection rate of mNGS (61.20%) was significantly higher than that of conventional microbiological culture (30.80%) and PCT (28%). The sensitivity (79.41%) and negative predictive value (63.16%) of mNGS were substantially greater than those of cultures (25% and 22.58%, respectively), with no significant difference in specificity and positive predictive value. Seven days post-surgery, a notable reduction in the percentage of neutrophils (NEUT%) was observed, while decreases in white blood cell count (WBC), erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP) were not statistically significant. At the last follow-up, there was a significant decrease in all patients' Visual Analogue Scale (VAS) scores, Oswestry Disability Index (ODI), and Japanese Orthopaedic Association (JOA) scores. Conclusion The efficacy of mNGS technology surpasses traditional microbiological culture in pathogen detection, exhibiting superior performance particularly in identifying rare and critical pathogens. Treatment protocols combining mNGS, microbiological cultures and pathological examinations are effective in the treatment of spinal infections and provide a valuable clinical reference.

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Improving Suspected Pulmonary Infection Diagnosis by Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing: a Multicenter Retrospective Study

Cited by 40 publications

References 40 publications

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

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

The clinical significance of in-house metagenomic next-generation sequencing for bronchoalveolar lavage fluid diagnostics in patients with lower respiratory tract infections

Spinal infections? mNGS combined with microculture and pathology for answers

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