High-throughput next-generation sequencing for identifying pathogens during early-stage post-lung transplantation

Lian, Qiaoyan; Chen, Ao; Zhang, Jianheng; Guan, Weijun; Xu, Xin; Wei, Bing; Huang, Danxia; He, Jianxing; Chen, Ju

doi:10.1186/s12890-021-01723-z

Cited by 10 publications

(10 citation statements)

References 42 publications

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“…Additionally, DSA should be present for AMR. Pulmonary infection was diagnosed based on our previous studies [27,28]. There were no pathogens in the AR or CLAD groups.…”

Section: Histopathology From Lung Biopsy Tissuementioning

confidence: 99%

Application of plasma donor-derived cell free DNA for lung allograft rejection diagnosis in lung transplant recipients

Chen

Zhang

et al. 2023

BMC Pulm Med

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Background Donor-derived cell-free DNA (dd-cfDNA) has been applied to monitor acute rejection (AR) in kidney and heart transplantation. This study was aimed to investigate the application of dd-cfDNA levels in the diagnosis of AR and chronic lung allograft dysfunction (CLAD) among the lung transplantation recipients (LTRs). Methods One hundred and seventy LTRs were enrolled at the First Affiliated Hospital of Guangzhou Medical University between 1 June 2015 and 30 March 2021. Patients were divided into 4 groups: stable group, AR group, infection group and CLAD group. The level of dd-cfDNA was analyzed using target region sequencing and the performance characteristics of dd-cfDNA for diagnosis of AR and CLAD were determined, respectively. Results Kruskal–Wallis test showed that there were some significant differences in the level of dd-cfDNA (%) among the 4 groups, with p < 0.001. Among them, the level of dd-cfDNA (%) was highest (median 2.17, IQR [1.40–3.82]) in AR group, and higher in CLAD group (median 1.07, IQR [0.98–1.31]), but lower in infection group (median 0.71, IQR [0.57–1.07]) and lowest in stable group (median 0.71, IQR [0.61–0.84]). AUC-ROC curve analysis showed that the threshold of dd-cfDNA for AR was 1.17%, with sensitivity being 89.19% and specificity being 86.47%, and the optimal threshold of 0.89% was determined of CLAD, with sensitivity being 95.00% and specificity of 76.99%. Conclusions Plasma dd-cfDNA could be a useful tool for the assessment of lung allograft rejection, including AR and CLAD, and holds promise as a noninvasive biomarker for “allograft injury” in both acute and chronic rejection following lung transplantation.

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“…Additionally, DSA should be present for AMR. Pulmonary infection was diagnosed based on our previous studies [27,28]. There were no pathogens in the AR or CLAD groups.…”

Section: Histopathology From Lung Biopsy Tissuementioning

confidence: 99%

Application of plasma donor-derived cell free DNA for lung allograft rejection diagnosis in lung transplant recipients

Chen

Zhang

et al. 2023

BMC Pulm Med

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“…was associated with reduced lung function [ 69 ]. When it comes to early symptomatic pulmonary infection after lung transplantation, NGS was superior to traditional pathogen detection (88.24% vs. 76.47%) [ 70 ]. In patients who underwent hematopoietic cell transplantation with pneumonia, cell-free plasma DNA sequencing (cfDNA-seq) detected infections involving more than a single pathogenic mold (especially non- Aspergillus species) in 38 of the 75 patients [ 71 ].…”

Section: Ngs and Fungal Infection In Different Organsmentioning

confidence: 99%

Next-Generation Sequencing Applications for the Study of Fungal Pathogens

Jiang

Chen

et al. 2022

Microorganisms

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Next-generation sequencing (NGS) has become a widely used technology in biological research. NGS applications for clinical pathogen detection have become vital technologies. It is increasingly common to perform fast, accurate, and specific detection of clinical specimens using NGS. Pathogenic fungi with high virulence and drug resistance cause life-threatening clinical infections. NGS has had a significant biotechnological impact on detecting bacteria and viruses but is not equally applicable to fungi. There is a particularly urgent clinical need to use NGS to help identify fungi causing infections and prevent negative impacts. This review summarizes current research on NGS applications for fungi and offers a visual method of fungal detection. With the development of NGS and solutions for overcoming sequencing limitations, we suggest clinicians test specimens as soon as possible when encountering infections of unknown cause, suspected infections in vital organs, or rapidly progressive disease.

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“…Among the fteen included studies, the highest positive likelihood ratio is found in Jiang J's study, whose value is 24.34 (95%CI, 10.73-55. 21). The lowest positive likelihood ratio occurs in the Pan T study with a value of 1.50 (95%CI, 0.57-39.95).…”

Section: Sensitivity Speci City Plr Nlr Diagnostic or And Sroc Curvementioning

confidence: 99%

Diagnostic value of NGS in bronchoalveolar lavage fluid for pulmonary fungal infection

Kuang

Liu

2022

Preprint

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Metagenomic sequencing (mNGS) has been approved to diagnose lung fungal diseases. However, the test performance of clinical mNGS has not been widely recognized. This study aims to evaluate the value of mNGS in the system of bronchoalveolar lavage fluid through the systematic evaluation of gathered analysis and related research. A total of 1113 patients (265 with proven or probable invasive fungal diseases), included in 6 studies, were analyzed. The pooled sensitivity, specificity, PLR, NLR, and diagnostic odds ratio were 0.89(95%CI, 0.75–0.96), 0.86 (95%CI, 0.78–0.91), 6.2 (95%CI, 4.0-9.6), 0.12 (95%CI, 0.05–0.32), and 50(95%CI, 15–163), respectively. The area under the summary receiver operating characteristic curve, with 95% confidence intervals, was 0.93(95%CI,0.90–0.95).The accuracy of the metagenomic sequencing (mNGS) is good, has certain clinical characteristics, can explain the results separately, and has the clinical value of early diagnosis of lung fungal infection. Purpose:This meta-analysis of randomized controlled trials aims to investigate the diagnostic utility and benefits of mNGS in comparison to conventional detection techniques for lung fungal infection in clinical patients. Patients and methods:A preliminary diagnosis of lung infection based on a patient's medical history, clinical symptoms, and imaging tests is a requirement for inclusion.Using the method of meta-analysis, the sensitivity, specificity, diagnostic odds ratio (OR), positive likelihood ratio (PLR), and negative likelihood ratio (NLR) of BAL-mNGS for identifying lung fungal illness were pooled. Results:6 studies involving a total of 1113 patients, 265 of whom had invasive fungal diseases that were proven or likely to have occurred, were examined. The diagnostic odds ratio, PLR, NLR, and diagnostic sensitivity were all pooled, and their respective values were 0.89 (95% CI, 0.75–0.96), 0.86 (95% CI, 0.78–0.91), 6.2 (95% CI, 4.0-9.6), 0.12 (95% CI, 0.05–0.32), and 50 (95% CI, 15–163). With 95% confidence intervals, the area under the summary receiver operating characteristic curve was 0.93 (95%CI, 0.90–0.95). Conclusion:The clinical value of metagenomic sequencing (mNGS) for the early diagnosis of lung fungal infection is that it is accurate, has specific clinical characteristics, can explain the results separately, and has clinical utility.

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High-throughput next-generation sequencing for identifying pathogens during early-stage post-lung transplantation

Cited by 10 publications

References 42 publications

Application of plasma donor-derived cell free DNA for lung allograft rejection diagnosis in lung transplant recipients

Application of plasma donor-derived cell free DNA for lung allograft rejection diagnosis in lung transplant recipients

Next-Generation Sequencing Applications for the Study of Fungal Pathogens

Diagnostic value of NGS in bronchoalveolar lavage fluid for pulmonary fungal infection

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