Reduction of Human DNA Contamination in Clinical Cerebrospinal Fluid Specimens Improves the Sensitivity of Metagenomic Next-Generation Sequencing

Ji, Xinchao; Zhou, Linfu; Li, Chaoyang; Shi, Yajun; Wu, Meng‐Hao; Zhang, Yun; Fei, Xiaofei; Zhao, Gang

doi:10.1007/s12031-019-01472-z

Cited by 41 publications

(44 citation statements)

References 32 publications

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“…The mNGS technology is a new detection method for all currently known pathogenic microorganisms, including MTB [12]. mNGS allows for an unbiased and detailed test of the total DNA or RNA content of the microbiome [32].…”

Section: Discussionmentioning

confidence: 99%

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Metagenomic next generation sequencing for the diagnosis of tuberculosis meningitis: A systematic review and meta-analysis

Yu¹,

Zhao²,

Shen³

et al. 2020

PLoS ONE

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Background Tuberculous meningitis (TBM) is a severe form of extrapulmonary tuberculosis and its early diagnosis is very difficult leading to present with severe disability or die. The current study aimed to assess the accuracy of metagenomic next generation sequencing (mNGS) for TBM, and to identify a new test for the early diagnosis of TBM. Methods We searched for articles published in Embase, PubMed, Cochrane Library, China National Knowledge Infrastructure, and Wanfang Data up to June 30, 2020 for studies that assessed the efficacy of mNGS for the diagnosis of TBM. Then, the accuracy between mNGS and a composite reference standard (CRS) in these articles was compared using the meta-analysis approach. Results Four independent studies with 342 samples comparing mNGS and a CRS were included in this study. The sensitivity of mNGS for TBM diagnosis ranged from 27% to 84%. The combined sensitivity of mNGS was 61%, and the I2 value was 92%. Moreover, the specificity of mNGS for TBM diagnosis ranged from 96% to 100%. The combined specificity of mNGS was 98%, and the I2 value was 74%. The heterogeneity between studies in terms of sensitivity and specificity was significant. The area under the curve (AUC) of the summary receiver operating characteristic curve (SROC) of mNGS for TBM was 0.98. Conclusions The sensitivity of mNGS for TBM diagnosis was moderate. Furthermore, the specificity was extremely high, and the AUC of the SROC indicated a very good diagnostic efficacy. mNGS could be used as an early diagnostic method for TBM, however, the results should be treated with caution for the heterogeneity between studies was extremely significant. Systematic review registration INPLASY202070100.

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Section: Discussionmentioning

confidence: 99%

“…The mNGS technology is a new detection method, which allows for an unbiased and detailed test of the total DNA or RNA content of all currently known pathogenic microorganisms [11]. Thus, it has been increasingly used [12]. mNGS could detect pathogenic microorganisms from a wide range of clinical specimens, including CSF [11,13,14].…”

Section: Introductionmentioning

confidence: 99%

Metagenomic next generation sequencing for the diagnosis of tuberculosis meningitis: A systematic review and meta-analysis

Yu¹,

Zhao²,

Shen³

et al. 2020

PLoS ONE

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“…Processing the samples before library construction can reduce the host genome proportion, significantly increase the sequence coverage of pathogens in the samples, and improve the detection sensitivity. [ 20 ] Further, centrifugation and filtration can be combined to enrich pathogenic microorganisms. For second‐generation sequencing to detect viruses, samples can be centrifuged at a low speed of 6000 × g for 10 min, and the supernatant filtered using a 0.80 µm filter to remove eukaryotic and bacterial cells without affecting the extraction of RNA viruses.…”

Section: The Challenges For Ngs In Pathogens Diagnosismentioning

confidence: 99%

“…[ 19 ] Specifically, the HiSeq series platform is generally used to carry out clinical pathogenic detection on large sample sizes due to its high‐throughput and relatively long sequencing read length, however, each run can take up to 3.5 days, which is not suitable for the rapid detection of single samples. [ 20–22 ] Alternatively, NextSeq500 and NextSeq550 series sequencing systems offer the advantages of moderate throughput and short running time (12–30 h per run), making them particularly suitable for the detection of clinical pathogens, for which they are widely used. [ 23–26 ]…”

Section: History Of Sequencing Technologymentioning

confidence: 99%

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

et al. 2020

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The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next‐generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third‐generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS‐related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.

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An umbrella review of the diagnostic value of next-generation sequencing in infectious diseases

Cao,

Chen,

et al. 2024

Int J Clin Pharm

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Reduction of Human DNA Contamination in Clinical Cerebrospinal Fluid Specimens Improves the Sensitivity of Metagenomic Next-Generation Sequencing

Cited by 41 publications

References 32 publications

Metagenomic next generation sequencing for the diagnosis of tuberculosis meningitis: A systematic review and meta-analysis

Metagenomic next generation sequencing for the diagnosis of tuberculosis meningitis: A systematic review and meta-analysis

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

An umbrella review of the diagnostic value of next-generation sequencing in infectious diseases

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