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      Diagnostic accuracy of nanopore sequencing for the rapid diagnosis of pulmonary tuberculosis: A protocol for a systematic review and meta-analysis

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      1 , 1 , 2 , 2 , * ,
      PLOS ONE
      Public Library of Science

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          Abstract

          Background

          Pulmonary tuberculosis (PTB) is the most common type of tuberculosis (TB). Rapid diagnosis of PTB can help in TB control. Although the use of molecular tests (such as the GeneXpert MTB/RIF) has improved the ability to rapidly diagnose PTB, there is still room for improvement. Nanopore sequencing is a novel means of rapid TB detection. The purpose of this study was to establish a systematic review and meta-analysis protocol for evaluating the accuracy of nanopore sequencing for the rapid diagnosis of PTB.

          Methods

          We completed this protocol according to the Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) statement and registered on the PROSPERO platform. We will screen studies related to nanopore sequencing for diagnosis of PTB by searching through PubMed, EMBASE, the Cochrane Library using English, and Wanfang database, CNKI (China National Knowledge Infrastructure) using Chinese. Eligible studies will be screened according to the inclusion and exclusion criteria established in the study protocol. We will evaluate the methodological quality of the individual included studies using Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2). We will use Stata (version 15.0) with the midas command and RevMan (version 5.3) for meta-analysis and forest plots and SROC curves generation. A p < 0.05 was treated as a statistically significant difference. When significant heterogeneity exists between studies, we will explore sources of heterogeneity through meta-regression analysis and subgroup analysis.

          Conclusion

          To the best of our knowledge, this will be the first systematic review and meta-analysis of nanopore sequencing for the diagnosis of PTB. We hope that this study will find a new and effective tool for the early diagnosis of PTB.

          PROSPERO Registration number

          CRD42023495593.

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          Most cited references27

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          Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement

          Systematic reviews should build on a protocol that describes the rationale, hypothesis, and planned methods of the review; few reviews report whether a protocol exists. Detailed, well-described protocols can facilitate the understanding and appraisal of the review methods, as well as the detection of modifications to methods and selective reporting in completed reviews. We describe the development of a reporting guideline, the Preferred Reporting Items for Systematic reviews and Meta-Analyses for Protocols 2015 (PRISMA-P 2015). PRISMA-P consists of a 17-item checklist intended to facilitate the preparation and reporting of a robust protocol for the systematic review. Funders and those commissioning reviews might consider mandating the use of the checklist to facilitate the submission of relevant protocol information in funding applications. Similarly, peer reviewers and editors can use the guidance to gauge the completeness and transparency of a systematic review protocol submitted for publication in a journal or other medium.
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            QUADAS-2: a revised tool for the quality assessment of diagnostic accuracy studies.

            In 2003, the QUADAS tool for systematic reviews of diagnostic accuracy studies was developed. Experience, anecdotal reports, and feedback suggested areas for improvement; therefore, QUADAS-2 was developed. This tool comprises 4 domains: patient selection, index test, reference standard, and flow and timing. Each domain is assessed in terms of risk of bias, and the first 3 domains are also assessed in terms of concerns regarding applicability. Signalling questions are included to help judge risk of bias. The QUADAS-2 tool is applied in 4 phases: summarize the review question, tailor the tool and produce review-specific guidance, construct a flow diagram for the primary study, and judge bias and applicability. This tool will allow for more transparent rating of bias and applicability of primary diagnostic accuracy studies.
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              Preferred Reporting Items for a Systematic Review and Meta-analysis of Diagnostic Test Accuracy Studies

              Systematic reviews of diagnostic test accuracy synthesize data from primary diagnostic studies that have evaluated the accuracy of 1 or more index tests against a reference standard, provide estimates of test performance, allow comparisons of the accuracy of different tests, and facilitate the identification of sources of variability in test accuracy.
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                Author and article information

                Contributors
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: SoftwareRole: Writing – original draftRole: Writing – review & editing
                Role: InvestigationRole: MethodologyRole: ResourcesRole: ValidationRole: VisualizationRole: Writing – original draft
                Role: Data curationRole: Formal analysisRole: ResourcesRole: Supervision
                Role: ConceptualizationRole: Project administrationRole: SoftwareRole: SupervisionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                PLOS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                6 June 2024
                2024
                : 19
                : 6
                : e0304162
                Affiliations
                [1 ] Department of Thoracic Surgery, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
                [2 ] Department of Nursing, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
                Gulu University, UGANDA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                https://orcid.org/0009-0009-5363-967X
                Article
                PONE-D-24-00653
                10.1371/journal.pone.0304162
                11156269
                38843269
                ab9e4bb5-25fc-412b-899e-4f3bb62c08f2
                © 2024 Yu et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 10 January 2024
                : 3 May 2024
                Page count
                Figures: 0, Tables: 0, Pages: 7
                Funding
                Funded by: Hangzhou Biomedicine and Health Industry Development Supporting Science and Technology Special Project
                Award ID: 2023WJC162
                Award Recipient :
                Funded by: Hangzhou Biomedicine and Health Industry Development Supporting Science and Technology Special Project
                Award ID: 2023WJC312
                Award Recipient :
                This work was supported by Hangzhou Biomedicine and Health Industry Development Supporting Science and Technology Special Project. Yanqin Shen, 2023WJC162; Guocan Yu, 2023WJC312. The funder does not have a role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Registered Report Protocol
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Sequencing Techniques
                Nanopore Sequencing
                Research and Analysis Methods
                Molecular Biology Techniques
                Sequencing Techniques
                Nanopore Sequencing
                Biology and Life Sciences
                Organisms
                Bacteria
                Actinobacteria
                Mycobacterium Tuberculosis
                Medicine and Health Sciences
                Medical Conditions
                Infectious Diseases
                Bacterial Diseases
                Tuberculosis
                Medicine and Health Sciences
                Medical Conditions
                Tropical Diseases
                Tuberculosis
                Research and Analysis Methods
                Mathematical and Statistical Techniques
                Statistical Methods
                Metaanalysis
                Physical Sciences
                Mathematics
                Statistics
                Statistical Methods
                Metaanalysis
                Medicine and Health Sciences
                Diagnostic Medicine
                Tuberculosis Diagnosis and Management
                Research and Analysis Methods
                Database and Informatics Methods
                Database Searching
                Research and Analysis Methods
                Research Assessment
                Systematic Reviews
                Biology and life sciences
                Molecular biology
                Molecular biology techniques
                Sequencing techniques
                DNA sequencing
                Gene Sequencing
                Research and analysis methods
                Molecular biology techniques
                Sequencing techniques
                DNA sequencing
                Gene Sequencing
                Custom metadata
                All relevant data are within the manuscript and its Supporting information files.

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                Uncategorized

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