Diagnostic accuracy of nanopore sequencing using respiratory specimens in the diagnosis of pulmonary tuberculosis

Yu, Guocan; Shen, Yanqin; Zhong, Fangming; Zhou, Lei; Chen, Gang; Fang, Lingling; Zhu, Pengfei; Sun, Lifang; Zhao, Wuchen; Yu, Wenfeng; Ye, Bo

doi:10.1016/j.ijid.2022.06.001

Cited by 20 publications

(18 citation statements)

References 31 publications

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“…Taken together, these results indicate that the nanopore sequencing assay can be used to detect infections caused by Mycobacterium spp. and can distinguish MTB from NTM, consistent with the results of previous studies [ 28 , 29 ]. This result is of great importance since rapid discrimination between MTB and NTM is required to ensure that specific and effective medications are administered to patients in order to maximize the effectiveness of anti-mycobacterial treatments.…”

Section: Discussionsupporting

confidence: 92%

“…A few reported studies have highlighted the diagnostic value of respiratory tract samples (sputum or BALF) collected from patients with suspected PTB when tested via nanopore sequencing. For example, Yu et al found that the sensitivity rate, specificity rate, PPV, and NPV of the nanopore sequencing assay for diagnosing PTB cases were 94.8%, 97.9%, 99.1%, and 88.7%, respectively [ 29 ]. Similarly, the results obtained by Liu et al, who conducted nanopore sequencing detection of BALF specimens obtained from 55 suspected PTB cases, showed values for the abovementioned indicators of 75.86%, 80.77%, 81.48%, and 75.00%, respectively [ 28 ].…”

Section: Discussionmentioning

confidence: 99%

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Accuracy of Nanopore Sequencing as a Diagnostic Assay for Pulmonary Tuberculosis versus Smear, Culture and Xpert MTB/RIF: A Head-to-Head Comparison

Yang,

Ye,

Zhang

et al. 2023

TropicalMed

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Early diagnosis of pulmonary tuberculosis (PTB) is pivotal for achieving effective tuberculosis (TB) control. This study aimed to assess the effectiveness of nanopore sequencing of sputum, bronchoalveolar lavage fluid (BALF), and pleural fluid samples for achieving early PTB diagnosis and provided head-to-head comparisons of nanopore sequencing results versus results obtained using smear, culture, and Xpert MTB/RIF assays. Patients admitted from October 2021 to April 2023 were screened for PTB using diagnostic imaging and electronic medical records. A total of 172 patients (129 PTB, 43 non-TB patients) were included in the final analysis after the exclusion of patients who did not meet the study’s inclusion criteria. PTB-positive rates were determined for each assay, and then, assay diagnostic efficacies were compared. The positive MTB-detection rates obtained using nanopore sequencing were 86.8% for all samples, 62.3% for BALF, and 84.6% for pleural fluid, all of which were significantly higher than the corresponding rates obtained using the other three assays. The overall sensitivity rates, specificity rates, and area under the curve (AUC) values obtained from smear testing were 5.4%, 95.3%, and 0.504, respectively, as compared to the respective results obtained via culture (18.6%, 100.0%, and 0.593), Xpert MTB/RIF (26.4%, 97.7%, and 0.620), and nanopore sequencing (85.3%, 95.4%, and 0.903). The diagnostic efficacy of nanopore sequencing surpassed the diagnostic efficacies of smear, culture, and Xpert MTB/RIF assays. Thus, nanopore sequencing holds promise as an alternative to Xpert MTB/RIF for early PTB detection, particularly for the testing of BALF and pleural fluid samples.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Accuracy of Nanopore Sequencing as a Diagnostic Assay for Pulmonary Tuberculosis versus Smear, Culture and Xpert MTB/RIF: A Head-to-Head Comparison

Yang,

Ye,

Zhang

et al. 2023

TropicalMed

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“…The modulation provides valuable information about the structure, 3 size, 4 interaction, 5 and other properties of molecules. Because nanopore technology is characterized by high resolution, 6 low cost, 7 and rapid detection, 8 it has been developed for detecting and analyzing molecules at the single-molecule level, including DNA, 9 proteins, 10 RNA, peptides, 11 and polysaccharides. 12 Based on the type of forming materials, nanopores are mainly divided into biological nanopores and solid-state nanopores.…”

Section: ■ Introductionmentioning

confidence: 99%

Conformation Influence of DNA on the Detection Signal through Solid-State Nanopores

Liu,

Ma,

Wang

et al. 2024

Langmuir

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The detection and identification of nanoscale molecules are crucial, but traditional technology comes with a high cost and requires skilled operators. Solid-state nanopores are new powerful tools for discerning the three-dimensional shape and size of molecules, enabling the translation of molecular structural information into electric signals. Here, DNA molecules with different shapes were designed to explore the effects of electroosmotic forces (EOF), electrophoretic forces (EPF), and volume exclusion on electric signals within solid-state nanopores. Our results revealed that the electroosmotic force was the main driving force for single-stranded DNA (ssDNA), whereas doublestranded DNA (dsDNA) was primarily dominated by electrophoretic forces in nanopores. Moreover, dsDNA caused greater amplitude signals and moved faster through the nanopore due to its larger diameter and carrying more charges. Furthermore, at the same charge level and amount of bases, circular dsDNA exhibited a tighter structure compared to brush DNA, resulting in a shorter length. Consequently, circular dsDNA caused higher current-blocking amplitudes and faster passage speeds. The characterization approach based on nanopores allows researchers to get molecular information about size and shape in real time. These findings suggest that nanopore detection has the potential to streamline nanoscale characterization and analysis, potentially reducing both the cost and complexity.

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“…There is little research from resource-constrained settings on the use of ONT platforms for TB diagnosis. Those publishing have often done so as individual research studies (24)(25)(26)(27)(28)(29). Previous studies often made use of the ligation-based ONT library preparation (25,28).…”

Section: Introductionmentioning

confidence: 99%

A pragmatic pipeline for drug resistance identification inMycobacterium tuberculosisusing whole genome sequencing

Elton,

Aydin,

Stoker

et al. 2024

Preprint

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Background: Delays in accurate diagnosis of drug resistant tuberculosis (DR-TB) can hinder treatment. Whole genome sequencing (WGS) provides more information than standard molecular and phenotypic testing, but commonly used platforms are expensive to implement, and data interpretation requires significant expertise. Aims: We aimed to optimise a TB WGS diagnostic pipeline balancing user-friendliness, cost-effectiveness and time to results, whilst ensuring accuracy. Materials and methods: Growth conditions, DNA extraction protocols and Oxford Nanopore Technologies (ONT) library preparation kits were compared. Software for basecalling and analysis were evaluated to find the most accurate resistance SNP and lineage predictor. Results: Optimally, a spin-column CTAB DNA extraction method was combined with the RBK110.96 library preparation kit, high accuracy basecalling and data analysis using TB-Profiler. Compared with Illumina, the pipeline was concordant for 16/17 (94%) isolates (lineage) and for 17/17 (100%) isolates (resistance SNPs). Our pipeline was 71% (12/17) concordant with phenotypic drug susceptibility test (DST) results. Time-to-diagnosis was around four weeks. Conclusions: This optimised TB sequencing pipeline requires less time expertise to run and analyse than Illumina, takes less time than phenotypic DSTs and the results are comparable with Illumina. The cost per sample is comparable with other methods. These features make it an important tool for incorporating into routine DR-TB diagnostic pipelines and larger scale drug resistance surveillance in all settings.

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Diagnostic accuracy of nanopore sequencing using respiratory specimens in the diagnosis of pulmonary tuberculosis

Cited by 20 publications

References 31 publications

Accuracy of Nanopore Sequencing as a Diagnostic Assay for Pulmonary Tuberculosis versus Smear, Culture and Xpert MTB/RIF: A Head-to-Head Comparison

Accuracy of Nanopore Sequencing as a Diagnostic Assay for Pulmonary Tuberculosis versus Smear, Culture and Xpert MTB/RIF: A Head-to-Head Comparison

Conformation Influence of DNA on the Detection Signal through Solid-State Nanopores

A pragmatic pipeline for drug resistance identification inMycobacterium tuberculosisusing whole genome sequencing

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