Accuracy of Nanopore Sequencing as a Diagnostic Assay for Pulmonary Tuberculosis versus Smear, Culture and Xpert MTB/RIF: A Head-to-Head Comparison
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 h...
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| Format: | Article |
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MDPI AG
2023-09-01
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| Series: | Tropical Medicine and Infectious Disease |
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| Online Access: | https://www.mdpi.com/2414-6366/8/9/441 |
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| author | Juan Yang Wei Ye Chao Zhang Wenhong Lin Lin Mei Shengsheng Liu Jie Liu |
| author_facet | Juan Yang Wei Ye Chao Zhang Wenhong Lin Lin Mei Shengsheng Liu Jie Liu |
| author_sort | Juan Yang |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T21:53:47Z |
| format | Article |
| id | doaj.art-90aa87fcc3984908a5ee9ecde55b0e9b |
| institution | Directory Open Access Journal |
| issn | 2414-6366 |
| language | English |
| last_indexed | 2024-03-10T21:53:47Z |
| publishDate | 2023-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Tropical Medicine and Infectious Disease |
| spelling | doaj.art-90aa87fcc3984908a5ee9ecde55b0e9b2023-11-19T13:16:56ZengMDPI AGTropical Medicine and Infectious Disease2414-63662023-09-018944110.3390/tropicalmed8090441Accuracy of Nanopore Sequencing as a Diagnostic Assay for Pulmonary Tuberculosis versus Smear, Culture and Xpert MTB/RIF: A Head-to-Head ComparisonJuan Yang0Wei Ye1Chao Zhang2Wenhong Lin3Lin Mei4Shengsheng Liu5Jie Liu6Department of Tuberculosis, Anhui Chest Hospital, Anhui Provincial Institute for Tuberculosis Prevention and Treatment, Hefei 230022, ChinaDepartment of Pathology, Anhui Chest Hospital, Anhui Provincial Institute for Tuberculosis Prevention and Treatment, Hefei 230022, ChinaDepartment of Tuberculosis, Anhui Chest Hospital, Anhui Provincial Institute for Tuberculosis Prevention and Treatment, Hefei 230022, ChinaDepartment of Tuberculosis, Anhui Chest Hospital, Anhui Provincial Institute for Tuberculosis Prevention and Treatment, Hefei 230022, ChinaDepartment of Tuberculosis, Anhui Chest Hospital, Anhui Provincial Institute for Tuberculosis Prevention and Treatment, Hefei 230022, ChinaDepartment of Tuberculosis, Anhui Chest Hospital, Anhui Provincial Institute for Tuberculosis Prevention and Treatment, Hefei 230022, ChinaDepartment of Tuberculosis Control and Prevention, Anhui Chest Hospital, Anhui Provincial Institute for Tuberculosis Prevention and Treatment, Hefei 230022, ChinaEarly 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.https://www.mdpi.com/2414-6366/8/9/441nanopore sequencing assaytuberculosisXpert MTB/RIFdiagnosis |
| spellingShingle | Juan Yang Wei Ye Chao Zhang Wenhong Lin Lin Mei Shengsheng Liu Jie Liu Accuracy of Nanopore Sequencing as a Diagnostic Assay for Pulmonary Tuberculosis versus Smear, Culture and Xpert MTB/RIF: A Head-to-Head Comparison Tropical Medicine and Infectious Disease nanopore sequencing assay tuberculosis Xpert MTB/RIF diagnosis |
| title | Accuracy of Nanopore Sequencing as a Diagnostic Assay for Pulmonary Tuberculosis versus Smear, Culture and Xpert MTB/RIF: A Head-to-Head Comparison |
| title_full | Accuracy of Nanopore Sequencing as a Diagnostic Assay for Pulmonary Tuberculosis versus Smear, Culture and Xpert MTB/RIF: A Head-to-Head Comparison |
| title_fullStr | Accuracy of Nanopore Sequencing as a Diagnostic Assay for Pulmonary Tuberculosis versus Smear, Culture and Xpert MTB/RIF: A Head-to-Head Comparison |
| title_full_unstemmed | Accuracy of Nanopore Sequencing as a Diagnostic Assay for Pulmonary Tuberculosis versus Smear, Culture and Xpert MTB/RIF: A Head-to-Head Comparison |
| title_short | Accuracy of Nanopore Sequencing as a Diagnostic Assay for Pulmonary Tuberculosis versus Smear, Culture and Xpert MTB/RIF: A Head-to-Head Comparison |
| title_sort | accuracy of nanopore sequencing as a diagnostic assay for pulmonary tuberculosis versus smear culture and xpert mtb rif a head to head comparison |
| topic | nanopore sequencing assay tuberculosis Xpert MTB/RIF diagnosis |
| url | https://www.mdpi.com/2414-6366/8/9/441 |
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