Diagnostic value of a nanopore sequencing assay of bronchoalveolar lavage fluid in pulmonary tuberculosis
Abstract Background To determine the diagnostic accuracy of a nanopore sequencing assay of PCR products from a M. tuberculosis complex-specific region for testing of bronchoalveolar lavage fluid (BALF) samples or sputum samples from suspected pulmonary tuberculosis (PTB) patients and compare the res...
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| Format: | Article |
| Language: | English |
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BMC
2023-03-01
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| Series: | BMC Pulmonary Medicine |
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| Online Access: | https://doi.org/10.1186/s12890-023-02337-3 |
| _version_ | 1797865652669644800 |
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| author | Zhifeng Liu Yang Yang Qingfeng Wang Lei Wang Wenjuan Nie Naihui Chu |
| author_facet | Zhifeng Liu Yang Yang Qingfeng Wang Lei Wang Wenjuan Nie Naihui Chu |
| author_sort | Zhifeng Liu |
| collection | DOAJ |
| description | Abstract Background To determine the diagnostic accuracy of a nanopore sequencing assay of PCR products from a M. tuberculosis complex-specific region for testing of bronchoalveolar lavage fluid (BALF) samples or sputum samples from suspected pulmonary tuberculosis (PTB) patients and compare the results to results obtained for MGIT and Xpert assays. Methods Cases with suspected PTB (n = 55) were diagnosed from January 2019 to December 2021 based on results of nanopore sequencing, MGIT culture, and Xpert MTB/RIF testing of BALF and sputum samples collected during hospitalization. Diagnostic accuracies of assays were compared. Results Ultimately, data from 29 PTB patients and 26 non-PTB cases were analyzed. PTB diagnostic sensitivities of MGIT, Xpert MTB/RIF, and nanopore sequencing assays were 48.28%, 41.38%, and 75.86%, respectively, thus demonstrating that nanopore sequencing provided greater sensitivity than was provided by MGIT culture and Xpert assays (P < 0.05). PTB diagnostic specificities of the respective assays were 65.38%, 100%, and 80.77%, which corresponded with kappa coefficient (κ) values of 0.14, 0.40, and 0.56, respectively. These results indicate that nanopore sequencing provided superior overall performance as compared to Xpert and MGIT culture assays and provided significantly greater PTB diagnostic accuracy than Xpert and sensitivity comparable to that of the MGIT culture assay. Conclusion Our findings suggest that improved detection of PTB in suspected cases was achieved using nanopore sequencing-based testing of BALF or sputum samples than was achieved using Xpert and MGIT culture-based assays, and nanopore sequencing results alone cannot be used to rule out PTB. |
| first_indexed | 2024-04-09T23:11:35Z |
| format | Article |
| id | doaj.art-18b864c4cdf64aaa9df493bbd8d1e0fc |
| institution | Directory Open Access Journal |
| issn | 1471-2466 |
| language | English |
| last_indexed | 2024-04-09T23:11:35Z |
| publishDate | 2023-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Pulmonary Medicine |
| spelling | doaj.art-18b864c4cdf64aaa9df493bbd8d1e0fc2023-03-22T10:19:18ZengBMCBMC Pulmonary Medicine1471-24662023-03-012311810.1186/s12890-023-02337-3Diagnostic value of a nanopore sequencing assay of bronchoalveolar lavage fluid in pulmonary tuberculosisZhifeng Liu0Yang Yang1Qingfeng Wang2Lei Wang3Wenjuan Nie4Naihui Chu5Beijing Emercency Mecial CenterTuberculosis Department, Beijing Chest Hospital Affiliated to Capital Medical UniversityTuberculosis Department, Beijing Chest Hospital Affiliated to Capital Medical UniversityTuberculosis Department, Dezhou Second People’s HospitalTuberculosis Department, Beijing Chest Hospital Affiliated to Capital Medical UniversityTuberculosis Department, Beijing Chest Hospital Affiliated to Capital Medical UniversityAbstract Background To determine the diagnostic accuracy of a nanopore sequencing assay of PCR products from a M. tuberculosis complex-specific region for testing of bronchoalveolar lavage fluid (BALF) samples or sputum samples from suspected pulmonary tuberculosis (PTB) patients and compare the results to results obtained for MGIT and Xpert assays. Methods Cases with suspected PTB (n = 55) were diagnosed from January 2019 to December 2021 based on results of nanopore sequencing, MGIT culture, and Xpert MTB/RIF testing of BALF and sputum samples collected during hospitalization. Diagnostic accuracies of assays were compared. Results Ultimately, data from 29 PTB patients and 26 non-PTB cases were analyzed. PTB diagnostic sensitivities of MGIT, Xpert MTB/RIF, and nanopore sequencing assays were 48.28%, 41.38%, and 75.86%, respectively, thus demonstrating that nanopore sequencing provided greater sensitivity than was provided by MGIT culture and Xpert assays (P < 0.05). PTB diagnostic specificities of the respective assays were 65.38%, 100%, and 80.77%, which corresponded with kappa coefficient (κ) values of 0.14, 0.40, and 0.56, respectively. These results indicate that nanopore sequencing provided superior overall performance as compared to Xpert and MGIT culture assays and provided significantly greater PTB diagnostic accuracy than Xpert and sensitivity comparable to that of the MGIT culture assay. Conclusion Our findings suggest that improved detection of PTB in suspected cases was achieved using nanopore sequencing-based testing of BALF or sputum samples than was achieved using Xpert and MGIT culture-based assays, and nanopore sequencing results alone cannot be used to rule out PTB.https://doi.org/10.1186/s12890-023-02337-3Nanopore sequencing assayPulmonary tuberculosisSensitivitySpecificity |
| spellingShingle | Zhifeng Liu Yang Yang Qingfeng Wang Lei Wang Wenjuan Nie Naihui Chu Diagnostic value of a nanopore sequencing assay of bronchoalveolar lavage fluid in pulmonary tuberculosis BMC Pulmonary Medicine Nanopore sequencing assay Pulmonary tuberculosis Sensitivity Specificity |
| title | Diagnostic value of a nanopore sequencing assay of bronchoalveolar lavage fluid in pulmonary tuberculosis |
| title_full | Diagnostic value of a nanopore sequencing assay of bronchoalveolar lavage fluid in pulmonary tuberculosis |
| title_fullStr | Diagnostic value of a nanopore sequencing assay of bronchoalveolar lavage fluid in pulmonary tuberculosis |
| title_full_unstemmed | Diagnostic value of a nanopore sequencing assay of bronchoalveolar lavage fluid in pulmonary tuberculosis |
| title_short | Diagnostic value of a nanopore sequencing assay of bronchoalveolar lavage fluid in pulmonary tuberculosis |
| title_sort | diagnostic value of a nanopore sequencing assay of bronchoalveolar lavage fluid in pulmonary tuberculosis |
| topic | Nanopore sequencing assay Pulmonary tuberculosis Sensitivity Specificity |
| url | https://doi.org/10.1186/s12890-023-02337-3 |
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