Diagnostic value of third-generation nanopore sequencing in extrapulmonary tuberculosis
BackgroundThis study aimed to explore the accuracy of third-generation nanopore sequencing to diagnose extrapulmonary tuberculosis (EPTB).MethodsSamples were collected from the lesions of 67 patients with suspected EPTB admitted between April 2022 and August 2023. Nanopore sequencing, acid-fast baci...
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Cellular and Infection Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fcimb.2024.1432446/full |
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| author | Chang Song Chang Song Chunyan Zhao Chunyan Zhao Yanrong Lin Yingxing Nong Aichun Huang Shaoyong Xi Xiaoying Wei Chunmei Zeng Shixiong Yang Qingdong Zhu |
| author_facet | Chang Song Chang Song Chunyan Zhao Chunyan Zhao Yanrong Lin Yingxing Nong Aichun Huang Shaoyong Xi Xiaoying Wei Chunmei Zeng Shixiong Yang Qingdong Zhu |
| author_sort | Chang Song |
| collection | DOAJ |
| description | BackgroundThis study aimed to explore the accuracy of third-generation nanopore sequencing to diagnose extrapulmonary tuberculosis (EPTB).MethodsSamples were collected from the lesions of 67 patients with suspected EPTB admitted between April 2022 and August 2023. Nanopore sequencing, acid-fast bacilli (AFB) staining, DNA testing, and X-pert and mycobacterial cultures were performed. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and area under the receiver operating characteristic curve (AUC) were calculated for different diagnostic methods, and their diagnostic accuracies were compared.ResultsNanopore sequencing demonstrated the highest correct diagnosis rate among 50 positive EPTB cases, independently diagnosing 19 positive cases missed by conventional methods. Its sensitivity (62.00%), specificity (94.10%), PPV (96.90%), NPV (45.70%) and AUC (0.781, 95% CI: 0.67–0.89) were superior to those of conventional methods, such as AFB staining, DNA testing, X-pert, and solid culture, indicating its significantly efficient advantage in EPTB detection.ConclusionNanopore sequencing technology significantly outperforms conventional methods such as AFB staining, DNA testing, X-pert, and mycobacterial culture to diagnose EPTB, promising to improve the diagnosis of EPTB. |
| format | Article |
| id | doaj-art-93e6bf6285d249f49ed301fceed2e38d |
| institution | Kabale University |
| issn | 2235-2988 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj-art-93e6bf6285d249f49ed301fceed2e38d2025-01-07T06:40:22ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882025-01-011410.3389/fcimb.2024.14324461432446Diagnostic value of third-generation nanopore sequencing in extrapulmonary tuberculosisChang Song0Chang Song1Chunyan Zhao2Chunyan Zhao3Yanrong Lin4Yingxing Nong5Aichun Huang6Shaoyong Xi7Xiaoying Wei8Chunmei Zeng9Shixiong Yang10Qingdong Zhu11Department of Tuberculosis, The Fourth People’s Hospital of Nanning, Nanning, ChinaGuangxi Medical University, Nanning, ChinaDepartment of Tuberculosis, The Fourth People’s Hospital of Nanning, Nanning, ChinaGuangxi Medical University, Nanning, ChinaDepartment of Tuberculosis, The Fourth People’s Hospital of Nanning, Nanning, ChinaDepartment of Medical, The Fourth People’s Hospital of Nanning, Nanning, ChinaDepartment of Tuberculosis, The Fourth People’s Hospital of Nanning, Nanning, ChinaDepartment of Clinical Laboratory, The Fourth People’s Hospital of Nanning, Nanning, ChinaDepartment of Tuberculosis, The Fourth People’s Hospital of Nanning, Nanning, ChinaDepartment of Tuberculosis, The Fourth People’s Hospital of Nanning, Nanning, ChinaAdministrative Office, The Fourth People’s Hospital of Nanning, Nanning, ChinaDepartment of Tuberculosis, The Fourth People’s Hospital of Nanning, Nanning, ChinaBackgroundThis study aimed to explore the accuracy of third-generation nanopore sequencing to diagnose extrapulmonary tuberculosis (EPTB).MethodsSamples were collected from the lesions of 67 patients with suspected EPTB admitted between April 2022 and August 2023. Nanopore sequencing, acid-fast bacilli (AFB) staining, DNA testing, and X-pert and mycobacterial cultures were performed. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and area under the receiver operating characteristic curve (AUC) were calculated for different diagnostic methods, and their diagnostic accuracies were compared.ResultsNanopore sequencing demonstrated the highest correct diagnosis rate among 50 positive EPTB cases, independently diagnosing 19 positive cases missed by conventional methods. Its sensitivity (62.00%), specificity (94.10%), PPV (96.90%), NPV (45.70%) and AUC (0.781, 95% CI: 0.67–0.89) were superior to those of conventional methods, such as AFB staining, DNA testing, X-pert, and solid culture, indicating its significantly efficient advantage in EPTB detection.ConclusionNanopore sequencing technology significantly outperforms conventional methods such as AFB staining, DNA testing, X-pert, and mycobacterial culture to diagnose EPTB, promising to improve the diagnosis of EPTB.https://www.frontiersin.org/articles/10.3389/fcimb.2024.1432446/fullnanopore sequencingextrapulmonary tuberculosisdiagnostic valueconventional methodsclinical microbiology |
| spellingShingle | Chang Song Chang Song Chunyan Zhao Chunyan Zhao Yanrong Lin Yingxing Nong Aichun Huang Shaoyong Xi Xiaoying Wei Chunmei Zeng Shixiong Yang Qingdong Zhu Diagnostic value of third-generation nanopore sequencing in extrapulmonary tuberculosis Frontiers in Cellular and Infection Microbiology nanopore sequencing extrapulmonary tuberculosis diagnostic value conventional methods clinical microbiology |
| title | Diagnostic value of third-generation nanopore sequencing in extrapulmonary tuberculosis |
| title_full | Diagnostic value of third-generation nanopore sequencing in extrapulmonary tuberculosis |
| title_fullStr | Diagnostic value of third-generation nanopore sequencing in extrapulmonary tuberculosis |
| title_full_unstemmed | Diagnostic value of third-generation nanopore sequencing in extrapulmonary tuberculosis |
| title_short | Diagnostic value of third-generation nanopore sequencing in extrapulmonary tuberculosis |
| title_sort | diagnostic value of third generation nanopore sequencing in extrapulmonary tuberculosis |
| topic | nanopore sequencing extrapulmonary tuberculosis diagnostic value conventional methods clinical microbiology |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2024.1432446/full |
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