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Yan X, Yang G, Wang Y, Wang Y, Cheng J, Xu P, Qiu X, Su L, Liu L, Geng R, You Y, Liu H, Chu N, Ma L, Nie W. Nanopore sequencing for smear-negative pulmonary tuberculosis-a multicentre prospective study in China. Ann Clin Microbiol Antimicrob 2024; 23:51. [PMID: 38877520 PMCID: PMC11179381 DOI: 10.1186/s12941-024-00714-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 06/05/2024] [Indexed: 06/16/2024] Open
Abstract
PURPOSE In this prospective study, the diagnosis accuracy of nanopore sequencing-based Mycobacterium tuberculosis (MTB) detection was determined through examining bronchoalveolar lavage fluid (BALF) samples from pulmonary tuberculosis (PTB) -suspected patients. Compared the diagnostic performance of nanopore sequencing, mycobacterial growth indicator tube (MGIT) culture and Xpert MTB/rifampin resistance (MTB/RIF) assays. METHODS Specimens collected from suspected PTB cases across China from September 2021 to April 2022 were tested then assay diagnostic accuracy rates were compared. RESULTS Among the 111 suspected PTB cases that were ultimately diagnosed as PTB, the diagnostic rate of nanopore sequencing was statistically significant different from other assays (P < 0.05). Fleiss' kappa values of 0.219 and 0.303 indicated fair consistency levels between MTB detection results obtained using nanopore sequencing versus other assays, respectively. Respective PTB diagnostic sensitivity rates of MGIT culture, Xpert MTB/RIF and nanopore sequencing of 36.11%, 40.28% and 83.33% indicated superior sensitivity of nanopore sequencing. Analysis of area under the curve (AUC), Youden's index and accuracy values and the negative predictive value (NPV) indicated superior MTB detection performance for nanopore sequencing (with Xpert MTB/RIF ranking second), while the PTB diagnostic accuracy rate of nanopore sequencing exceeded corresponding rates of the other methods. CONCLUSIONS In comparison with MGIT culture and Xpert MTB/RIF assays, BALF's nanopore sequencing provided superior MTB detection sensitivity and thus is suitable for testing of sputum-scarce suspected PTB cases. However, negative results obtained using these assays should be confirmed based on additional evidence before ruling out a PTB diagnosis.
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Affiliation(s)
- Xiaojing Yan
- Medical Quality Control Center, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, PR China
| | - Guoli Yang
- Tuberculosis Department, Tuberculosis Hospital of Jilin Province (Jilin Provincial Infectious Disease Hospital), Changchun, 130500, PR China
| | - Yunfei Wang
- Department of Medicine, Hangzhou Shengting Medical Technolog, Ltd, Zhejiang, Hangzhou, 310000, PR China
| | - Yuqing Wang
- The Fourth People's Hospital of Qinghai Province, Xining, 510650, PR China
| | - Jie Cheng
- Tuberculosis Department, Anhui Provincial Chest Hospital, Hefei, 230022, PR China
| | - Peisong Xu
- Department of Medicine, Hangzhou Shengting Medical Technolog, Ltd, Zhejiang, Hangzhou, 310000, PR China
| | - Xiaoli Qiu
- Department of Medicine, Hangzhou Shengting Medical Technolog, Ltd, Zhejiang, Hangzhou, 310000, PR China
| | - Lei Su
- Tuberculosis Department, Henan Province Anyang City Tuberculosis Prevention and Control Institute, Henan Province, Anyang City, 455000, PR China
| | - Lina Liu
- Tuberculosis Department, Hengshui Third People's Hospital, Hengshui City, Henan Province, 053099, PR China
| | - Ruixue Geng
- Tuberculosis Department, Hohhot Second Hospital, Hohhot City, Inner Mongolia Autonomous Region, 010020, PR China
| | - Yingxia You
- Tuberculosis Department, Zhengzhou Sixth People's Hospital, Zhengzhou City, Henan Province, 450015, PR China
| | - Hui Liu
- Medical Quality Control Center, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, PR China
| | - Naihui Chu
- Tuberculosis Department, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, PR China.
| | - Li Ma
- Department of medical oncology, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, PR China.
| | - Wenjuan Nie
- Tuberculosis Department, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, PR China.
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Liu Z, Yang Y, Wang Q, Wang L, Nie W, Chu N. Diagnostic value of a nanopore sequencing assay of bronchoalveolar lavage fluid in pulmonary tuberculosis. BMC Pulm Med 2023; 23:77. [PMID: 36890507 PMCID: PMC9996878 DOI: 10.1186/s12890-023-02337-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 01/23/2023] [Indexed: 03/10/2023] Open
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.
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Affiliation(s)
- Zhifeng Liu
- Beijing Emercency Mecial Center, Beijing, 100031, People's Republic of China
| | - Yang Yang
- Tuberculosis Department, Beijing Chest Hospital Affiliated to Capital Medical University, No 9, Beiguan Street, Tongzhou District, Beijing, 101149, People's Republic of China
| | - Qingfeng Wang
- Tuberculosis Department, Beijing Chest Hospital Affiliated to Capital Medical University, No 9, Beiguan Street, Tongzhou District, Beijing, 101149, People's Republic of China
| | - Lei Wang
- Tuberculosis Department, Dezhou Second People's Hospital, Textile Street, Canal Economic Development Zone, Dezhou, 253007, People's Republic of China
| | - Wenjuan Nie
- Tuberculosis Department, Beijing Chest Hospital Affiliated to Capital Medical University, No 9, Beiguan Street, Tongzhou District, Beijing, 101149, People's Republic of China.
| | - Naihui Chu
- Tuberculosis Department, Beijing Chest Hospital Affiliated to Capital Medical University, No 9, Beiguan Street, Tongzhou District, Beijing, 101149, People's Republic of China.
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Xing F, Lo SKF, Ma Y, Ip JD, Chan WM, Zhou M, Gong M, Lau SKP, Woo PCY. Rapid Diagnosis of Mycobacterium marinum Infection by Next-Generation Sequencing: A Case Report. Front Med (Lausanne) 2022; 9:824122. [PMID: 35187006 PMCID: PMC8854760 DOI: 10.3389/fmed.2022.824122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
We present the first report of histology- and culture-proven Mycobacterium marinum infection diagnosed by next-generation sequencing (NGS). It took <2 days to make a microbiological diagnosis using the Oxford Nanopore Technologies' MinION device, compared to 20 days for the mycobacterium to be isolated from the tissue biopsy. NGS is particularly useful for culture-negative and slow-growing microorganism infections, such as mycobacterial, fungal and partially treated pyogenic bacterial infections. Due to its low equipment cost, short turn-around-time and portable size, the Oxford Nanopore Technologies' MinION device is a useful platform for NGS in routine clinical microbiology laboratories.
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Affiliation(s)
- Fanfan Xing
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Simon K. F. Lo
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Yuanchao Ma
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Jonathan Daniel Ip
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Wan-Mui Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Meixun Zhou
- Department of Pathology, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Miaozi Gong
- Department of Pathology, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Susanna K. P. Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Patrick C. Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- *Correspondence: Patrick C. Y. Woo
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Deng C, Naler LB, Lu C. Microfluidic epigenomic mapping technologies for precision medicine. LAB ON A CHIP 2019; 19:2630-2650. [PMID: 31338502 PMCID: PMC6697104 DOI: 10.1039/c9lc00407f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Epigenomic mapping of tissue samples generates critical insights into genome-wide regulations of gene activities and expressions during normal development and disease processes. Epigenomic profiling using a low number of cells produced by patient and mouse samples presents new challenges to biotechnologists. In this review, we first discuss the rationale and premise behind profiling epigenomes for precision medicine. We then examine the existing literature on applying microfluidics to facilitate low-input and high-throughput epigenomic profiling, with emphasis on technologies enabling interfacing with next-generation sequencing. We detail assays on studies of histone modifications, DNA methylation, 3D chromatin structures and non-coding RNAs. Finally, we discuss what the future may hold in terms of method development and translational potential.
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Affiliation(s)
- Chengyu Deng
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
| | - Lynette B Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
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Papageorgiou L, Eleni P, Raftopoulou S, Mantaiou M, Megalooikonomou V, Vlachakis D. Genomic big data hitting the storage bottleneck. EMBNET.JOURNAL 2018; 24:e910. [PMID: 29782620 PMCID: PMC5958914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
During the last decades, there is a vast data explosion in bioinformatics. Big data centres are trying to face this data crisis, reaching high storage capacity levels. Although several scientific giants examine how to handle the enormous pile of information in their cupboards, the problem remains unsolved. On a daily basis, there is a massive quantity of permanent loss of extensive information due to infrastructure and storage space problems. The motivation for sequencing has fallen behind. Sometimes, the time that is spent to solve storage space problems is longer than the one dedicated to collect and analyse data. To bring sequencing to the foreground, scientists have to slide over such obstacles and find alternative ways to approach the issue of data volume. Scientific community experiences the data crisis era, where, out of the box solutions may ease the typical research workflow, until technological development meets the needs of Bioinformatics.
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Affiliation(s)
- Louis Papageorgiou
- Laboratory of Genetics, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece,Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, Athens, Greece
| | - Picasi Eleni
- Laboratory of Genetics, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - Sofia Raftopoulou
- Laboratory of Genetics, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece,Sotiria Chest Diseases Hospital, Athens, Greece,Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | | | - Vasileios Megalooikonomou
- Computer Engineering and Informatics Department, School of Engineering, University of Patras, Patras, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece,Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece,Computer Engineering and Informatics Department, School of Engineering, University of Patras, Patras, Greece
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