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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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Zhou L, Zou X, Yong Y, Hu Q. Using cerebrospinal fluid nanopore sequencing assay to diagnose tuberculous meningitis: a retrospective cohort study in China. BMJ Open 2024; 14:e080904. [PMID: 38862231 PMCID: PMC11168130 DOI: 10.1136/bmjopen-2023-080904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 04/30/2024] [Indexed: 06/13/2024] Open
Abstract
OBJECTIVE This study aimed to evaluate the efficiency of nanopore sequencing for the early diagnosis of tuberculous meningitis (TBM) using cerebrospinal fluid and compared it with acid-fast bacilli (AFB) smear, mycobacterial growth indicator tube culture and Xpert Mycobacterium tuberculosis (MTB)/rifampicin (RIF). DESIGN Single-centre retrospective study. SETTING The Tuberculosis Diagnosis and Treatment Center of Zhejiang Chinese and Western Medicine Integrated Hospital. PARTICIPANTS We enrolled 64 adult patients with presumptive TBM admitted to our hospital from August 2021 to August 2023. METHODS We calculated the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of AFB smear, culture, Xpert MTB/RIF and nanopore sequencing to evaluate their diagnostic efficacy compared with a composite reference standard for TBM. RESULTS Among these 64 patients, all tested negative for TBM by AFB smear. The sensitivity, specificity, PPV and NPV were 11.11%, 100%, 100% and 32.2% for culture, 13.33%, 100%, 100% and 2.76% for Xpert MTB/RIF, and 77.78%, 100%, 100% and 65.52% for nanopore sequencing, respectively. CONCLUSION The diagnostic accuracy of the nanopore sequencing test was significantly higher than that of conventional testing methods used to detect TBM.
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Affiliation(s)
- Lihong Zhou
- Tuberculosis Diagnosis and Treatment Center, Integrated Traditional Chinese and Western Medicine Hospital of Zhejiang Province, Hangzhou, China
| | - Xingwu Zou
- Tuberculosis Diagnosis and Treatment Center, Integrated Traditional Chinese and Western Medicine Hospital of Zhejiang Province, Hangzhou, China
| | - Yan Yong
- Tuberculosis Diagnosis and Treatment Center, Integrated Traditional Chinese and Western Medicine Hospital of Zhejiang Province, Hangzhou, China
| | - Qin Hu
- Tuberculosis Diagnosis and Treatment Center, Integrated Traditional Chinese and Western Medicine Hospital of Zhejiang Province, Hangzhou, China
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Schwab TC, Perrig L, Göller PC, Guebely De la Hoz FF, Lahousse AP, Minder B, Günther G, Efthimiou O, Omar SV, Egger M, Fenner L. Targeted next-generation sequencing to diagnose drug-resistant tuberculosis: a systematic review and meta-analysis. THE LANCET. INFECTIOUS DISEASES 2024:S1473-3099(24)00263-9. [PMID: 38795712 DOI: 10.1016/s1473-3099(24)00263-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/05/2024] [Accepted: 04/12/2024] [Indexed: 05/28/2024]
Abstract
BACKGROUND Targeted next-generation sequencing (NGS) can rapidly and simultaneously detect mutations associated with resistance to tuberculosis drugs across multiple gene targets. The use of targeted NGS to diagnose drug-resistant tuberculosis, as described in publicly available data, has not been comprehensively reviewed. We aimed to identify targeted NGS assays that diagnose drug-resistant tuberculosis, determine how widely this technology has been used, and assess the diagnostic accuracy of these assays. METHODS In this systematic review and meta-analysis, we searched MEDLINE, Embase, Cochrane Library, Web of Science Core Collection, Global Index Medicus, Google Scholar, ClinicalTrials.gov, and the WHO International Clinical Trials Registry Platform for published and unpublished reports on targeted NGS for drug-resistant tuberculosis from Jan 1, 2005, to Oct 14, 2022, with updates to our search in Embase and Google Scholar until Feb 13, 2024. Studies eligible for the systematic review described targeted NGS approaches to predict drug resistance in Mycobacterium tuberculosis infections using primary samples, reference strain collections, or cultured isolates from individuals with presumed or confirmed tuberculosis. Our search had no limitations on study type or language, although only reports in English, German, and French were screened for eligibility. For the meta-analysis, we included test accuracy studies that used any reference standard, and we assessed risk of bias using the Quality Assessment of Diagnostic Accuracy Studies-2 tool. The primary outcomes for the meta-analysis were sensitivity and specificity of targeted NGS to diagnose drug-resistant tuberculosis compared to phenotypic and genotypic drug susceptibility testing. We used a Bayesian bivariate model to generate summary receiver operating characteristic plots and diagnostic accuracy measures, overall and stratified by drug and sample type. This study is registered with PROSPERO, CRD42022368707. FINDINGS We identified and screened 2920 reports, of which 124 were eligible for our systematic review, including 37 review articles and 87 reports of studies collecting samples for targeted NGS. Sequencing was mainly done in the USA (14 [16%] of 87), western Europe (ten [11%]), India (ten [11%]), and China (nine [10%]). We included 24 test accuracy studies in the meta-analysis, in which 23 different tuberculosis drugs or drug groups were assessed, covering first-line drugs, injectable drugs, and fluoroquinolones and predominantly comparing targeted NGS with phenotypic drug susceptibility testing. The combined sensitivity of targeted NGS across all drugs was 94·1% (95% credible interval [CrI] 90·9-96·3) and specificity was 98·1% (97·0-98·9). Sensitivity for individual drugs ranged from 76·5% (52·5-92·3) for capreomycin to 99·1% (98·3-99·7) for rifampicin; specificity ranged from 93·1% (88·0-96·3) for ethambutol to 99·4% (98·3-99·8) for amikacin. Diagnostic accuracy was similar for primary clinical samples and culture isolates overall and for rifampicin, isoniazid, ethambutol, streptomycin, and fluoroquinolones, and similar after excluding studies at high risk of bias (overall sensitivity 95·2% [95% CrI 91·7-97·1] and specificity 98·6% [97·4-99·3]). INTERPRETATION Targeted NGS is highly sensitive and specific for detecting drug resistance across panels of tuberculosis drugs and can be performed directly on clinical samples. There is a paucity of data on performance for some currently recommended drugs. The barriers preventing the use of targeted NGS to diagnose drug-resistant tuberculosis in high-burden countries need to be addressed. FUNDING National Institutes of Allergy and Infectious Diseases and Swiss National Science Foundation.
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Affiliation(s)
- Tiana Carina Schwab
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Lisa Perrig
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | | | | | - Beatrice Minder
- Public Health and Primary Care Library, University Library of Bern, University of Bern, Bern, Switzerland
| | - Gunar Günther
- Department of Pulmonology and Allergology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department of Medical Science, Faculty of Health Sciences, University of Namibia, Windhoek, Namibia
| | - Orestis Efthimiou
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Institute of Primary Health Care (BIHAM), University of Bern, Bern, Switzerland
| | - Shaheed Vally Omar
- Centre for Tuberculosis, National & WHO Supranational TB Reference Laboratory, National Institute for Communicable Diseases, a division of the National Health Laboratory Services, Johannesburg, South Africa
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Centre for Infectious Disease Epidemiology & Research, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Lukas Fenner
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
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Liu A, Liu S, Lv K, Zhu Q, Wen J, Li J, Liang C, Huang X, Gong C, Sun Q, Gu H. Rapid detection of multidrug resistance in tuberculosis using nanopore-based targeted next-generation sequencing: a multicenter, double-blind study. Front Microbiol 2024; 15:1349715. [PMID: 38495513 PMCID: PMC10940340 DOI: 10.3389/fmicb.2024.1349715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/13/2024] [Indexed: 03/19/2024] Open
Abstract
Background Resistance to anti-tuberculous drugs is a major challenge in the treatment of tuberculosis (TB). We aimed to evaluate the clinical availability of nanopore-based targeted next-generation sequencing (NanoTNGS) for the diagnosis of drug-resistant tuberculosis (DR-TB). Methods This study enrolled 253 patients with suspected DR-TB from six hospitals. The diagnostic efficacy of NanoTNGS for detecting Mycobacterium tuberculosis and its susceptibility or resistance to first- and second-line anti-tuberculosis drugs was assessed by comparing conventional phenotypic drug susceptibility testing (pDST) and Xpert MTB/RIF assays. NanoTNGS can be performed within 12 hours from DNA extraction to the result delivery. Results NanoTNGS showed a remarkable concordance rate of 99.44% (179/180) with the culture assay for identifying the Mycobacterium tuberculosis complex. The sensitivity of NanoTNGS for detecting drug resistance was 93.53% for rifampicin, 89.72% for isoniazid, 85.45% for ethambutol, 74.00% for streptomycin, and 88.89% for fluoroquinolones. Specificities ranged from 83.33% to 100% for all drugs tested. Sensitivity for rifampicin-resistant tuberculosis using NanoTNGS increased by 9.73% compared to Xpert MTB/RIF. The most common mutations were S531L (codon in E. coli) in the rpoB gene, S315T in the katG gene, and M306V in the embB gene, conferring resistance to rifampicin, isoniazid, and ethambutol, respectively. In addition, mutations in the pncA gene, potentially contributing to pyrazinamide resistance, were detected in 32 patients. Other prevalent variants, including D94G in the gyrA gene and K43R in the rpsL gene, conferred resistance to fluoroquinolones and streptomycin, respectively. Furthermore, the rv0678 R94Q mutation was detected in one sample, indicating potential resistance to bedaquiline. Conclusion NanoTNGS rapidly and accurately identifies resistance or susceptibility to anti-TB drugs, outperforming traditional methods. Clinical implementation of the technique can recognize DR-TB in time and provide guidance for choosing appropriate antituberculosis agents.
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Affiliation(s)
- Aimei Liu
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Sang Liu
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Kangyan Lv
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Qingdong Zhu
- Department of Tuberculosis, The Fourth People's Hospital of Nanning, Nanning, Guangxi, China
| | - Jun Wen
- Department of Pulmonary Medicine, The Third People's Hospital of Guilin, Guilin, Guangxi, China
| | - Jianpeng Li
- Department of Pulmonary Medicine, The Third People's Hospital of Wuzhou, Wuzhou, Guangxi, China
| | - Chengyuan Liang
- Department of Infectious Diseases, The People's Hospital of Baise, Baise, Guangxi, China
| | - Xuegang Huang
- Department of Infectious Diseases, The First People's Hospital of Fangchenggang, Fangchenggang, Guangxi, China
| | - Chunming Gong
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Qingfeng Sun
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Hongcang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
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Feng X, Liu Y, Zhao Y, Sun Z, Xu N, Zhao C, Xia W. Recombinase Polymerase Amplification-Based Biosensors for Rapid Zoonoses Screening. Int J Nanomedicine 2023; 18:6311-6331. [PMID: 37954459 PMCID: PMC10637217 DOI: 10.2147/ijn.s434197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 10/21/2023] [Indexed: 11/14/2023] Open
Abstract
Recent, outbreaks of new emergency zoonotic diseases have prompted an urgent need to develop fast, accurate, and portable screening assays for pathogen infections. Recombinase polymerase amplification (RPA) is sensitive and specific and can be conducted at a constant low temperature with a short response time, making it especially suitable for on-site screening and making it a powerful tool for preventing or controlling the spread of zoonoses. This review summarizes the design principles of RPA-based biosensors as well as various signal output or readout technologies involved in fluorescence detection, lateral flow assays, enzymatic catalytic reactions, spectroscopic techniques, electrochemical techniques, chemiluminescence, nanopore sequencing technologies, microfluidic digital RPA, and clustered regularly interspaced short palindromic repeats/CRISPR-associated systems. The current status and prospects of the application of RPA-based biosensors in zoonoses screening are highlighted. RPA-based biosensors demonstrate the advantages of rapid response, easy-to-read result output, and easy implementation for on-site detection, enabling development toward greater portability, automation, and miniaturization. Although there are still problems such as high cost with unstable signal output, RPA-based biosensors are increasingly becoming one of the most important means of on-site pathogen screening in complex samples involving environmental, water, food, animal, and human samples for controlling the spread of zoonotic diseases.
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Affiliation(s)
- Xinrui Feng
- College of Public Health, Jilin Medical University, Jilin, 132013, People’s Republic of China
- Medical College, Yanbian University, Yanji, 136200, People’s Republic of China
| | - Yan Liu
- College of Public Health, Jilin Medical University, Jilin, 132013, People’s Republic of China
| | - Yang Zhao
- Department of Emergency and Intensive Medicine, No. 965 Hospital of PLA Joint Logistic Support Force, Jilin, 132013, People’s Republic of China
| | - Zhe Sun
- College of Public Health, Jilin Medical University, Jilin, 132013, People’s Republic of China
- College of Medical Technology, Beihua University, Jilin, 132013, People’s Republic of China
| | - Ning Xu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, People’s Republic of China
| | - Chen Zhao
- College of Public Health, Jilin Medical University, Jilin, 132013, People’s Republic of China
| | - Wei Xia
- College of Medical Technology, Beihua University, Jilin, 132013, People’s Republic of China
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Huang YY, Li QS, Li ZD, Sun AH, Hu SP. Rapid diagnosis of Mycobacterium marinum infection using targeted nanopore sequencing: a case report. Front Cell Infect Microbiol 2023; 13:1238872. [PMID: 37965260 PMCID: PMC10642934 DOI: 10.3389/fcimb.2023.1238872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Mycobacterium marinum (M. marinum) is a non-tuberculous mycobacterium (NTM) that can cause infectious diseases in aquatic animals and humans. Culture-based pathogen detection is the gold standard for diagnosing NTM infection. However, this method is time-consuming and has low positivity rates for fastidious organisms. Oxford Nanopore MinION sequencing is an emerging third-generation sequencing technology that can sequence DNA or RNA directly in a culture-independent manner and offers rapid microbial identification. Further benefits include low cost, short turnaround time, long read lengths, and small equipment size. Nanopore sequencing plays a crucial role in assessing drug resistance, clinical identification of microbes, and monitoring infectious diseases. Some reports on Mycobacterium tuberculosis (MTB) using nanopore sequencing have been published, however, there are few reports on NTM, such as M. marinum. Here, we report the use of nanopore sequencing for the diagnosis of M. marinum.
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Affiliation(s)
- Yan-Ying Huang
- Department of Pathology, Hangzhou Red Cross Hospital, Hangzhou, China
| | - Qiu-Shi Li
- Department of Ophthalmology, Hangzhou Red Cross Hospital, Hangzhou, China
| | - Zhao-Dong Li
- Department of Clinical laboratory, Hangzhou Red Cross Hospital, Hangzhou, China
| | - Ai-Hua Sun
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Sheng-Ping Hu
- Department of Orthopaedic, Hangzhou Red Cross Hospital, Hangzhou, China
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Faye LM, Hosu MC, Oostvogels S, Dippenaar A, Warren RM, Sineke N, Vasaikar S, Apalata T. The Detection of Mutations and Genotyping of Drug-Resistant Mycobacterium tuberculosis Strains Isolated from Patients in the Rural Eastern Cape Province. Infect Dis Rep 2023; 15:403-416. [PMID: 37489395 PMCID: PMC10366782 DOI: 10.3390/idr15040041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023] Open
Abstract
Drug-resistant tuberculosis (DR-TB) is still a major public health concern in South Africa. Mutations in M. tuberculosis can cause varying levels of phenotypic resistance to anti-TB medications. There have been no prior studies on gene mutations and the genotyping of DR-TB in the rural Eastern Cape Province; hence, we aimed to identify DR-TB mutations, genetic diversity, and allocated lineages among patients in this area. Using Xpert® MTB/RIF, we assessed the rifampin resistance of sputum samples collected from 1157 patients suspected of having tuberculosis. GenoType MTBDR plus VER 2.0 was used for the detection of mutations causing resistance to anti-TB medications. The next step was to spoligotype 441 isolates. The most prevalent rifampin resistance-conferring mutations were in rpoB codon S531L in INH-resistant strains; the katG gene at codon S315TB and the inhA gene at codon C-15TB had the most mutations; 54.5% and 24.7%, respectively. In addition, 24.6% of strains showed mutations in both the rpoB and inhA genes, while 69.9% of strains showed mutations in both the katG and rpoB genes. Heteroresistance was seen in 17.9% of all cases in the study. According to spoligotyping analysis, Beijing families predominated. Investigation of the evolutionary lineages of M. tuberculosis isolates can be carried out using the information provided by the study's diversity of mutations. In locations wherein these mutations have been discovered, decision-making regarding the standardization of treatment regimens or individualized treatment may be aided by the detection frequency of rpoB, katG, and inhA mutations in various study areas.
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Affiliation(s)
- Lindiwe M Faye
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Mojisola C Hosu
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Selien Oostvogels
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, BE-2000 Antwerp, Belgium
| | - Anzaan Dippenaar
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, BE-2000 Antwerp, Belgium
| | - Robin M Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council, Parowvallei, Cape Town 7505, South Africa
- Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Ncomeka Sineke
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Sandeep Vasaikar
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Teke Apalata
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
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Murphy SG, Smith C, Lapierre P, Shea J, Patel K, Halse TA, Dickinson M, Escuyer V, Rowlinson MC, Musser KA. Direct detection of drug-resistant Mycobacterium tuberculosis using targeted next generation sequencing. Front Public Health 2023; 11:1206056. [PMID: 37457262 PMCID: PMC10340549 DOI: 10.3389/fpubh.2023.1206056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/07/2023] [Indexed: 07/18/2023] Open
Abstract
Mycobacterium tuberculosis complex (MTBC) infections are treated with combinations of antibiotics; however, these regimens are not as efficacious against multidrug and extensively drug resistant MTBC. Phenotypic (growth-based) drug susceptibility testing on slow growing bacteria like MTBC requires many weeks to months to complete, whereas sequencing-based approaches can predict drug resistance (DR) with reduced turnaround time. We sought to develop a multiplexed, targeted next generation sequencing (tNGS) assay that can predict DR and can be performed directly on clinical respiratory specimens. A multiplex PCR was designed to amplify a group of thirteen full-length genes and promoter regions with mutations known to be involved in resistance to first- and second-line MTBC drugs. Long-read amplicon libraries were sequenced with Oxford Nanopore Technologies platforms and high-confidence resistance mutations were identified in real-time using an in-house developed bioinformatics pipeline. Sensitivity, specificity, reproducibility, and accuracy of the tNGS assay was assessed as part of a clinical validation study. In total, tNGS was performed on 72 primary specimens and 55 MTBC-positive cultures and results were compared to clinical whole genome sequencing (WGS) performed on paired patient cultures. Complete or partial susceptibility profiles were generated from 82% of smear positive primary specimens and the resistance mutations identified by tNGS were 100% concordant with WGS. In addition to performing tNGS on primary clinical samples, this assay can be used to sequence MTBC cultures mixed with other mycobacterial species that would not yield WGS results. The assay can be effectively implemented in a clinical/diagnostic laboratory with a two to three day turnaround time and, even if batched weekly, tNGS results are available on average 15 days earlier than culture-derived WGS results. This study demonstrates that tNGS can reliably predict MTBC drug resistance directly from clinical specimens or cultures and provide critical information in a timely manner for the appropriate treatment of patients with DR tuberculosis.
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Fukushima K, Matsumoto Y, Matsuki T, Saito H, Motooka D, Komukai S, Fukui E, Yamuchi J, Nitta T, Niitsu T, Abe Y, Nabeshima H, Nagahama Y, Nii T, Tsujino K, Miki K, Kitada S, Kumanogoh A, Akira S, Nakamura S, Kida H. MGIT-seq for the Identification of Nontuberculous Mycobacteria and Drug Resistance: a Prospective Study. J Clin Microbiol 2023; 61:e0162622. [PMID: 36946719 PMCID: PMC10117113 DOI: 10.1128/jcm.01626-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Because nontuberculous mycobacterial pulmonary disease is a considerable health burden, a simple and clinically applicable analytical protocol enabling the identification of subspecies and drug-resistant disease is required to determine the treatment strategy. We aimed to develop a simplified workflow consisting only of direct sequencing of mycobacterial growth indicator tube cultures (MGIT-seq). In total, 138 patients were prospectively enrolled between April 2021 and May 2022, and culture-positive MGIT broths were subjected to sequencing using MinION, a portable next-generation sequencer. Sequence analysis was conducted to identify species using core genome multilocus sequence typing and to predict macrolide and amikacin (AMK) resistance based on previously reported mutations in rrl, rrs, and erm(41). The results were compared to clinical tests for species identification and drug susceptibility. A total of 116 patients with positive MGIT cultures were included in the analysis. MGIT-seq yielded 99.1% accuracy in species-level identification and identified 98 isolates (84.5%) at the subspecies level. Macrolide and AMK resistance were detected in 19.4% and 1.9% of Mycobacterium avium complex (MAC) and Mycobacterium abscessus isolates. The predicted macrolide and AMK resistance was consistent with the results of conventional drug susceptibility tests, with specificities of 97.6% and 100.0%, respectively. Direct MGIT-seq has achieved comprehensive identification and drug resistance detection of nontuberculous mycobacteria, which could be applicable to determine the treatment strategy by a single test in clinical practice.
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Affiliation(s)
- Kiyoharu Fukushima
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
- Global Center for Medical Engineering and Informatics, Suita, Osaka, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Takanori Matsuki
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Haruko Saito
- Department of Clinical Laboratory, National Hospital Organization, Osaka Toneyama Medical Centre, Toyonaka, Osaka, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
| | - Sho Komukai
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
- Department of Biomedical Statistics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Eriko Fukui
- Department of General Thoracic surgery, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - June Yamuchi
- Department of Clinical Laboratory, National Hospital Organization, Osaka Toneyama Medical Centre, Toyonaka, Osaka, Japan
| | - Tadayoshi Nitta
- Department of Clinical Laboratory, National Hospital Organization, Osaka Toneyama Medical Centre, Toyonaka, Osaka, Japan
| | - Takayuki Niitsu
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yuko Abe
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Hiroshi Nabeshima
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
| | - Yasuharu Nagahama
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
| | - Takuro Nii
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Kazuyuki Tsujino
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Keisuke Miki
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | | | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Japan for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - Shizuo Akira
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Japan for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - Hiroshi Kida
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
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10
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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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11
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Moller AG, Petit RA, Davis MH, Read TD. Development of an Amplicon Nanopore Sequencing Strategy for Detection of Mutations Conferring Intermediate Resistance to Vancomycin in Staphylococcus aureus Strains. Microbiol Spectr 2023; 11:e0272822. [PMID: 36688645 PMCID: PMC9927139 DOI: 10.1128/spectrum.02728-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/03/2023] [Indexed: 01/24/2023] Open
Abstract
Staphylococcus aureus is a major cause of bacteremia and other hospital-acquired infections. The cell-wall active antibiotic vancomycin is commonly used to treat both methicillin-resistant (MRSA) and sensitive (MSSA) infections. Vancomycin intermediate S. aureus (VISA) variants can arise through de novo mutations. Here, we performed pilot experiments to develop a combined PCR/long-read sequencing-based method for detection of previously known VISA-causing mutations. Primers were designed to generate 10 amplicons covering 16 genes associated with the VISA phenotype. We sequenced amplicon pools as long reads with Oxford Nanopore adapter ligation on Flongle flow cells. We then detected mutations by mapping reads against a parental consensus or known reference sequence and comparing called variants against a database of known VISA mutations from laboratory selection. Each amplicon in the pool was sequenced to high (>1,000×) coverage, and no relationship was found between amplicon length and coverage. We also were able to detect the causative mutation (walK 646C>G) in a VISA mutant derived from the USA300 strain (N384-3 from parental strain N384). Mixing mutant (N384-3) and parental (N384) DNA at various ratios from 0 to 1 mutant suggested a mutation detection threshold of the average minor allele frequency (6.5%) at 95% confidence (two standard errors above mean mutation frequency). The study lays the groundwork for direct S. aureus antibiotic resistance genotype inference using rapid nanopore sequencing from clinical samples. IMPORTANCE Bacteremia mortality is known to increase rapidly with time after infection, making rapid diagnostics and treatment necessary. Successful treatment depends on correct administration of antibiotics based on knowledge of strain antibiotic susceptibility. Staphylococcus aureus is a major causative agent of bacteremia that is also commonly antibiotic resistant. In this work, we develop a method to accelerate detection of a complex, polygenic antibiotic resistance phenotype in S. aureus, vancomycin-intermediate resistance (VISA), through long-read genomic sequencing of amplicons representing genes most commonly mutated in VISA selection. This method both rapidly identifies VISA genotypes and incorporates the most comprehensive database of VISA genetic determinants known to date.
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Affiliation(s)
- Abraham G. Moller
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
- Microbiology and Molecular Genetics (MMG), Graduate Division of Biological and Biomedical Sciences (GDBBS), Emory University, Atlanta, Georgia, USA
| | - Robert A. Petit
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
- Theiagen Genomics, Highlands Ranch, Colorado, USA
| | - Michelle H. Davis
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
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12
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Zou X, Zhu Y, Qin Y, Fei F, Chen Y, Wang P, Zhou L, Lang Y. Value analysis of next-generation sequencing combined with Xpert in early precise diagnosis of pulmonary tuberculosis. Diagn Microbiol Infect Dis 2023. [PMID: 37478548 DOI: 10.1016/j.diagmicrobio.2023.115921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The current study aims to investigate the value of combination of NGS with Xpert MTB/RIF in the diagnosis of early pulmonary tuberculosis (PTB). A total of 85 patients with suspected PTB were analyzed retrospectively. The positive detection rates of PTB by Xpert MTB/RIF, TBseq Ultra, TB-DNA, and TB-RNA were significantly higher than those by acid-fast staining. Xpert MTB/RIF, TBseq Ultra, TB-DNA, and TB-RNA possessed higher sensitivity and accuracy than acid-fast stained smears. Kappa agreement analysis showed good agreement between Xpert MTB/RIF and TBseq Ultra. Combined diagnosis improves the detection sensitivity compared with a single diagnostic method. ROC curve analysis showed that Xpert MTB/RIF combined with TBseq Ultra showed the highest area under the curve (0.886). In conclusion, the combined diagnosis of TBseq Ultra and Xpert MTB/RIF harbors the characteristics of short cycle, high specificity and accuracy, which demonstrated a promising application value in the early diagnosis of PTB.
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13
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Wang M, Liu H, Ren J, Huang Y, Deng Y, Liu Y, Chen Z, Chow FWN, Leung PHM, Li S. Enzyme-Assisted Nucleic Acid Amplification in Molecular Diagnosis: A Review. BIOSENSORS 2023; 13:bios13020160. [PMID: 36831926 PMCID: PMC9953907 DOI: 10.3390/bios13020160] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 06/12/2023]
Abstract
Infectious diseases and tumors have become the biggest medical challenges in the 21st century. They are driven by multiple factors such as population growth, aging, climate change, genetic predispositions and more. Nucleic acid amplification technologies (NAATs) are used for rapid and accurate diagnostic testing, providing critical information in order to facilitate better follow-up treatment and prognosis. NAATs are widely used due their high sensitivity, specificity, rapid amplification and detection. It should be noted that different NAATs can be selected according to different environments and research fields; for example, isothermal amplification with a simple operation can be preferred in developing countries or resource-poor areas. In the field of translational medicine, CRISPR has shown great prospects. The core component of NAAT lies in the activity of different enzymes. As the most critical material of nucleic acid amplification, the key role of the enzyme is self-evident, playing the upmost important role in molecular diagnosis. In this review, several common enzymes used in NAATs are compared and described in detail. Furthermore, we summarize both the advances and common issues of NAATs in clinical application.
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Affiliation(s)
- Meiling Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Jie Ren
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yunqi Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yuan Liu
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Polly Hang-Mei Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
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14
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Chapman R, D'Angelo A, Bagby S. Nanopore-based metagenomic sequencing: a diagnostic tool in respiratory tract infection. ERJ Open Res 2022; 8:00461-2022. [PMID: 36545212 PMCID: PMC9761407 DOI: 10.1183/23120541.00461-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 09/16/2022] [Indexed: 12/24/2022] Open
Abstract
This correspondence highlights the burden of respiratory tract infection and focuses on nanopore sequencing as a promising approach in diagnostics https://bit.ly/3fgs8zg.
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Affiliation(s)
- Robert Chapman
- Princess Alexandra Hospital NHS Trust, Harlow, UK,Robert Chapman ()
| | | | - Stefan Bagby
- Department of Life Sciences, University of Bath, Bath, UK
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15
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Mehta K, Narayanan N, Heysell SK, Bisson GP, Subbian S, Kurepina N, Kreiswirth BN, Vinnard C. Pharmacogenetic variability and the probability of site of action target attainment during tuberculosis meningitis treatment: A physiologically based pharmacokinetic modeling and simulations study. Tuberculosis (Edinb) 2022; 137:102271. [PMID: 36375279 DOI: 10.1016/j.tube.2022.102271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/01/2022] [Accepted: 10/12/2022] [Indexed: 11/22/2022]
Abstract
OBJECTIVE AND METHODS Our objective was to investigate the role of patient pharmacogenetic variability in determining site of action target attainment during tuberculous meningitis (TBM) treatment. Rifampin and isoniazid PBPK model that included SLCO1B1 and NAT2 effects on exposures respectively were obtained from literature, modified, and validated using available cerebrospinal-fluid (CSF) concentrations. Population simulations of isoniazid and rifampin concentrations in brain interstitial fluid and probability of target attainment according to genotypes and M. tuberculosis MIC levels, under standard and intensified dosing, were conducted. RESULTS The rifampin and isoniazid model predicted steady-state drug concentration within brain interstitial fluid matched with the observed CSF concentrations. At MIC level of 0.25 mg/L, 57% and 23% of the patients with wild type and heterozygous SLCO1B1 genotype respectively attained the target in CNS with rifampin standard dosing, improving to 98% and 91% respectively with 35 mg/kg dosing. At MIC level of 0.25 mg/L, 33% of fast acetylators attained the target in CNS with isoniazid standard dosing, improving to 90% with 7.5 mg/kg dosing. CONCLUSION In this study, the combined effects of pharmacogenetic and M. tuberculosis MIC variability were potent determinants of target attainment in CNS. The potential for genotype-guided dosing during TBM treatment should be further explored in prospective clinical studies.
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Affiliation(s)
| | | | - Scott K Heysell
- University of Virginia, Division of Infectious Diseases and International Health, Charlottesville, VA, USA
| | - Gregory P Bisson
- University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Selvakumar Subbian
- Public Health Research Institute, New Jersey Medical School, Newark, NJ, USA
| | - Natalia Kurepina
- Center for Discovery & Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Barry N Kreiswirth
- Center for Discovery & Innovation, Hackensack Meridian Health, Nutley, NJ, USA
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16
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Ness TE, DiNardo A, Farhat MR. High Throughput Sequencing for Clinical Tuberculosis: An Overview. Pathogens 2022; 11:pathogens11111343. [PMID: 36422596 PMCID: PMC9695813 DOI: 10.3390/pathogens11111343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
High throughput sequencing (HTS) can identify the presence of Mycobacterium tuberculosis DNA in a clinical sample while also providing information on drug susceptibility. Multiple studies have provided a context for exploring the clinical application of HTS for TB diagnosis. The workflow challenges, strengths and limitations of the various sequencing platforms, and tools used for analysis are presented to provide a framework for further innovations in the field.
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Affiliation(s)
- Tara E. Ness
- Division of Pediatric Infectious Diseases, Baylor College of Medicine/Texas Children’s Hospital, Houston, TX 77030, USA
- Global TB Program, Baylor College of Medicine/Texas Childrens Hospital, Houston, TX 77030, USA
- Correspondence:
| | - Andrew DiNardo
- Global TB Program, Baylor College of Medicine/Texas Childrens Hospital, Houston, TX 77030, USA
| | - Maha R. Farhat
- Harvard Medical School Biomedical Informatics and Pulmonary and Critical Care Massachusetts General Hospital, Boston, MA 02115, USA
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17
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Tiberi S, Utjesanovic N, Galvin J, Centis R, D'Ambrosio L, van den Boom M, Zumla A, Migliori GB. Drug resistant TB - latest developments in epidemiology, diagnostics and management. Int J Infect Dis 2022; 124 Suppl 1:S20-S25. [PMID: 35342000 DOI: 10.1016/j.ijid.2022.03.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/13/2022] [Accepted: 03/15/2022] [Indexed: 12/14/2022] Open
Abstract
AIM The aim of this review is to inform the reader on the latest developments in epidemiology, diagnostics and management. EPIDEMIOLOGY Drug-resistant Tuberculosis (DR-TB) continues to be a current global health threat, and is defined by higher morbidity and mortality, sequelae, higher cost and complexity. The WHO classifies drug-resistant TB into 5 categories: isoniazid-resistant TB, rifampicin resistant (RR)-TB and MDR-TB, (TB resistant to isoniazid and rifampicin), pre-extensively drug-resistant TB (pre-XDR-TB) which is MDR-TB with resistance to a fluoroquinolone and finally XDR-TB that is TB resistant to rifampicin, plus any fluoroquinolone, plus at least one further priority A drug (bedaquiline or linezolid). Of 500,000 estimated new cases of RR-TB in 2020, only 157 903 cases are notified. Only about a third of cases are detected and treated annually. DIAGNOSTICS Recently newer rapid diagnostic methods like the GeneXpert, whole genome sequencing and Myc-TB offer solutions for rapid detection of resistance. TREATMENT The availability of new TB drugs and shorter treatment regimens have been recommended for the management of DR-TB. CONCLUSION Despite advances in diagnostics and treatments we still have to find and treat two thirds of the drug resistant cases that go undetected and therefore go untreated each year. Control of TB and elimination will only occur if cases are detected, diagnosed and treated promptly.
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Affiliation(s)
- Simon Tiberi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London. Department of Infection, Royal London Hospital, Barts Health NHS Trust, London UK.
| | - Natasa Utjesanovic
- Department of Clinical Virology, University College London Hospital, UCL Hospitals NHS Foundation Trust, London UK
| | - Jessica Galvin
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London. Department of Infection, Royal London Hospital, Barts Health NHS Trust, London UK
| | - Rosella Centis
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri IRCCS, Tradate, Italy
| | | | | | - Alimuddin Zumla
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, and National Institute for Health Research Biomedical Research Centre, UCL Hospitals NHS Foundation Trust, London, UK
| | - Giovanni Battista Migliori
- Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Istituti Clinici Scientifici Maugeri IRCCS, Tradate, Italy
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18
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Bian Y, Deng M, Zhang Q, Hou G. Global trends of research on tuberculous pleurisy over the past 15 years: A bibliometric analysis. Front Cell Infect Microbiol 2022; 12:937811. [PMID: 36111237 PMCID: PMC9468418 DOI: 10.3389/fcimb.2022.937811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022] Open
Abstract
Tuberculous pleurisy (TP) is a common type of extrapulmonary tuberculosis (EPTB). With the development of research and changes in TP patient characteristics, an increasing number of studies have revealed the prevalence, risk factors, and novel diagnosis techniques. Thus, this bibliometric analysis was performed to identify global scientific output characteristics and research hotspots and frontiers for TP over the past 15 years. We searched the Web of Science Core Collection (WoSCC) Science Citation Index Expanded (SCI-expanded) for literature published between 2007 and 2021 and recorded their information. The Bibliometrix software package was used for bibliometric indicator analysis, and VOSviewer was used to visualize the trends of and hotspots in TP research. A total of 1,464 original articles were reviewed, and the results indicated that the annual number of publications (Np) focusing on TP has increased over the past 15 years. China had the largest number of papers and the highest H-index, and the United States ranked first for number of citations (Nc). EGYPTIAN KNOWLEDGE BANK and PLOS ONE were the most prolific unit and journal, respectively. The use of the Xpert assay and immune-related biomarker detection to diagnose TP appears to be a recent research hotspot. This bibliometric study demonstrated that the number of publications related to TP have tended to increase. China is a major producer, and the United States is an influential country in this field. Research in the past 15 years has been predominantly clinical research. The diagnosis of TP was the focus of research, and the exploration of novel diagnostic techniques, verification of diagnostic markers, and combination of diagnostic methods have been recent research hotspots. Immune-related biomarkers should be given more attention in the field of TP diagnosis.
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Affiliation(s)
- Yiding Bian
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Mingming Deng
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Qin Zhang
- Department of Pulmonary and Critical Care Medicine, First Hospital of China Medical University, Shenyang, China
| | - Gang Hou
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- National Center for Respiratory Medicine, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- *Correspondence: Gang Hou,
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19
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Gómez-González PJ, Campino S, Phelan JE, Clark TG. Portable sequencing of Mycobacterium tuberculosis for clinical and epidemiological applications. Brief Bioinform 2022; 23:6650479. [PMID: 35894606 PMCID: PMC9487601 DOI: 10.1093/bib/bbac256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/23/2022] [Accepted: 06/01/2022] [Indexed: 11/14/2022] Open
Abstract
With >1 million associated deaths in 2020, human tuberculosis (TB) caused by the bacteria Mycobacterium tuberculosis remains one of the deadliest infectious diseases. A plethora of genomic tools and bioinformatics pipelines have become available in recent years to assist the whole genome sequencing of M. tuberculosis. The Oxford Nanopore Technologies (ONT) portable sequencer is a promising platform for cost-effective application in clinics, including personalizing treatment through detection of drug resistance-associated mutations, or in the field, to assist epidemiological and transmission investigations. In this study, we performed a comparison of 10 clinical isolates with DNA sequenced on both long-read ONT and (gold standard) short-read Illumina HiSeq platforms. Our analysis demonstrates the robustness of the ONT variant calling for single nucleotide polymorphisms, despite the high error rate. Moreover, because of improved coverage in repetitive regions where short sequencing reads fail to align accurately, ONT data analysis can incorporate additional regions of the genome usually excluded (e.g. pe/ppe genes). The resulting extra resolution can improve the characterization of transmission clusters and dynamics based on inferring closely related isolates. High concordance in variants in loci associated with drug resistance supports its use for the rapid detection of resistant mutations. Overall, ONT sequencing is a promising tool for TB genomic investigations, particularly to inform clinical and surveillance decision-making to reduce the disease burden.
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Affiliation(s)
- Paula J Gómez-González
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK.,Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
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20
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Zhou Y, Ren M, Zhang P, Jiang D, Yao X, Luo Y, Yang Z, Wang Y. Application of Nanopore Sequencing in the Detection of Foodborne Microorganisms. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:1534. [PMID: 35564242 PMCID: PMC9100974 DOI: 10.3390/nano12091534] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 12/21/2022]
Abstract
Foodborne pathogens have become the subject of intense interest because of their high incidence and mortality worldwide. In the past few decades, people have developed many methods to solve this challenge. At present, methods such as traditional microbial culture methods, nucleic acid or protein-based pathogen detection methods, and whole-genome analysis are widely used in the detection of pathogenic microorganisms in food. However, these methods are limited by time-consuming, cumbersome operations or high costs. The development of nanopore sequencing technology offers the possibility to address these shortcomings. Nanopore sequencing, a third-generation technology, has the advantages of simple operation, high sensitivity, real-time sequencing, and low turnaround time. It can be widely used in the rapid detection and serotyping of foodborne pathogens. This review article discusses foodborne diseases, the principle of nanopore sequencing technology, the application of nanopore sequencing technology in foodborne pathogens detection, as well as its development prospects.
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Affiliation(s)
| | | | | | | | | | | | | | - Yin Wang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (M.R.); (P.Z.); (D.J.); (X.Y.); (Y.L.); (Z.Y.)
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