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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Google Scholar, ClinicalTrials.gov, and the WHO International Clinical Trials Registry Platform for published and unpublished reports on targeted NGS for drug-resistant tuberculosis from Jan 1, 2005, to Oct 14, 2022, with updates to our search in Embase and Google Scholar until Feb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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Alavifard H, Nabavi-Rad A, Baghaei K, Sadeghi A, Yadegar A, Zali MR. Pyrosequencing analysis for rapid and accurate detection of clarithromycin resistance-associated mutations in Iranian Helicobacter pylori isolates. BMC Res Notes 2023; 16:136. [PMID: 37415212 DOI: 10.1186/s13104-023-06420-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Treatment of Helicobacter pylori (H. pylori) infection has become challenging following the development of primary antibiotic resistance. A primary therapeutic regimen for H. pylori eradication includes clarithromycin; however, the presence of point mutations within the 23S rRNA sequence of H. pylori contributes to clarithromycin resistance and eradication failure. Thus, we aimed to develop a rapid and precise method to determine clarithromycin resistance-related point mutations using the pyrosequencing method. METHODS AND RESULTS H. pylori was isolated from 82 gastric biopsy samples and minimal inhibitory concentration (MIC) was evaluated using the agar dilution method. Clarithromycin resistance-associated point mutations were detected by Sanger sequencing, from which 11 isolates were chosen for pyrosequencing. Our results demonstrated a 43.9% (36/82) prevalence in resistance to clarithromycin. The A2143G mutation was detected in 8.3% (4/48) of H. pylori isolates followed by A2142G (6.2%), C2195T (4.1%), T2182C (4.1%), and C2288T (2%). Although the C2195T mutation was only detected by Sanger sequencing, the overall results from pyrosequencing and Sanger sequencing platforms were comparable. CONCLUSIONS Pyrosequencing could be used as a rapid and practical platform in clinical laboratories to determine the susceptibility profile of H. pylori isolates. This might pave the way for efficient H. pylori eradication upon detection.
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Affiliation(s)
- Helia Alavifard
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Nabavi-Rad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kaveh Baghaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Sadeghi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Sharma A, Sharma A, Malhotra R, Singh P, Chakrabortty RK, Mahajan S, Pandit AK. An accurate artificial intelligence system for the detection of pulmonary and extra pulmonary Tuberculosis. Tuberculosis (Edinb) 2021; 131:102143. [PMID: 34794086 DOI: 10.1016/j.tube.2021.102143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 12/01/2022]
Abstract
Tuberculosis (TB) is the greatest irresistible illness in humans, caused by microbes Mycobacterium TB (MTB) bacteria and is an infectious disease that spreads from one individual to another through the air. It principally influences lung, which is termed Pulmonary TB (PTB). However, it can likewise influence other parts of the body such as the brain, bones and lymph nodes. Hence, it is also referred to as Extra Pulmonary TB (EPTB). TB has normal symptoms, so without proper testing, it is hard to detect if a patient has TB or not. In this paper, an accurate and novel system for diagnosing TB (PTB and EPTB) has been designed using image processing and AI-based classification techniques. The designed system is comprised of two phases. Firstly, the X-Ray image is processed using preprocessing, segmentation and features extraction and then, three different AI-based techniques are applied for classification. For image processing, 'Histogram Filter' and 'Median Filter' are applied with the CLAHE process to retrieve the segmented image. Then, classification based on AI techniques is done. The designed system produces the accuracy of 98%, 83%, and 89% for Decision Tree, SVM, and Naïve Bayes Classifier, respectively and has been validated by the doctors of the Jalandhar, India.
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Affiliation(s)
| | | | | | | | | | - Shubham Mahajan
- School of Electronics & Communication Engineering, Shri Mata Vaishno Devi University, Katra, 182320, India.
| | - Amit Kant Pandit
- School of Electronics & Communication Engineering, Shri Mata Vaishno Devi University, Katra, 182320, India
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Agashe VM, Johari AN, Shah M, Anjum R, Romano C, Drago L, Sharma HK, Benzakour T. Diagnosis of Osteoarticular Tuberculosis: Perceptions, Protocols, Practices, and Priorities in the Endemic and Non-Endemic Areas of the World-A WAIOT View. Microorganisms 2020; 8:microorganisms8091312. [PMID: 32872175 PMCID: PMC7563388 DOI: 10.3390/microorganisms8091312] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/18/2020] [Accepted: 08/23/2020] [Indexed: 02/07/2023] Open
Abstract
There has been a major resurgence of tuberculosis (TB) and drug-resistant tuberculosis in the last few decades. Although it has been brought under control in most Western countries, it is still a major cause of death in endemic regions like India. Osteoarticular tuberculosis (OA TB) forms a small proportion of the total cases of tuberculosis. Perceptions and practices of orthopedic surgeons are entirely different in endemic and non-endemic regions around the world, due to the vast difference in exposure. Literature from endemic areas puts stress on clinico-radiological diagnosis and empirical anti-tubercular treatment (ATT). Such practices, although non-invasive, simple to implement, and economical, carry a significant risk of missing TB mimics and developing drug resistance. However, OA TB is still perceived as a “diagnostic enigma” in non-endemic regions, leading to a delay in diagnosis. Hence, a high index of suspicion, especially in a high-risk population, is needed to improve the diagnosis. Evolving drug resistance continues to thwart efforts to control the disease globally. This review article discusses the perceptions and practices in different parts of the world, with India as an example of the endemic world, and lays down priorities for overcoming the challenges of diagnosing osteoarticular TB.
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Affiliation(s)
| | - Ashok N. Johari
- ENABLE International Centre for Paediatric Musculoskeletal Care, Mumbai 400016, India;
| | - Mudit Shah
- Dr. Agashe’s Maternity and Surgical Nursing Home, 116 Bazar ward, MN, Road Kurla, Mumbai 400070, India;
| | - Rashid Anjum
- Department of Orthopaedics, ASCOMS and Hospital, J and K, Jammu 180017, India
- Correspondence:
| | - Carlo Romano
- Studio Medico Associato Cecca-Romanò, 20121 Milano, Italy;
| | - Lorenzo Drago
- Clinical Microbiology, University of Milan, 20100 Milan, Italy;
| | - Hemant K. Sharma
- Hull University Teaching Hospitals, Anlaby Road, Hull HU3 2JZ, UK;
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Qin L, Wang J, Lu J, Yang H, Zheng R, Liu Z, Huang X, Feng Y, Hu Z, Ge B. A deletion in the RD105 region confers resistance to multiple drugs in Mycobacterium tuberculosis. BMC Biol 2019; 17:7. [PMID: 30683096 PMCID: PMC6347829 DOI: 10.1186/s12915-019-0628-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/10/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb), especially those that are multidrug resistant poses a serious threat to global tuberculosis control. However, the mechanism underlying the occurrence of drug resistance against more than one drug is poorly understood. Given that the Beijing/W strains are associated with outbreaks and multidrug resistance, they may harbor a genetic advantage and provide useful insight into the disease. One marker found in all Beijing/W Mtb strains is a deletion of RD105 region that results in a gene fusion, Rv0071/74, with a variable number (3-9 m) of VDP (V: Val, D: Asp; P: Pro) repeats (coded by gtggacccg repeat sequences) at the N-terminal. Here, we report that this variable number of VDP repeats in Rv0071/74 regulates the development of multidrug resistance. RESULTS We collected and analyzed 1255 Beijing/W clinical strains. The results showed that the number of VDP repeats in Rv0071/74 was related to the development of multidrug resistance, and the deletion of Rv0071/74-9 m from Beijing/W clinical strain restored drug susceptibility. Rv0071/74-9 m also increased resistance to multiple drugs when transferred to different mycobacterial strains. Cell-free assays indicate that the domain carrying 4-9 VDP repeats (4-9 m) showed a variable binding affinity with peptidoglycan and Rv0071/74 cleaves peptidoglycan. Furthermore, Rv0071/74-9 m increased cell wall thickness and reduced the intracellular concentration of antibiotics. CONCLUSIONS These findings not only identify Rv0071/74 with VDP repeats as a newly identified multidrug resistance gene but also provide a new model for the development of multiple drug resistance.
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Affiliation(s)
- Lianhua Qin
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Jie Wang
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Junmei Lu
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Hua Yang
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Ruijuan Zheng
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Zhonghua Liu
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Xiaochen Huang
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Yonghong Feng
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Zhongyi Hu
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Baoxue Ge
- Shanghai Key Laboratory of Tuberculosis, Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China.
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Chen J, Peng P, Du Y, Ren Y, Chen L, Rao Y, Wang W. Early detection of multidrug- and pre-extensively drug-resistant tuberculosis from smear-positive sputum by direct sequencing. BMC Infect Dis 2017; 17:300. [PMID: 28438132 PMCID: PMC5402665 DOI: 10.1186/s12879-017-2409-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 04/19/2017] [Indexed: 01/06/2023] Open
Abstract
Background Emergence of multidrug- and extensively drug-resistant tuberculosis (M/XDR-TB) is a major hurdle for TB control programs especially in developing countries like China. Resistance to fluoroquinolones is high among MDR-TB patients. Early diagnosis of MDR/pre-XDR-TB is essential for lowering transmission of drug-resistant TB and adjusting the treatment regimen. Methods Smear-positive sputum specimens (n = 186) were collected from Wuhan Institute for Tuberculosis Control. The DNA was extracted from the specimens and run through a Sanger sequencing assay to detect mutations associated with MDR/pre-XDR-TB including the rpoB core region for rifampicin (RIF) resistance; katG and inhA promoter for isoniazid (INH) resistance; and gyrA for fluoroquinolone (FQ) resistance. Sequencing data were compared to phenotypic Lowenstein-Jensen (L-J) proportion method drug susceptibility testing (DST) results for performance analysis. Results By comparing the mutation data with phenotypic results, the detection rates of MDR-TB and pre-XDR-TB were 84.31% (43/51) and 83.33% (20/24), respectively. The sequencing assay illustrated good sensitivity for the detection of resistance to RIF (96.92%), INH (86.89%), FQ (77.50%). The specificities of the assay were 98.35% for RIF, 99.20% for INH, and 97.26% for FQ. Conclusions The sequencing assay is an efficient, accurate method for detection of MDR-TB and pre-XDR-TB from clinical smear-positive sputum specimens, should be considered as a supplemental method for obtaining early DST results before the availability of phenotypic DST results. This could be of benefit to early diagnosis, adjusting the treatment regimen and controlling transmission of drug-resistant TB.
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Affiliation(s)
- Jun Chen
- Department of Laboratory Medicine, Wuhan Institute for Tuberculosis Control, Wuhan Pulmonary Hospital, Wuhan, 430030, China
| | - Peng Peng
- Department of Internal Medicine, Wuhan Institute for Tuberculosis Control, Wuhan Pulmonary Hospital, Wuhan, 430030, China
| | - Yixiang Du
- Department of Tuberculosis Control, Wuhan Institute for Tuberculosis Control, Wuhan Pulmonary Hospital, Wuhan, 430030, China
| | - Yi Ren
- Department of Laboratory Medicine, Wuhan Institute for Tuberculosis Control, Wuhan Pulmonary Hospital, Wuhan, 430030, China
| | - Lifeng Chen
- Department of Laboratory Medicine, Wuhan Institute for Tuberculosis Control, Wuhan Pulmonary Hospital, Wuhan, 430030, China
| | - Youyi Rao
- Department of Laboratory Medicine, Wuhan Institute for Tuberculosis Control, Wuhan Pulmonary Hospital, Wuhan, 430030, China
| | - Weihua Wang
- Department of Internal Medicine, Wuhan Institute for Tuberculosis Control, Wuhan Pulmonary Hospital, Wuhan, 430030, China.
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Thanchomnang T, Tantrawatpan C, Intapan PM, Sanpool O, Lulitanond V, Tourtip S, Yamasaki H, Maleewong W. Rapid identification of nine species of diphyllobothriidean tapeworms by pyrosequencing. Sci Rep 2016; 6:37228. [PMID: 27853295 PMCID: PMC5112553 DOI: 10.1038/srep37228] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/26/2016] [Indexed: 01/08/2023] Open
Abstract
The identification of diphyllobothriidean tapeworms (Cestoda: Diphyllobothriidea) that infect humans and intermediate/paratenic hosts is extremely difficult due to their morphological similarities, particularly in the case of Diphyllobothrium and Spirometra species. A pyrosequencing method for the molecular identification of pathogenic agents has recently been developed, but as of yet there have been no reports of pyrosequencing approaches that are able to discriminate among diphyllobothriidean species. This study, therefore, set out to establish a pyrosequencing method for differentiating among nine diphyllobothriidean species, Diphyllobothrium dendriticum, Diphyllobothrium ditremum, Diphyllobothrium latum, Diphyllobothrium nihonkaiense, Diphyllobothrium stemmacephalum, Diplogonoporus balaenopterae, Adenocephalus pacificus, Spirometra decipiens and Sparganum proliferum, based on the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene as a molecular marker. A region of 41 nucleotides in the cox1 gene served as a target, and variations in this region were used for identification using PCR plus pyrosequencing. This region contains nucleotide variations at 12 positions, which is enough for the identification of the selected nine species of diphyllobothriidean tapeworms. This method was found to be a reliable tool not only for species identification of diphyllobothriids, but also for epidemiological studies of cestodiasis caused by diphyllobothriidean tapeworms at public health units in endemic areas.
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Affiliation(s)
- Tongjit Thanchomnang
- Faculty of Medicine, Mahasarakham University, Mahasarakham, 44000, Thailand.,Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chairat Tantrawatpan
- Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, 40002, Thailand.,Division of Cell Biology, Department of Preclinical Sciences, Faculty of Medicine, Thammasat University, Rangsit Campus, Pathum Thani, 12120, Thailand
| | - Pewpan M Intapan
- Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, 40002, Thailand.,Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Oranuch Sanpool
- Faculty of Medicine, Mahasarakham University, Mahasarakham, 44000, Thailand.,Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, 40002, Thailand.,Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Viraphong Lulitanond
- Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, 40002, Thailand.,Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Somjintana Tourtip
- Faculty of Medicine, Mahasarakham University, Mahasarakham, 44000, Thailand
| | - Hiroshi Yamasaki
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Wanchai Maleewong
- Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, 40002, Thailand.,Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
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Rapid Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates Directly from Clinical Samples by Use of Amplicon Sequencing: a Proof-of-Concept Study. J Clin Microbiol 2016; 54:2058-67. [PMID: 27225403 PMCID: PMC4963505 DOI: 10.1128/jcm.00535-16] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/19/2016] [Indexed: 11/20/2022] Open
Abstract
Increasingly complex drug-resistant tuberculosis (DR-TB) is a major global health concern and one of the primary reasons why TB is now the leading infectious cause of death worldwide. Rapid characterization of a DR-TB patient's complete drug resistance profile would facilitate individualized treatment in place of empirical treatment, improve treatment outcomes, prevent amplification of resistance, and reduce the transmission of DR-TB. The use of targeted next-generation sequencing (NGS) to obtain drug resistance profiles directly from patient sputum samples has the potential to enable comprehensive evidence-based treatment plans to be implemented quickly, rather than in weeks to months, which is currently needed for phenotypic drug susceptibility testing (DST) results. In this pilot study, we evaluated the performance of amplicon sequencing of Mycobacterium tuberculosis DNA from patient sputum samples using a tabletop NGS technology and automated data analysis to provide a rapid DST solution (the Next Gen-RDST assay). One hundred sixty-six out of 176 (94.3%) sputum samples from the Republic of Moldova yielded complete Next Gen-RDST assay profiles for 7 drugs of interest. We found a high level of concordance of our Next Gen-RDST assay results with phenotypic DST (97.0%) and pyrosequencing (97.8%) results from the same clinical samples. Our Next Gen-RDST assay was also able to estimate the proportion of resistant-to-wild-type alleles down to mixtures of ≤1%, which demonstrates the ability to detect very low levels of resistant variants not detected by pyrosequencing and possibly below the threshold for phenotypic growth methods. The assay as described here could be used as a clinical or surveillance tool.
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Abstract
Tuberculosis (TB) remains one of the world's most lethal infectious diseases. Preventive and control strategies among other high-risk groups, such as the elderly population, continues to be a challenge. Clinical features of TB in older adults may be atypical and confused with age-related diseases. Diagnosis and management of TB in the elderly person can be difficult; treatment can be associated with adverse drug reactions. This article reviews the current global epidemiology, pathogenesis, clinical characteristics, diagnosis, management, and prevention of Mycobacterium tuberculosis infection in community-dwelling and institutionalized aging adults.
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Affiliation(s)
- Shobita Rajagopalan
- Los Angeles County Department of Public Health, 123 West Manchester Boulevard, Inglewood, CA 90301, USA; Charles R. Drew University of Medicine and Science, Los Angeles, CA, USA.
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Sanpool O, Tantrawatpan C, Thanchomnang T, Janwan P, Intapan PM, Rodpai R, Lulitanond V, Taweethavonsawat P, Maleewong W. Pyrosequencing Using SL and 5S rRNA as Molecular Markers for Identifying Zoonotic Filarial Nematodes in Blood Samples and Mosquitoes. Vector Borne Zoonotic Dis 2016; 16:326-33. [PMID: 27008279 DOI: 10.1089/vbz.2015.1914] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUNDS Lymphatic filariasis is principally caused by Wuchereria bancrofti, and Brugia malayi. The other two filarial nematode species, Brugia pahangi and Dirofilaria immitis, possibly cause human zoonotic diseases. METHODS We propose the development of a PCR assay linked with DNA pyrosequencing as a rapid tool to identify W. bancrofti, B. malayi, B. pahangi, and D. immitis in blood samples and mosquitoes. Primers targeting the fragment of the 5S ribosomal RNA and spliced leader sequences were newly designed and developed to identify these four filarial nematodes. Analytical sensitivity and specificity were evaluated. RESULTS Pyrosequencing determination of nucleotide variations within 36 nucleotides for B. malayi and B. pahangi, and 32 nucleotides for W. bancrofti and D. immitis is sufficient for differentiation of those filarial nematodes, and for detection of intraspecies genetic variation of B. malayi. This analysis could detect a single B. malayi, B. pahangi, W. bancrofti, and D. immitis microfilaria in blood samples. CONCLUSIONS Overall, the PCR-linked pyrosequencing-based method was faster than direct sequencing and less expensive than real-time PCR or direct sequencing. This is the possibility of choice that can be applied in a high-throughput platform for identification and surveillance of reservoirs and vectors infected with lymphatic filaria in endemic areas.
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Affiliation(s)
- Oranuch Sanpool
- 1 Department of Parasitology, Faculty of Medicine, Khon Kaen University , Khon Kaen, Thailand .,2 Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University , Khon Kaen, Thailand .,3 Faculty of Medicine, Mahasarakham University , Mahasarakham, Thailand
| | - Chairat Tantrawatpan
- 2 Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University , Khon Kaen, Thailand .,4 Division of Cell Biology, Department of Preclinical Sciences, Faculty of Medicine, Thammasat University , Pathum Thani, Thailand
| | - Tongjit Thanchomnang
- 2 Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University , Khon Kaen, Thailand .,3 Faculty of Medicine, Mahasarakham University , Mahasarakham, Thailand
| | - Penchom Janwan
- 2 Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University , Khon Kaen, Thailand .,5 Department of Medical Technology, School of Allied Health Sciences and Public Health, Walailak University , Nakhon Si Thammarat, Thailand
| | - Pewpan M Intapan
- 1 Department of Parasitology, Faculty of Medicine, Khon Kaen University , Khon Kaen, Thailand .,2 Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University , Khon Kaen, Thailand
| | - Rutchanee Rodpai
- 1 Department of Parasitology, Faculty of Medicine, Khon Kaen University , Khon Kaen, Thailand .,2 Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University , Khon Kaen, Thailand
| | - Viraphong Lulitanond
- 2 Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University , Khon Kaen, Thailand .,6 Department of Microbiology, Faculty of Medicine, Khon Kaen University , Khon Kaen, Thailand
| | - Piyanan Taweethavonsawat
- 7 Parasitology Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University , Bangkok, Thailand
| | - Wanchai Maleewong
- 1 Department of Parasitology, Faculty of Medicine, Khon Kaen University , Khon Kaen, Thailand .,2 Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University , Khon Kaen, Thailand
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Affiliation(s)
- Diala Faddoul
- Descanso Pediatrics, Huntington Medical Foundation, 1346 Foothill Boulevard Suite 201, La Canada, CA 91011, USA.
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Abstract
The challenge of diagnosing childhood tuberculosis (TB) results from its paucibacillary nature and the difficulties of sputum collection in children. Mycobacterial culture, the diagnostic gold standard, provides microbiological confirmation in only 30% to 40% of childhood pulmonary TB cases and takes up to 6 weeks to result. Conventional drug susceptibility testing requires an additional 2 to 4 weeks after culture confirmation. In response to the low sensitivity and long wait time of the traditional diagnostic approach, many new assays have been developed. These new tools have shortened time to result; however, none of them offer greater sensitivity than culture.
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Affiliation(s)
- Silvia S Chiang
- Section of Infectious Diseases, Department of Pediatrics, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA; Department of Global Health and Social Medicine, Harvard Medical School, 641 Huntington Avenue, Boston, MA 02115, USA
| | - Douglas S Swanson
- Division of Infectious Diseases, Department of Pediatrics, University of Missouri-Kansas City School of Medicine, 2401 Gillham Road, Kansas City, MO 64108, USA
| | - Jeffrey R Starke
- Section of Infectious Diseases, Department of Pediatrics, Baylor College of Medicine, 1102 Bates Street, Suite 1150, Houston, TX 77030, USA.
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Recent Advances in Tuberculosis Diagnosis: IGRAs and Molecular Biology. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2014. [DOI: 10.1007/s40506-014-0034-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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