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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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Caruso CR, Yang Z. Molecular diagnostics of infectious disease: Detection and characterization of microbial agents in cytology samples. Diagn Cytopathol 2023; 51:68-82. [PMID: 36263664 DOI: 10.1002/dc.25064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/30/2022] [Accepted: 10/10/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Cytology samples are widely used to diagnose various infectious diseases by detection and identification of causative infectious agents, including bacteria, fungi, and viruses. The role of cytopathology in infectious disease has expanded tremendously in the past decades with the advances in molecular techniques. Molecular diagnostic methods, compared to conventional methods, have shown improved patient outcome, reduction in cost, and shortened hospital stay times. The aim of this article is to review molecular testing in cytology samples for diagnosis of infectious diseases. METHODS The literature search for molecular testing in common cytology samples for diagnosis of infectious diseases was performed. The findings of the studies were summarized. The common cytology samples included in this article were gynecologic specimens, cerebrospinal fluid, bronchoalveolar lavage, and urine samples. CONCLUSIONS There are a number of molecular diagnostic tests that are available to be used in common cytology samples to detect infectious agents. Each test has its own advantages and limitations. It is our hope that upon reading this review article, the readers will have better understanding of molecular diagnostic testing of infectious diseases utilizing commonly sampled cytology specimens in daily practice.
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Affiliation(s)
- Carla R Caruso
- Department of Pathology and Anatomic Sciences, University of Missouri, Columbia, Missouri, USA
| | - Zhongbo Yang
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
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Finci I, Albertini A, Merker M, Andres S, Bablishvili N, Barilar I, Cáceres T, Crudu V, Gotuzzo E, Hapeela N, Hoffmann H, Hoogland C, Kohl TA, Kranzer K, Mantsoki A, Maurer FP, Nicol MP, Noroc E, Plesnik S, Rodwell T, Ruhwald M, Savidge T, Salfinger M, Streicher E, Tukvadze N, Warren R, Zemanay W, Zurek A, Niemann S, Denkinger CM. Investigating resistance in clinical Mycobacterium tuberculosis complex isolates with genomic and phenotypic antimicrobial susceptibility testing: a multicentre observational study. THE LANCET. MICROBE 2022; 3:e672-e682. [PMID: 35907429 PMCID: PMC9436784 DOI: 10.1016/s2666-5247(22)00116-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/10/2022] [Accepted: 04/14/2022] [Indexed: 01/01/2023]
Abstract
BACKGROUND Whole-genome sequencing (WGS) of Mycobacterium tuberculosis complex has become an important tool in diagnosis and management of drug-resistant tuberculosis. However, data correlating resistance genotype with quantitative phenotypic antimicrobial susceptibility testing (AST) are scarce. METHODS In a prospective multicentre observational study, 900 clinical M tuberculosis complex isolates were collected from adults with drug-resistant tuberculosis in five high-endemic tuberculosis settings around the world (Georgia, Moldova, Peru, South Africa, and Viet Nam) between Dec 5, 2014, and Dec 12, 2017. Minimum inhibitory concentrations (MICs) and resulting binary phenotypic AST results for up to nine antituberculosis drugs were determined and correlated with resistance-conferring mutations identified by WGS. FINDINGS Considering WHO-endorsed critical concentrations as reference, WGS had high accuracy for prediction of resistance to isoniazid (sensitivity 98·8% [95% CI 98·5-99·0]; specificity 96·6% [95% CI 95·2-97·9]), levofloxacin (sensitivity 94·8% [93·3-97·6]; specificity 97·1% [96·7-97·6]), kanamycin (sensitivity 96·1% [95·4-96·8]; specificity 95·0% [94·4-95·7]), amikacin (sensitivity 97·2% [96·4-98·1]; specificity 98·6% [98·3-98·9]), and capreomycin (sensitivity 93·1% [90·0-96·3]; specificity 98·3% [98·0-98·7]). For rifampicin, pyrazinamide, and ethambutol, the specificity of resistance prediction was suboptimal (64·0% [61·0-67·1], 83·8% [81·0-86·5], and 40·1% [37·4-42·9], respectively). Specificity for rifampicin increased to 83·9% when borderline mutations with MICs overlapping with the critical concentration were excluded. Consequently, we highlighted mutations in M tuberculosis complex isolates that are often falsely identified as susceptible by phenotypic AST, and we identified potential novel resistance-conferring mutations. INTERPRETATION The combined analysis of mutations and quantitative phenotypes shows the potential of WGS to produce a refined interpretation of resistance, which is needed for individualised therapy, and eventually could allow differential drug dosing. However, variability of MIC data for some M tuberculosis complex isolates carrying identical mutations also reveals limitations of our understanding of the genotype and phenotype relationships (eg, including epistasis and strain genetic background). FUNDING Bill & Melinda Gates Foundation, German Centre for Infection Research, German Research Foundation, Excellence Cluster Precision Medicine of Inflammation (EXC 2167), and Leibniz ScienceCampus EvoLUNG.
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Affiliation(s)
- Iris Finci
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | | | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; Evolution of the Resistome, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Sönke Andres
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Nino Bablishvili
- National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Tatiana Cáceres
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Valeriu Crudu
- Phthisiopneumology Institute Chiril Draganiuc, Chisinau, Moldova
| | - Eduardo Gotuzzo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Nchimunya Hapeela
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Harald Hoffmann
- SYNLAB Gauting, SYNLAB MVZ Dachau, Gauting, Germany; Institute of Microbiology and Laboratory Medicine (IML Red), WHO Supranational TB Reference Laboratory, Gauting, Germany
| | | | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Katharina Kranzer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK; Biomedical Research and Training Institute, Harare, Zimbabwe
| | | | - Florian P Maurer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mark P Nicol
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Ecaterina Noroc
- Phthisiopneumology Institute Chiril Draganiuc, Chisinau, Moldova
| | - Sara Plesnik
- Institute of Microbiology and Laboratory Medicine (IML Red), WHO Supranational TB Reference Laboratory, Gauting, Germany
| | - Timothy Rodwell
- FIND, Geneva, Switzerland; Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Theresa Savidge
- Advanced Diagnostic Laboratories, National Jewish Health, Denver, CO, USA; Alaska State Public Health Laboratories, Anchorage, AK, USA
| | - Max Salfinger
- College of Public Health, University of South Florida, Tampa, FL, USA; Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Elizabeth Streicher
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nestani Tukvadze
- National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Robin Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Widaad Zemanay
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anna Zurek
- Advanced Diagnostic Laboratories, National Jewish Health, Denver, CO, USA
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Claudia M Denkinger
- FIND, Geneva, Switzerland; German Center for Infection Research, Heidelberg, Germany; Division of Clinical Tropical Medicine and German Centre for Infection Research, Heidelberg University Hospital, Heidelberg, Germany.
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Use of Whole-Genome Sequencing to Predict Mycobacterium tuberculosis Complex Drug Resistance from Early Positive Liquid Cultures. Microbiol Spectr 2022; 10:e0251621. [PMID: 35311541 PMCID: PMC9045259 DOI: 10.1128/spectrum.02516-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Our objective was to evaluate the performance of whole-genome sequencing (WGS) from early positive liquid cultures for predicting Mycobacterium tuberculosis complex (MTBC) drug resistance. Clinical isolates were obtained from tuberculosis patients at Shanghai Pulmonary Hospital (SPH). Antimicrobial susceptibility testing (AST) was performed, and WGS from early Bactec mycobacterial growth indicator tube (MGIT) 960-positive liquid cultures was performed to predict the drug resistance using the TB-Profiler informatics platform. A total of 182 clinical isolates were enrolled in this study. Using phenotypic AST as the gold standard, the overall sensitivity and specificity for WGS were, respectively, 97.1% (89.8 to 99.6%) and 90.4% (83.4 to 95.1%) for rifampin, 91.0% (82.4 to 96.3%) and 95.2% (89.1 to 98.4%) for isoniazid, 100.0% (89.4 to 100.0%) and 87.3% (80.8 to 92.1%) for ethambutol, 96.6% (88.3 to 99.6%) and 61.8% (52.6 to 70.4%) for streptomycin, 86.8% (71.9 to 95.6%) and 95.8% (91.2 to 98.5%) for moxifloxacin, 86.5% (71.2 to 91.5%) and 95.2% (90.3 to 98.0%) for ofloxacin, 100.0% (54.1 to 100.0%) and 67.6% (60.2 to 74.5%) for amikacin, 100.0% (63.1 to 100.0%) and 67.2% (59.7 to 74.2%) for kanamycin, 62.5% (24.5 to 91.5%) and 88.5% (82.8 to 92.8%) for ethionamide, 33.3% (4.3 to 77.7%) and 98.3% (95.1 to 99.7%) for para-aminosalicylic acid, and 0.0% (0.0 to 12.3%) and 100.0% (97.6 to 100.0%) for cycloserine. The concordances of WGS-based AST and phenotypic AST were as follows: rifampin (92.9%), isoniazid (93.4%), ethambutol (89.6%), streptomycin (73.1%), moxifloxacin (94.0%), ofloxacin (93.4%), amikacin (68.7%), kanamycin (68.7%), ethionamide (87.4%), para-aminosalicylic acid (96.2%) and cycloserine (84.6%). We conclude that WGS could be a promising approach to predict MTBC resistance from early positive liquid cultures. IMPORTANCE In this study, we used whole-genome sequencing (WGS) from early positive liquid (MGIT) cultures instead of solid cultures to predict drug resistance of 182 Mycobacterium tuberculosis complex (MTBC) clinical isolates to predict drug resistance using the TB-Profiler informatics platform. Our study indicates that WGS may be a promising method for predicting MTBC resistance using early positive liquid cultures.
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5
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Lee SK, Baek SH, Hong MS, Lee JS, Cho EJ, Lee JI, Cho SN, Eum SY. A rapid assessing method of drug susceptibility using flow cytometry for Mycobacterium tuberculosis isolates resistant to INH, RIF and EMB. Tuberc Respir Dis (Seoul) 2022; 85:264-272. [PMID: 35196443 PMCID: PMC9263347 DOI: 10.4046/trd.2021.0134] [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: 09/27/2021] [Accepted: 02/22/2022] [Indexed: 11/24/2022] Open
Abstract
Background The current conventional drug susceptibility test (DST) for Mycobacterium tuberculosis (Mtb) takes several weeks of incubation to obtain results. As a rapid method, molecular DST requires only a few days to get the results but does not fully cover the phenotypic resistance. A new rapid method based on the ability of viable Mtb bacilli to hydrolyze fluorescein diacetate to free fluorescein with detection of fluorescent mycobacteria by flow cytometric analysis, was recently developed. Methods To evaluate this cytometric method, we tested 39 clinical isolates which were susceptible or resistant to isoniazid (INH) or rifampin (RIF), or ethambutol (EMB) by phenotypic or molecular DST methods and compared the results. Results The susceptibility was determined by measuring the viability rate of Mtb and all the isolates which were tested with INH, RIF, and EMB showed susceptibility results concordant with those by the phenotypic solid and liquid media methods. The isolates having no mutations in the molecular DST but resistance in the conventional phenotypic DST were also resistant in this cytometric method. These results suggest that the flow cytometric DST method is faster than conventional agar phenotypic DST and may complement the results of molecular DST. Conclusion In conclusion, the cytometric method could provide quick and more accurate information that would help clinicians to choose more effective drugs.
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Affiliation(s)
- Sun-Kyoung Lee
- Division of Immunopathology and Cellular Immunology & Division of Microbiology, International Tuberculosis Research Center,Seoul, Republic of Korea
| | - Seung-Hun Baek
- ChangWon, Department of Microbiology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Min-Sun Hong
- Division of Immunopathology and Cellular Immunology & Division of Microbiology, International Tuberculosis Research Center,Seoul, Republic of Korea
| | - Jong-Seok Lee
- Division of Immunopathology and Cellular Immunology & Division of Microbiology, International Tuberculosis Research Center,Seoul, Republic of Korea
| | - Eun-Jin Cho
- Division of Immunopathology and Cellular Immunology & Division of Microbiology, International Tuberculosis Research Center,Seoul, Republic of Korea
| | - Ji-Im Lee
- Division of Immunopathology and Cellular Immunology & Division of Microbiology, International Tuberculosis Research Center,Seoul, Republic of Korea
| | - Sang-Nae Cho
- Division of Immunopathology and Cellular Immunology & Division of Microbiology, International Tuberculosis Research Center,Seoul, Republic of Korea.,ChangWon, Department of Microbiology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seok-Yong Eum
- Division of Immunopathology and Cellular Immunology & Division of Microbiology, International Tuberculosis Research Center,Seoul, Republic of Korea
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Du J, Li Q, Liu M, Wang Y, Xue Z, Huo F, Zhang X, Shang Y, Li S, Huang H, Pang Y. Distinguishing Relapse From Reinfection With Whole-Genome Sequencing in Recurrent Pulmonary Tuberculosis: A Retrospective Cohort Study in Beijing, China. Front Microbiol 2021; 12:754352. [PMID: 34956119 PMCID: PMC8693897 DOI: 10.3389/fmicb.2021.754352] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/08/2021] [Indexed: 11/18/2022] Open
Abstract
Background: Tuberculosis recurrence is still a major problem for the control of tuberculosis, and the cause of the recurrence is still unclear. Methods: We retrospectively recruited 68 pairs of samples of Mycobacterium tuberculosis (MTB) from recurrent TB cases in Beijing Chest Hospital between January 2008 and December 2019. The whole-genome sequencing was conducted to analyze single-nucleotide polymorphism (SNP) and to identify whether recurrent disease was due to relapse or reinfection. The BACTEC MGIT was performed to compare differences in drug susceptibility profiles between two episodes. Results: 62 (91.2%) out of 68 confirmed recurrence were due to relapse, whereas the remaining six (8.8%) were due to reinfection. And there was a strong association between earlier relapse and underlying chronic diseases. In addition, the MTB isolates from non-diabetic patients had a higher mutation rate than those from diabetic patients. A community transmission was also identified in our cohort. Levofloxacin resistance was the most frequently observed drug resistance for 12.9% relapse cases. Conclusion: The relapse of a previous episode in Beijing. The underlying chronic diseases are associated with an earlier TB relapse. MTB isolates were more prone to develop levofloxacin resistance than moxifloxacin resistance after FQ exposure. The patients at high-risk for relapses deserve more careful investigation.
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Affiliation(s)
- Jian Du
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Qing Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Min Liu
- Provincial Center for Tuberculosis Control and Prevention, Liaoning Provincial Center for Disease Control and Prevention, Shenyang, China
| | - Yufeng Wang
- Department of Laboratory Quality Control, Innovation Alliance on Tuberculosis Diagnosis and Treatment (Beijing), Beijing, China
| | - Zhongtan Xue
- Department of Laboratory Quality Control, Innovation Alliance on Tuberculosis Diagnosis and Treatment (Beijing), Beijing, China
| | - Fengmin Huo
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Xuxia Zhang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Shanshan Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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Kendall EA, Malhotra S, Cook-Scalise S, Dowdy DW, Denkinger CM. Clinical Impact of Rapid Drug Susceptibility Testing to Accompany Fluoroquinolone-Containing Universal Tuberculosis Regimens: A Markov Model. Clin Infect Dis 2021; 71:2889-2896. [PMID: 31813958 DOI: 10.1093/cid/ciz1179] [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: 09/10/2019] [Accepted: 12/06/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND To appropriately treat tuberculosis (TB) with regimens that combine novel and older drugs, evidence-based, context-specific strategies for drug-susceptibility testing (DST) will be required. METHODS We created a Markov state-transition model of 100 000 adults with TB receiving a novel, fluoroquinolone (FQ)-containing regimen. We estimated clinical outcomes and resource utilization with no FQ-DST, universal FQ-DST, or FQ-DST only for patients with rifampin-resistant TB ("targeted FQ-DST"). We considered scenarios of stronger (South Africa) and weaker (Southeast Asia) correlation of fluoroquinolone resistance with rifampin resistance, with sensitivity analysis for other setting and regimen characteristics. RESULTS Relative to no FQ-DST, targeted FQ-DST increased cure of FQ-resistant TB by 7.5% (interquartile range [IQR], 6.7%-9.2%) in South Africa and 1.7% (IQR, 0.7%-2.5%) in Southeast Asia. However, rare FQ resistance among the more prevalent rifampin-susceptible TB accounted for 50% of FQ-resistant TB in South Africa and 83% in Southeast Asia. As a result, universal FQ-DST further increased cure of FQ-resistant TB by 3.4% (IQR, 2.3%-5.4%) in South Africa and 5.8% (IQR, 5.1%-6.3%) in Southeast Asia. With targeted FQ-DST, 1 additional patient was cured per 50 (IQR, 42-70) tests in South Africa and 44 (IQR, 37-51) in Southeast Asia. When expanding from targeted to universal FQ-DST, 1 additional cure required 3500 (IQR, 2300-5500) tests in South Africa and 410 (IQR, 370-450) in Southeast Asia. CONCLUSIONS FQ-DST improved patient outcomes and was particularly important for high-risk patient groups and less robust regimens. A universal strategy was favored in generalized epidemics of fluoroquinolone resistance.
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Affiliation(s)
- Emily A Kendall
- Division of Infectious Diseases and Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Shelly Malhotra
- Global Alliance for Tuberculosis Drug Development, New York, New York, USA
| | - Sarah Cook-Scalise
- Global Alliance for Tuberculosis Drug Development, New York, New York, USA
| | - David W Dowdy
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Claudia M Denkinger
- Division of Tropical Medicine, Center of Infectious Disease, Heidelberg University, Heidelberg, Germany.,Foundation for Innovative New Diagnostics, Geneva, Switzerland
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Torpey K, Agyei-Nkansah A, Ogyiri L, Forson A, Lartey M, Ampofo W, Akamah J, Puplampu P. Management of TB/HIV co-infection: the state of the evidence. Ghana Med J 2020; 54:186-196. [PMID: 33883764 PMCID: PMC8042796 DOI: 10.4314/gmj.v54i3.10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis (TB) and HIV are strongly linked. There is a 19 times increased risk of developing active TB in people living with HIV than in HIV-negative people with Sub-Saharan Africa being the hardest hit region. According to the WHO, 1.3 million people died from TB, and an additional 300,000 TB-related deaths among people living with HIV. Although some progress has been made in reducing TB-related deaths among people living with HIV due to the evolution of diagnostics, treatment and antiretroviral HIV treatment, multi drug resistant TB is becoming a source of worry. Though significant progress has been made at the national level, understanding the state of the evidence and the challenges will better inform the national response of the opportunities for improved patient outcomes. FUNDING None.
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Affiliation(s)
- Kwasi Torpey
- Department of Population, Family and Reproductive Health, University of Ghana School of Public Health
- Department of Medicine and Therapeutics, University of Ghana Medical School
| | | | - Lily Ogyiri
- Department of Population, Family and Reproductive Health, University of Ghana School of Public Health
| | - Audrey Forson
- Department of Medicine and Therapeutics, University of Ghana Medical School
| | - Margaret Lartey
- Department of Medicine and Therapeutics, University of Ghana Medical School
| | - William Ampofo
- Department of Virology, University of Ghana Noguchi Memorial Institute of Medical Research
| | - Joseph Akamah
- Department of Medicine and Therapeutics, University of Ghana Medical School
| | - Peter Puplampu
- Department of Medicine and Therapeutics, University of Ghana Medical School
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9
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Acharya B, Acharya A, Gautam S, Ghimire SP, Mishra G, Parajuli N, Sapkota B. Advances in diagnosis of Tuberculosis: an update into molecular diagnosis of Mycobacterium tuberculosis. Mol Biol Rep 2020; 47:4065-4075. [DOI: 10.1007/s11033-020-05413-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 03/28/2020] [Indexed: 01/02/2023]
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Rakhmawatie MD, Wibawa T, Lisdiyanti P, Pratiwi WR, Mustofa. Evaluation of crystal violet decolorization assay and resazurin microplate assay for antimycobacterial screening. Heliyon 2019; 5:e02263. [PMID: 31497667 PMCID: PMC6722264 DOI: 10.1016/j.heliyon.2019.e02263] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/28/2019] [Accepted: 08/06/2019] [Indexed: 11/29/2022] Open
Abstract
The main obstacle in antimycobacterial discovery is the extremely slow growth rates of pathogenic mycobacteria that lead to the long incubation times needed in antimycobacterial screening. Some in vitro testings has been developed and are currently available for antimycobacterial screening. The aim of the study was to compare Resazurin Microplate Assay (REMA) and Crystal Violet Decolorization Assay (CVDA) for testing mycobacteria susceptibility to isoniazid and rifampicin as well as for antimycobacterial screening of natural products (NP). Mycobacterium tuberculosis strain H37Rv and Mycobacterium smegmatis strain mc2 155 were used as tested mycobacteria. Serial two-fold dilutions from 0.0625 to 1.0 μg/mL for the isoniazid and rifampicin and from 6.25 to 100.0 μg/mL for the NP A and B were prepared. Tested mycobacteria were then incubated with tested drugs or NPs in each growth medium at 37 °C for 7 days for M. tuberculosis and 3 days for M. smegmatis. MIC values against M. tuberculosis were interpreted 24-48 h after adding resazurin or at least 72 h after adding crystal violet, whereas MIC values against M. smegmatis were interpreted 1 h after adding resazurin or 24 h after adding crystal violet. The MIC values against M. tuberculosis interpreted by REMA were 0.0625, 0.0625, 6.25, and >100 μg/mL for rifampicin, isoniazid, NP A, and NP B, respectively, and those interpreted by CVDA were 0.0625, 0.0625, 6.25, and >100 μg/mL for rifampicin, isoniazid, NP A, and NP B, respectively. Moreover, the MIC values against M. smegmatis interpreted by REMA were 0.0625, >1, 6.25, and 100 μg/mL for rifampicin, isoniazid, NP A, and NP B, respectively, and those interpreted by CVDA were 0.125, >1, 6.25, and >100 μg/mL for rifampicin, isoniazid, NP A, NP B respectively. In conclusion, REMA is faster and easier than CVDA to interpret MIC values, however CVDA produces higher MIC values than REMA for rifampicin and NP B in M. smegmatis susceptibility testing. Therefore, REMA and CVDA can be used for antimycobacterial screening.
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Affiliation(s)
- Maya Dian Rakhmawatie
- Doctoral Program in Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Muhammadiyah Semarang, Semarang, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Puspita Lisdiyanti
- Research Center for Biotechnology, Indonesian Institute of Sciences, Bogor, Indonesia
| | - Woro Rukmi Pratiwi
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mustofa
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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11
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Li G, Xu Z, Jiang Y, Liu H, Zhao LL, Li M, Xu D, Zhao X, Liu Z, Wang R, Wan K. Synergistic activities of clofazimine with moxifloxacin or capreomycin against Mycobacterium tuberculosis in China. Int J Antimicrob Agents 2019; 54:642-646. [PMID: 31200023 DOI: 10.1016/j.ijantimicag.2019.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 04/19/2019] [Accepted: 06/02/2019] [Indexed: 11/25/2022]
Abstract
Clofazimine (CFZ) is a promising candidate drug for use in the management of multidrug-resistant tuberculosis (MDR-TB) patients. In this study, the minimum inhibitory concentration (MIC) method and checkerboard method were used to investigate potential synergies between CFZ and moxifloxacin (MOX) or capreomycin (CAP). Thirty Mycobacterium tuberculosis strains were collected, including 13 MDR strains, 2 extensively drug-resistant (XDR) strains, 3 pan-sensitive strains and 12 strains resistant to other drugs. When the minimum fractional inhibitory concentration indexes (FICIs) were calculated, synergy was found in 21 (70.00%) M. tuberculosis strains against the CFZ/CAP combination and 29 (96.67%) against the CFZ/MOX combination. When the maximum FICIs were calculated, 10 of 15 MDR/XDR strains and 2 of 15 other drug-resistant or pan-sensitive strains showed antagonism against the CFZ/CAP combination, whilst 8 of 15 MDR/XDR strains and 1 of 15 other drug-resistant or pan-sensitive strains showed antagonism against the CFZ/MOX combination, respectively. In conclusion, these findings demonstrate that the combination of CFZ and MOX shows better synergism than the combination of CFZ and CAP. The MDR/XDR isolates are more likely to show antagonism than the other drug-resistant or pan-sensitive strains in both the CFZ/MOX and CFZ/CAP combinations. CFZ in combination with MOX may be a promising drug regimen for the treatment of MDR-TB, particularly for susceptible M. tuberculosis infections.
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Affiliation(s)
- Guilian Li
- Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Zhengquan Xu
- Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Yi Jiang
- Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Haican Liu
- Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Li-Li Zhao
- Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Machao Li
- Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Donglei Xu
- Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Xiuqin Zhao
- Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Zhiguang Liu
- Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Ruibai Wang
- Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Kanglin Wan
- Tuberculosis branch, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
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12
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Redefining MDR-TB: Comparison of Mycobacterium tuberculosis clinical isolates from Russia and Taiwan. INFECTION GENETICS AND EVOLUTION 2018; 72:141-146. [PMID: 30593924 DOI: 10.1016/j.meegid.2018.12.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 12/21/2018] [Accepted: 12/26/2018] [Indexed: 12/22/2022]
Abstract
Multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis are global challenges due to the limited number of effective drugs for treatment. Treatment with less than 4-5 effective drugs might lead to the further emergence of drug resistance and poor clinical outcomes. For better prediction of treatment outcomes, we compared drug-resistance profiles of consecutive clinical MDR Mycobacterium tuberculosis isolates from high- and low-burden settings. This was a retrospective cohort study. We analysed 225 and 229 MDR isolates from Moscow (Russia) and Taiwan, respectively, obtained between 2014 and 2015. Drug susceptibility testing was performed by the Bactec MGIT 960 automated system and the agar proportion method. Detection of resistance-associated mutations in the M. tuberculosis genome was carried out by an array and/or sequencing of selected loci. The principal differences between resistance profiles of MDR isolates in the two countries were the percentages of pre-XDR (40.9% vs. 14.8%) and XDR (34.7% vs. 1.7%) isolates, both of which were significantly higher in Moscow isolates. Forty-eight (33%) of 147 MDR and pre-XDR Russian isolates fall into a group with less than four effective drugs, which accounts for 40% (N = 120) of these isolates. The other 60% in this group were XDR strains (N = 72). Consequently, the average number of effective anti-tuberculosis drugs for MDR-TB treatment was lower for Russian isolates (3 vs. 7). Furthermore, a notable percentage (9%) of isolates resistant to kanamycin harboured mutations in the whiB7 locus, which was not detected by molecular tests targeting common mutations in the rrs and eis loci. We found that 98.2% and 45.9% of MDR isolates from Moscow and Taiwan, respectively, were resistant to streptomycin. Molecular tests for detecting resistance to drugs other than rifampicin, isoniazid, fluoroquinolones, and second-line injectable drugs are needed for individualized therapy. The conventional MDR treatment schemes most probably fail in these cases due to the limited number of effective drugs.
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13
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Ezewudo M, Borens A, Chiner-Oms Á, Miotto P, Chindelevitch L, Starks AM, Hanna D, Liwski R, Zignol M, Gilpin C, Niemann S, Kohl TA, Warren RM, Crook D, Gagneux S, Hoffner S, Rodrigues C, Comas I, Engelthaler DM, Alland D, Rigouts L, Lange C, Dheda K, Hasan R, McNerney R, Cirillo DM, Schito M, Rodwell TC, Posey J. Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase. Sci Rep 2018; 8:15382. [PMID: 30337678 PMCID: PMC6194142 DOI: 10.1038/s41598-018-33731-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/11/2018] [Indexed: 12/30/2022] Open
Abstract
Drug-resistant tuberculosis poses a persistent public health threat. The ReSeqTB platform is a collaborative, curated knowledgebase, designed to standardize and aggregate global Mycobacterium tuberculosis complex (MTBC) variant data from whole genome sequencing (WGS) with phenotypic drug susceptibility testing (DST) and clinical data. We developed a unified analysis variant pipeline (UVP) ( https://github.com/CPTR-ReSeqTB/UVP ) to identify variants and assign lineage from MTBC sequence data. Stringent thresholds and quality control measures were incorporated in this open source tool. The pipeline was validated using a well-characterized dataset of 90 diverse MTBC isolates with conventional DST and DNA Sanger sequencing data. The UVP exhibited 98.9% agreement with the variants identified using Sanger sequencing and was 100% concordant with conventional methods of assigning lineage. We analyzed 4636 publicly available MTBC isolates in the ReSeqTB platform representing all seven major MTBC lineages. The variants detected have an above 94% accuracy of predicting drug based on the accompanying DST results in the platform. The aggregation of variants over time in the platform will establish confidence-graded mutations statistically associated with phenotypic drug resistance. These tools serve as critical reference standards for future molecular diagnostic assay developers, researchers, public health agencies and clinicians working towards the control of drug-resistant tuberculosis.
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Affiliation(s)
- Matthew Ezewudo
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Amanda Borens
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Álvaro Chiner-Oms
- Joint unit Infection and Public Health FISABIO-CSISP/University of Valencia, Institute of integrative Systems Biology, Valencia, Spain
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132, Milano, Italy
| | - Leonid Chindelevitch
- School of Computing Science, Simon Fraser University, 8888 University Ave, Burnaby, BC, V5A 1S6, Canada
| | - Angela M Starks
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road MS F08, Atlanta, GA, 30329, USA
| | - Debra Hanna
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Richard Liwski
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Matteo Zignol
- Global Tuberculosis Program, World Health Organization, Geneva, Switzerland
| | - Christopher Gilpin
- Global Tuberculosis Program, World Health Organization, Geneva, Switzerland
| | - Stefan Niemann
- German Center for Infection Research, Partner Site Borstel, Borstel, Germany
| | - Thomas Andreas Kohl
- Molecular and Experimental Mycobacteriology, Priority area Infections, Research Center Borstel, Borstel, Germany
| | - Robin M Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Derrick Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | | | - Sven Hoffner
- Department of Public Health Sciences, Karolinska institute, Stockholm, Sweden
| | | | - Iñaki Comas
- Tuberculosis Genomics Unit, Biomedicine Institute of Valencia (IBV-CSIC), Street Jaime Roig 11. P.O., 4010, Valencia, Spain
| | - David M Engelthaler
- Translational Genomics Research Institute, 3051 W. Shamrell Blvd. Ste 106, Flagstaff, AZ, 86005, USA
| | - David Alland
- Center for Emerging Pathogens, Rutgers-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ, 07103, USA
| | - Leen Rigouts
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Christoph Lange
- Division of Clinical Infectious Diseases and German Center for Infection Research Tuberculosis Unit, Research Center Borstel, Borstel, Germany
| | - Keertan Dheda
- Lung Infection and Immunity Unit, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Old Main Building, Groote Schuur Hospital, Observatory, Cape Town, South Africa
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Stadium Road, Karachi, Pakistan
| | - Ruth McNerney
- Department of Medicine, Division of Pulmonology, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132, Milano, Italy
| | - Marco Schito
- Critical Path Institute, 1730 E River Rd., Tucson, AZ, 85718, USA
| | - Timothy C Rodwell
- Department of Medicine, University of California, San Diego, CA, USA.,The Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - James Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road MS F08, Atlanta, GA, 30329, USA.
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14
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Sng LH, Peh JWL, Kee MTL, Ya'akob NBM, Ong RTH, Wong CW, Chee CBE, Wang YT. Clofazimine drug susceptibility testing for Mycobacterium tuberculosis: the case of using the right diluent. Pathology 2018; 50:549-553. [PMID: 29891191 DOI: 10.1016/j.pathol.2018.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 01/05/2018] [Accepted: 01/22/2018] [Indexed: 11/19/2022]
Abstract
Accurate and reliable drug susceptibility testing (DST) is essential for the effective treatment and control of tuberculosis. With the increase in drug-resistant organisms, newer and less conventional antimicrobial agents are used for treatment. Recently, we found an unprecedented rise in the number of clofazimine-resistant Mycobacterium tuberculosis isolates in our laboratory. An investigation found that this phenomenon was due to a change in the method of drug preparation. We performed studies to assess the impact of water and dimethyl sulfoxide (DMSO) as a final diluent for clofazimine drug testing. Based on our findings, the use of DMSO as a solvent for M. tuberculosis DST was optimised using the BACTEC MGIT 960 platform.
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Affiliation(s)
- Li-Hwei Sng
- Central Tuberculosis Laboratory, Singapore General Hospital, Singapore.
| | | | | | | | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University Health Singapore, National University of Singapore, Singapore
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15
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Xu C, Pang Y, Li R, Ruan Y, Wang L, Chen M, Zhang H. Clinical outcome of multidrug-resistant tuberculosis patients receiving standardized second-line treatment regimen in China. J Infect 2018; 76:348-353. [PMID: 29374587 DOI: 10.1016/j.jinf.2017.12.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/18/2017] [Accepted: 12/14/2017] [Indexed: 11/30/2022]
Abstract
OBJECTIVES The aim of this study was to retrospectively analyze the clinical outcome and the risk factors associated with poor outcome of MDR-TB patients receiving standardized second-line treatment regimen in China. METHODS Between January 2008 and December 2010, a total of 12,100 clinical diagnosed TB cases at high risk of drug-resistant TB (DR-TB) were enrolled in this study. Routine follow-up tests were conducted every month during the 6-month intensive phase, and every two months during the 18-month continuation phase. RESULTS On the basis of phenotypical drug susceptibility test (DST) results, 2322 MDR-TB patients were confirmed, of which 1542 further received standardized second-line anti-TB regimen. The treatment success rate was 47.6% (734/1542): 688 patients (44.6%) were cured and 46 (3.0%) completed treatment. The percentage of cases with favorable outcome in previously untreated patients (57.6%) was significantly higher than that in treatment-experienced patients (46.1%, OR: 1.58, 95% CI: 1.17-2.14). In addition, a significant lower percentage of male MDR-TB cases with favorable outcome (45.8%) was observed using female MDR-TB cases as a reference (52.0%, OR: 1.31, 95% CI: 1.03-1.60). The proportion of MDR-TB cases with favorable outcome was significantly decreased in older age groups. CONCLUSIONS In conclusion, our data demonstrate that less than half of these patients receiving standardized second-line treatment regimen meet the definition of successful treatment during a 3-year period in China. More attention should be paid to the MDR-TB population at high-risk of poor clinical outcome, including male, elderly age, and those who have received prior treatment.
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Affiliation(s)
- Caihong Xu
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yu Pang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Renzhong Li
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yunzhou Ruan
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lixia Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mingting Chen
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Zhang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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16
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Abstract
Rapid and accurate diagnosis is critical for timely initiation of anti-tuberculosis (TB) treatment, but many people with TB (or TB symptoms) do not have access to adequate initial diagnosis. In many countries, TB diagnosis is still reliant on sputum microscopy, a test with known limitations. However, new diagnostics are starting to change the landscape. Stimulated, in part, by the success and rollout of Xpert MTB/RIF, an automated, molecular test, there is now considerable interest in new technologies. The landscape looks promising with a pipeline of new tools, particularly molecular diagnostics, and well over 50 companies actively engaged in product development, and many tests have been reviewed by WHO for policy endorsement. However, new diagnostics are yet to reach scale, and there needs to be greater convergence between diagnostics development and the development of shorter TB drug regimens. Another concern is the relative absence of non-sputum-based diagnostics in the pipeline for children, and of biomarker tests for triage, cure, and latent TB progression. Increased investments are necessary to support biomarker discovery, validation, and translation into clinical tools. While transformative tools are being developed, high-burden countries will need to improve the efficiency of their health care delivery systems, ensure better uptake of new technologies, and achieve greater linkages across the TB and HIV care continuum. While we wait for next-generation technologies, national TB programs must scale up the best diagnostics currently available, and use implementation science to get the maximum impact.
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17
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Méndez-Samperio P. Diagnosis of Tuberculosis in HIV Co-infected Individuals: Current Status, Challenges and Opportunities for the Future. Scand J Immunol 2017; 86:76-82. [PMID: 28513865 DOI: 10.1111/sji.12567] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 05/07/2017] [Indexed: 02/03/2023]
Abstract
Tuberculosis (TB) remains one of the most important causes of death among people co-infected with human immunodeficiency virus (HIV). The diagnosis of TB remains challenging in HIV co-infected individuals, due to a high frequency of smear-negative disease and high rates of extrapulmonary TB. Accurate, ease of use and rapid diagnosis of active TB are critical to the World Health Organization (WHO) End TB Strategy by 2050. Traditional laboratory techniques do not provide rapid and accurate results to effectively manage HIV co-infected patients. Over the last decade, molecular methods have provided significant steps in the fight against TB. However, many HIV co-infected patients do not have access to these molecular diagnostic tests. Given the costs closely related with confirming a TB diagnosis in HIV patients, an overtreatment for TB is used in this patient population. Nowadays, an estimated US $8 billion a year is required to provide TB treatment, which is very high compared with making an important strategy to improve the current diagnostic tests. This review focuses on current advances in diagnosing active TB with an emphasis on the diagnosis of HIV-associated TB. Also discussed are the main challenges that need to be overcome for improving an adequate initial diagnosis of active TB in HIV-positive patients.
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Affiliation(s)
- P Méndez-Samperio
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, IPN, México, México
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18
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Pathmanathan I, Date A, Coggin WL, Nkengasong J, Piatek AS, Alexander H. Rolling Out Xpert ® MTB/RIF for TB Detection in HIV-Infected Populations:An Opportunity for Systems Strengthening. Afr J Lab Med 2017; 6. [PMID: 28785533 PMCID: PMC5523912 DOI: 10.4102/ajlm.v6i2.460] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background To eliminate preventable deaths, disease and suffering due to tuberculosis, improved diagnostic capacity is critical. The Cepheid Xpert MTB/RIF® assay is recommended by the World Health Organization as the initial diagnostic test for people with suspected HIV-associated tuberculosis. However, despite high expectations, its scale-up in real-world settings has faced challenges, often due to the systems that support it. Opportunities for System Strengthening In this commentary, we discuss needs and opportunities for systems strengthening to support widespread scale-up of Xpert MTB/RIF as they relate to each step within the tuberculosis diagnostic cascade, from finding presumptive patients, to collecting, transporting and testing sputum specimens, to reporting and receiving results, to initiating and monitoring treatment and, ultimately, to ensuring successful and timely treatment and cure. Investments in evidence-based interventions at each step along the cascade and within the system as a whole will augment not only the utility of Xpert MTB/RIF, but also the successful implementation of future diagnostic tests. Conclusion Xpert MTB/RIF will only improve patient outcomes if optimally implemented within the context of strong tuberculosis programmes and systems. Roll-out of this technology to people living with HIV and others in resource-limited settings offers the opportunity to leverage current tuberculosis and HIV laboratory, diagnostic and programmatic investments, while also addressing challenges and strengthening coordination between laboratory systems, laboratory-programme interfaces, and tuberculosis-HIV programme interfaces. If successful, the benefits of this tool could extend beyond progress toward global End TB Strategy goals, to improve system-wide capacity for global disease detection and control.
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Affiliation(s)
- Ishani Pathmanathan
- Division of Global HIV and TB, U.S. Centers for Disease Control & Prevention, Atlanta, USA.,Epidemic Intelligence Service, U.S. Centers for Disease Control & Prevention, Atlanta, USA
| | - Anand Date
- Division of Global HIV and TB, U.S. Centers for Disease Control & Prevention, Atlanta, USA
| | - William L Coggin
- Division of Global HIV and TB, U.S. Centers for Disease Control & Prevention, Atlanta, USA
| | - John Nkengasong
- Division of Global HIV and TB, U.S. Centers for Disease Control & Prevention, Atlanta, USA
| | - Amy S Piatek
- Global Health Bureau, United States Agency for International Development, Washington DC, USA
| | - Heather Alexander
- Division of Global HIV and TB, U.S. Centers for Disease Control & Prevention, Atlanta, USA
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19
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Abstract
Whole-genome sequencing has taken a leading role in epidemiologic studies of tuberculosis, but thus far, its real-time clinical utility has been low, in part because of the requirement for culture. In their report in this issue, Votintseva et al. (A. A. Votintseva, P. Bradley, L. Pankhurst, C. del Ojo Elias, M. Loose, K. Nilgiriwala, A. Chatterjee, E. G. Smith, N. Sanderson, T. M. Walker, M. R. Morgan, D. H. Wyllie, A. S. Walker, T. E. A. Peto, D. W. Crook, and Z. Iqbal, J Clin Microbiol 55:1285-1298, 2017, https://doi.org/10.1128/JCM.02483-16) present a new method for extracting Mycobacterium tuberculosis DNA directly from smear-positive respiratory samples, making it feasible to generate drug resistance predictions and phylogenetic trees in 44 h with the Illumina MiSeq. They also illustrate the potential for a <24-h turnaround time from DNA extraction to clinically relevant results with Illumina MiniSeq and Oxford Nanopore Technologies MinION. We comment on the promise and limitations of these approaches.
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20
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Evolution of Phenotypic and Molecular Drug Susceptibility Testing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:221-246. [PMID: 29116638 DOI: 10.1007/978-3-319-64371-7_12] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Drug Resistant Tuberculosis (DRTB) is an emerging problem world-wide. In order to control the disease and decrease the number of cases overtime a prompt diagnosis followed by an appropriate treatment should be provided to patients. Phenotypic DST based on liquid automated culture has greatly reduced the time needed to generate reliable data but has the drawback to be expensive and prone to contamination in the absence of appropriate infrastructures. In the past 10 years molecular biology tools have been developed. Those tools target the main mutations responsible for DRTB and are now globally accessible in term of cost and infrastructures needed for the implementation. The dissemination of the Xpert MTB/rif has radically increased the capacity to perform the detection of rifampicin resistant TB cases. One of the main challenges for the large scale implementation of molecular based tests is the emergence of conflicting results between phenotypic and genotypic tests. This mines the confidence of clinicians in the molecular tests and delays the initiation of an appropriate treatment. A new technique is revolutionizing the genotypic approach to DST: the WGS by Next-Generation Sequencing technologies. This methodology promises to become the solution for a rapid access to universal DST, able indeed to overcome the limitations of the current phenotypic and genotypic assays. Today the use of the generated information is still challenging in decentralized facilities due to the lack of automation for sample processing and standardization in the analysis.The growing knowledge of the molecular mechanisms at the basis of drug resistance and the introduction of high-performing user-friendly tools at peripheral level should allow the very much needed accurate diagnosis of DRTB in the near future.
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Prothionamide susceptibility testing of Mycobacterium tuberculosis using the resazurin microtitre assay and the BACTECMGIT 960 system. Eur J Clin Microbiol Infect Dis 2016; 36:779-782. [PMID: 28000029 DOI: 10.1007/s10096-016-2859-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/29/2016] [Indexed: 10/20/2022]
Abstract
Resazurin microtitre assay (RMA) has been successfully used to detect minimal inhibitory concentrations (MICs) of both first-line and several second-line drugs in drug susceptibility testing (DST) of Mycobacterium tuberculosis (MTB). In this study, we firstly compared prothionamide (PTH) susceptibility testing of Mycobacterium tuberculosis (MTB) using resazurin microtitre assay (RMA) and MGIT. Overall, the sensitivity and specificity of RMA for detecting PTH susceptibility was 96.5% [95% confidence interval (CI): 91.7-100.0] and 93.2% (95% CI: 89.6-96.8) respectively. In addition, the median time to positivity was significantly shorter for RMA than for the automated MGIT 960 (RMA, 8 days [range: 8-8 days] vs MGIT, 10.1 days, [range: 5.0-13.0]; P < 0.01). Concordance rate for MICs between RMA and MGIT for PTH-resistant group was 64.3% (95% CI: 46.5-82.0), which was significantly lower than that of PTH-susceptible group (85.9%, 95% CI: 78.8-93.0; P= 0.01). In conclusion, our data demonstrated that RMA can be used as an acceptable alternative for determination of PTH susceptibility with shorter turn-around time. When compared with MGIT 960, RMA method was prone to produce higher MICs for PTH-resistant MTB strains.
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MacLean E, Huddart S, Pai M. Molecular diagnosis of tuberculosis: we need solutions that span the healthcare value chain. Expert Rev Mol Diagn 2016; 17:5-7. [PMID: 27892734 DOI: 10.1080/14737159.2017.1265889] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Emily MacLean
- a Department of Epidemiology & Biostatistics , McGill University , Montreal , Canada.,b McGill International TB Centre , McGill University , Montreal , Canada
| | - Sophie Huddart
- a Department of Epidemiology & Biostatistics , McGill University , Montreal , Canada.,b McGill International TB Centre , McGill University , Montreal , Canada
| | - Madhukar Pai
- a Department of Epidemiology & Biostatistics , McGill University , Montreal , Canada.,b McGill International TB Centre , McGill University , Montreal , Canada
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Abstract
Tuberculosis (TB) is an airborne infectious disease caused by organisms of the Mycobacterium tuberculosis complex. Although primarily a pulmonary pathogen, M. tuberculosis can cause disease in almost any part of the body. Infection with M. tuberculosis can evolve from containment in the host, in which the bacteria are isolated within granulomas (latent TB infection), to a contagious state, in which the patient will show symptoms that can include cough, fever, night sweats and weight loss. Only active pulmonary TB is contagious. In many low-income and middle-income countries, TB continues to be a major cause of morbidity and mortality, and drug-resistant TB is a major concern in many settings. Although several new TB diagnostics have been developed, including rapid molecular tests, there is a need for simpler point-of-care tests. Treatment usually requires a prolonged course of multiple antimicrobials, stimulating efforts to develop shorter drug regimens. Although the Bacillus Calmette-Guérin (BCG) vaccine is used worldwide, mainly to prevent life-threatening TB in infants and young children, it has been ineffective in controlling the global TB epidemic. Thus, efforts are underway to develop newer vaccines with improved efficacy. New tools as well as improved programme implementation and financing are necessary to end the global TB epidemic by 2035.
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Ombura IP, Onyango N, Odera S, Mutua F, Nyagol J. Prevalence of Drug Resistance Mycobacterium Tuberculosis among Patients Seen in Coast Provincial General Hospital, Mombasa, Kenya. PLoS One 2016; 11:e0163994. [PMID: 27711122 PMCID: PMC5053611 DOI: 10.1371/journal.pone.0163994] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 09/19/2016] [Indexed: 11/29/2022] Open
Abstract
Background Although prevention and control of spread of multi-drug resistant tuberculosis strains is a global challenge, there is paucity of data on the prevalence of DR-TB in patients diagnosed with TB in referral hospitals in Kenya. The present study assessed patients’ characteristics and prevalence of drug resistant TB in sputa smear positive TB patients presenting to Coast Provincial General Hospital (CPGH) in Mombasa, Kenya. Methods Drug resistance was evaluated in 258 randomly selected sputa smear TB positive cases between the periods of November 2011 to February 2012 at the CPGH-Mombasa. Basic demographic data was obtained using administered questionnaires, and clinical history extracted from the files. For laboratory analyses, 2mls of sputum was obtained, decontaminated and subjected to mycobacteria DNA analyses. Detection of first line drug resistance genes was done using MDRTDR plus kit. This was followed with random selection of 83 cases for second line drug resistance genes testing using Genotype MDRTBsl probe assay kit (HAINS Lifesciences, GmbH, Germany), in which ethambutol mutation probes were included. The data was then analyzed using SPSS statistical package version 19.0. Results Male to female ratio was 1:2. Age range was 9 to 75 years, with median of 30 years. New treatment cases constituted 253(98%), among which seven turned out to be PTB negative, and further grouped as 4 (1.6%) PTB negative and 3(1.1%) NTM. 237(91.7%) new cases were fully susceptible to INH and RIF. The remaining, 8 (3.1%) and 1(0.4%) had mono- resistance to INH and RIF, respectively. All the retreatment cases were fully susceptible to the first line drugs. HIV positivity was found in 48 (18.6%) cases, of which 46(17.8%) were co-infected with TB. Of these, 44 (17.1%) showed full susceptibility to TB drugs, while 2 (0.8%) were INH resistant. For the second line drugs, one case each showed mono resistance to both and FQ. Also, one case each showed drug cross poly resistance to both ETH and FQ, with second line injectable antibiotics. However, no significant statistical correlation was established between TB and resistance to the second line drugs p = 0.855. Conclusion The findings of this study showed the existence of resistance to both first and second line anti-tubercular drugs, but no MDR-TB and XDR-TB was detected among patients attending TB clinic at CPGH using molecular techniques.
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Affiliation(s)
- Ida Pam Ombura
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Noel Onyango
- Department of Clinical Medicine and Therapeutics, Unit of Medical Oncology, University of Nairobi, Nairobi, Kenya
| | - Susan Odera
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Florence Mutua
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Joshua Nyagol
- Department of Human Pathology, Unit of Immunology, University of Nairobi, Nairobi, Kenya
- * E-mail:
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Zignol M, Dean AS, Alikhanova N, Andres S, Cabibbe AM, Cirillo DM, Dadu A, Dreyer A, Driesen M, Gilpin C, Hasan R, Hasan Z, Hoffner S, Husain A, Hussain A, Ismail N, Kamal M, Mansjö M, Mvusi L, Niemann S, Omar SV, Qadeer E, Rigouts L, Ruesch-Gerdes S, Schito M, Seyfaddinova M, Skrahina A, Tahseen S, Wells WA, Mukadi YD, Kimerling M, Floyd K, Weyer K, Raviglione MC. Population-based resistance of Mycobacterium tuberculosis isolates to pyrazinamide and fluoroquinolones: results from a multicountry surveillance project. THE LANCET. INFECTIOUS DISEASES 2016; 16:1185-1192. [PMID: 27397590 PMCID: PMC5030278 DOI: 10.1016/s1473-3099(16)30190-6] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 05/31/2016] [Accepted: 06/10/2016] [Indexed: 02/06/2023]
Abstract
Background Pyrazinamide and fluoroquinolones are essential antituberculosis drugs in new rifampicin-sparing regimens. However, little information about the extent of resistance to these drugs at the population level is available. Methods In a molecular epidemiology analysis, we used population-based surveys from Azerbaijan, Bangladesh, Belarus, Pakistan, and South Africa to investigate resistance to pyrazinamide and fluoroquinolones among patients with tuberculosis. Resistance to pyrazinamide was assessed by gene sequencing with the detection of resistance-conferring mutations in the pncA gene, and susceptibility testing to fluoroquinolones was conducted using the MGIT system. Findings Pyrazinamide resistance was assessed in 4972 patients. Levels of resistance varied substantially in the surveyed settings (3·0–42·1%). In all settings, pyrazinamide resistance was significantly associated with rifampicin resistance. Among 5015 patients who underwent susceptibility testing to fluoroquinolones, proportions of resistance ranged from 1·0–16·6% for ofloxacin, to 0·5–12·4% for levofloxacin, and 0·9–14·6% for moxifloxacin when tested at 0·5 μg/mL. High levels of ofloxacin resistance were detected in Pakistan. Resistance to moxifloxacin and gatifloxacin when tested at 2 μg/mL was low in all countries. Interpretation Although pyrazinamide resistance was significantly associated with rifampicin resistance, this drug may still be effective in 19–63% of patients with rifampicin-resistant tuberculosis. Even though the high level of resistance to ofloxacin found in Pakistan is worrisome because it might be the expression of extensive and unregulated use of fluoroquinolones in some parts of Asia, the negligible levels of resistance to fourth-generation fluoroquinolones documented in all survey sites is an encouraging finding. Rational use of this class of antibiotics should therefore be ensured to preserve its effectiveness. Funding Bill & Melinda Gates Foundation, United States Agency for International Development, Global Alliance for Tuberculosis Drug Development.
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Affiliation(s)
- Matteo Zignol
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland.
| | - Anna S Dean
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
| | | | - Sönke Andres
- National and Supranational Reference Laboratory for Mycobacterium, Borstel, Germany
| | | | | | - Andrei Dadu
- Regional Office for Europe, World Health Organization, Copenhagen, Denmark
| | - Andries Dreyer
- National Institute for Communicable Diseases, Sandringham, South Africa
| | - Michèle Driesen
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Christopher Gilpin
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Sven Hoffner
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden; Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Ashaque Husain
- National Tuberculosis Control Programme, Dhaka, Bangladesh
| | - Alamdar Hussain
- National Tuberculosis Reference Laboratory, National Tuberculosis Control Programme, Islamabad, Pakistan
| | - Nazir Ismail
- National Institute for Communicable Diseases, Sandringham, South Africa; University of Pretoria, Pretoria, South Africa
| | - Mostofa Kamal
- National Institute of Diseases of the Chest and Hospital, Dhaka, Bangladesh
| | - Mikael Mansjö
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Lindiwe Mvusi
- Tuberculosis Control and Management, National Department of Health, Pretoria, South Africa
| | - Stefan Niemann
- National and Supranational Reference Laboratory for Mycobacterium, Borstel, Germany
| | - Shaheed V Omar
- National Institute for Communicable Diseases, Sandringham, South Africa
| | - Ejaz Qadeer
- National Tuberculosis Control Programme, Ministry of National Health Services, Regulation and Coordination, Islamabad, Pakistan
| | - Leen Rigouts
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Sabine Ruesch-Gerdes
- National and Supranational Reference Laboratory for Mycobacterium, Borstel, Germany
| | | | | | - Alena Skrahina
- Republican Research and Practical Centre for Pulmonology and Tuberculosis, Minsk, Belarus
| | - Sabira Tahseen
- National Tuberculosis Reference Laboratory, National Tuberculosis Control Programme, Islamabad, Pakistan
| | - William A Wells
- Bureau for Global Health, US Agency for International Development, Washington, DC, USA
| | - Ya Diul Mukadi
- Bureau for Global Health, US Agency for International Development, Washington, DC, USA
| | | | - Katherine Floyd
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
| | - Karin Weyer
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
| | - Mario C Raviglione
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
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Dowdy DW, Houben R, Cohen T, Pai M, Cobelens F, Vassall A, Menzies NA, Gomez GB, Langley I, Squire SB, White R. Impact and cost-effectiveness of current and future tuberculosis diagnostics: the contribution of modelling. Int J Tuberc Lung Dis 2016; 18:1012-8. [PMID: 25189546 PMCID: PMC4436823 DOI: 10.5588/ijtld.13.0851] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The landscape of diagnostic testing for tuberculosis (TB) is changing rapidly, and stakeholders need urgent guidance on how to develop, deploy and optimize TB diagnostics in a way that maximizes impact and makes best use of available resources. When decisions must be made with only incomplete or preliminary data available, modelling is a useful tool for providing such guidance. Following a meeting of modelers and other key stakeholders organized by the TB Modelling and Analysis Consortium, we propose a conceptual framework for positioning models of TB diagnostics. We use that framework to describe modelling priorities in four key areas: Xpert® MTB/RIF scale-up, target product profiles for novel assays, drug susceptibility testing to support new drug regimens, and the improvement of future TB diagnostic models. If we are to maximize the impact and cost-effectiveness of TB diagnostics, these modelling priorities should figure prominently as targets for future research.
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Affiliation(s)
- D W Dowdy
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - R Houben
- Department of Infectious Disease Epidemiology and TB Modelling Group, London School of Hygiene & Tropical Medicine, London, UK
| | - T Cohen
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - M Pai
- Department of Epidemiology and Biostatistics & McGill International TB Centre, McGill University, Montreal, Quebec, Canada
| | - F Cobelens
- Department of Global Health and Amsterdam Institute for Global Health and Development, Academic Medical Center, Amsterdam, The Netherlands
| | - A Vassall
- SAME Modelling and Economics, Department of Global Health and Development, London School of Hygiene & Tropical Medicine, London, UK
| | - N A Menzies
- Center for Health Decision Science, Harvard School of Public Health, Boston, Massachusetts, USA
| | - G B Gomez
- Department of Global Health and Amsterdam Institute for Global Health and Development, Academic Medical Center, Amsterdam, The Netherlands
| | - I Langley
- Department of Clinical Sciences and Centre for Applied Health Research & Delivery, Liverpool School of Tropical Medicine, Liverpool, UK
| | - S B Squire
- Department of Clinical Sciences and Centre for Applied Health Research & Delivery, Liverpool School of Tropical Medicine, Liverpool, UK
| | - R White
- Department of Infectious Disease Epidemiology and TB Modelling Group, London School of Hygiene & Tropical Medicine, London, UK
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White PJ, Abubakar I. Improving Control of Tuberculosis in Low-Burden Countries: Insights from Mathematical Modeling. Front Microbiol 2016; 7:394. [PMID: 27199896 PMCID: PMC4853635 DOI: 10.3389/fmicb.2016.00394] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/14/2016] [Indexed: 12/20/2022] Open
Abstract
Tuberculosis control and elimination remains a challenge for public health even in low-burden countries. New technology and novel approaches to case-finding, diagnosis, and treatment are causes for optimism but they need to be used cost-effectively. This in turn requires improved understanding of the epidemiology of TB and analysis of the effectiveness and cost-effectiveness of different interventions. We describe the contribution that mathematical modeling can make to understanding epidemiology and control of TB in different groups, guiding improved approaches to public health interventions. We emphasize that modeling is not a substitute for collecting data but rather is complementary to empirical research, helping determine what are the key questions to address to maximize the public-health impact of research, helping to plan studies, and making maximal use of available data, particularly from surveillance, and observational studies. We provide examples of how modeling and related empirical research inform policy and discuss how a combination of these approaches can be used to address current questions of key importance, including use of whole-genome sequencing, screening and treatment for latent infection, and combating drug resistance.
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Affiliation(s)
- Peter J White
- MRC Centre for Outbreak Analysis and Modelling and NIHR Health Protection Research Unit in Modelling Methodology, Imperial College London School of Public HealthLondon, UK; Modelling and Economics Unit, Centre for Infectious Disease Surveillance and Control, Public Health EnglandLondon, UK
| | - Ibrahim Abubakar
- TB Section, Respiratory Diseases Department, Centre for Infectious Disease Surveillance and Control, Public Health EnglandLondon, UK; Research Department of Infection and Population Health, University College LondonLondon, UK; MRC Clinical Trials Unit, University College LondonLondon, UK
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28
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Ssengooba W, Meehan CJ, Lukoye D, Kasule GW, Musisi K, Joloba ML, Cobelens FG, de Jong BC. Whole genome sequencing to complement tuberculosis drug resistance surveys in Uganda. INFECTION GENETICS AND EVOLUTION 2016; 40:8-16. [PMID: 26917365 PMCID: PMC4856735 DOI: 10.1016/j.meegid.2016.02.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 01/20/2016] [Accepted: 02/15/2016] [Indexed: 11/29/2022]
Abstract
Understanding the circulating Mycobacterium tuberculosis resistance mutations is vital for better TB control strategies, especially to inform a new MDR-TB treatment programme. We complemented the phenotypic drug susceptibility testing (DST) based drug resistance surveys (DRSs) conducted in Uganda between 2008 and 2011 with Whole Genome Sequencing (WGS) of 90 Mycobacterium tuberculosis isolates phenotypically resistant to rifampicin and/or isoniazid to better understand the extent of drug resistance. A total of 31 (34.4 %) patients had MDR-TB, 5 (5.6 %) mono-rifampicin resistance and 54 (60.0 %) mono-isoniazid resistance by phenotypic DST. Pyrazinamide resistance mutations were identified in 32.3% of the MDR-TB patients. Resistance to injectable agents was detected in 4/90 (4.4%), and none to fluoroquinolones or novel drugs. Compensatory mutations in rpoC were identified in two patients. The sensitivity and specificity of drug resistance mutations compared to phenotypic DST were for rpoB 88.6% and 98.1%, katG 60.0% and 100%, fabG1 16.5% and 100%, katG and/or fabG1 71.8% and 100%, embCAB 63.0% and 82.5%, rrs 11.4% and 100%, rpsL 20.5% and 95.7% and rrs and/or rpsL 31.8% and 95.7%. Phylogenetic analysis showed dispersed MDR-TB isolate, with only one cluster of three Beijing family from South West Uganda. Among tuberculosis patients in Uganda, resistance beyond first-line drugs as well as compensatory mutations remain low, and MDR-TB isolates did not arise from a dominant clone. Our findings show the potential use of sequencing for complementing DRSs or surveillance in this setting, with good specificity compared to phenotypic DST. The reported high confidence mutations can be included in molecular assays, and population-based studies can track transmission of MDR-TB including the Beijing family strains in the South West of the country.
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Affiliation(s)
- Willy Ssengooba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda; Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Department of Global Health and Amsterdam Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Conor J Meehan
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Deus Lukoye
- National Tuberculosis Reference Laboratory, Ministry of Health, Kampala, Uganda
| | | | - Kenneth Musisi
- National Tuberculosis Reference Laboratory, Ministry of Health, Kampala, Uganda
| | - Moses L Joloba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda; National Tuberculosis Reference Laboratory, Ministry of Health, Kampala, Uganda
| | - Frank G Cobelens
- Department of Global Health and Amsterdam Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; KNCV Tuberculosis Foundation, The Hague, The Netherlands
| | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Division of Infectious Diseases, New York University, New York, NY, USA
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29
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Tackling the tuberculosis epidemic in sub-Saharan Africa--unique opportunities arising from the second European Developing Countries Clinical Trials Partnership (EDCTP) programme 2015-2024. Int J Infect Dis 2016; 32:46-9. [PMID: 25809755 DOI: 10.1016/j.ijid.2014.12.039] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 12/17/2014] [Accepted: 12/18/2014] [Indexed: 10/23/2022] Open
Abstract
Tuberculosis (TB) today remains a global emergency affecting 9.0 million people globally. The African Region bears the highest global TB/HIV burden and over 50% of TB cases in SSA are co-infected with HIV. An estimated 1.5 million died from the TB globally in 2013. A large majority of the 360,000 HIV-positive TB cases who died were from sub-Saharan Africa. Research and development is an important pillar of the WHO post-2015 global TB strategy. Advances in development of diagnostics, drugs, host-directed therapies, and vaccines will require evaluation under field conditions through multi-centre clinical trials at different geographical locations. Thus it is critically important that these evaluations are fully supported by all African governments and the capacity, trained staff and infrastructure required to perform the research and evaluations is built and made available. This viewpoint article reviews the opportunities provided by recently launched second programme (2015-2024) of the European & Developing Countries Clinical Trials Partnership (EDCTP2) for tackling the TB epidemic in Africa through its magnanimous portfolio. The unique opportunities provided by EDCTP2 for leadership of scientific research in TB and other diseases fully devolving to Africa are also covered.
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30
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Grobusch MP, Schaumburg F, Altpeter E, Bélard S. [Drug-resistant tuberculosis. Epidemiology, diagnostics and therapy]. Internist (Berl) 2016; 57:126-35. [PMID: 26795948 DOI: 10.1007/s00108-015-0010-x] [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: 11/30/2022]
Abstract
Drug-resistant tuberculosis (DR-TB) is one of the serious problems in the fight against tuberculosis on a global scale. This review article describes in brief the global epidemiology, diagnostics and treatment of DR-TB. The situation in Germany, Switzerland and Austria is addressed in detail. The article concludes with a presentation of current research topics in the field of resistant TB.
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Affiliation(s)
- M P Grobusch
- Zentrum für Tropen- und Reisemedizin, Abteilung Infektiologie, Akademisch-Medizinisches Zentrum, Universität von Amsterdam, 22660, 1100 DD, Amsterdam, Niederlande. .,Institut für Tropenmedizin, Eberhard Karls Universität Tübingen, Tübingen, Deutschland.
| | - F Schaumburg
- Institut für Medizinische Mikrobiologie, Universitätsklinikum Münster, Münster, Deutschland
| | - E Altpeter
- Abteilung Übertragbare Krankheiten, Bundesamt für Gesundheit, Bern, Schweiz
| | - S Bélard
- Zentrum für Tropen- und Reisemedizin, Abteilung Infektiologie, Akademisch-Medizinisches Zentrum, Universität von Amsterdam, 22660, 1100 DD, Amsterdam, Niederlande.,Pädiatrische Pneumologie und Immunologie, Charité - Universitätsmedizin, Berlin, Deutschland
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32
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Schito M, Dolinger DL. A Collaborative Approach for "ReSeq-ing" Mycobacterium tuberculosis Drug Resistance: Convergence for Drug and Diagnostic Developers. EBioMedicine 2015; 2:1262-5. [PMID: 26629499 PMCID: PMC4634747 DOI: 10.1016/j.ebiom.2015.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 10/05/2015] [Indexed: 11/30/2022] Open
Affiliation(s)
- Marco Schito
- Critical Path Institute, 1730 E River Rd, Suite 200, Tucson, Arizona, United States
| | - David L Dolinger
- FIND, Campus Biotech, Building B2, Level 0, 9, Chemin des Mines, 1202 Geneva, Switzerland
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Trauner A, Borrell S, Reither K, Gagneux S. Evolution of drug resistance in tuberculosis: recent progress and implications for diagnosis and therapy. Drugs 2015; 74:1063-72. [PMID: 24962424 PMCID: PMC4078235 DOI: 10.1007/s40265-014-0248-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Drug-resistant tuberculosis is a growing threat to global public health. Recent efforts to understand the evolution of drug resistance have shown that changes in drug–target interactions are only the first step in a longer adaptive process. The emergence of transmissible drug-resistant Mycobacterium tuberculosis is the result of a multitude of additional genetic mutations, many of which interact, a phenomenon known as epistasis. The varied effects of these epistatic interactions include compensating for the reduction of the biological cost associated with the development of drug resistance, increasing the level of resistance, and possibly accommodating broader changes in the physiology of resistant bacteria. Knowledge of these processes and our ability to detect them as they happen informs the development of diagnostic tools and better control strategies. In particular, the use of whole genome sequencing combined with surveillance efforts in the field could provide a powerful instrument to prevent future epidemics of drug-resistant tuberculosis.
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Affiliation(s)
- Andrej Trauner
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Klaus Reither
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Basel, Switzerland
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34
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Denkinger CM, Dolinger D, Schito M, Wells W, Cobelens F, Pai M, Zignol M, Cirillo DM, Alland D, Casenghi M, Gallarda J, Boehme CC, Perkins MD. Target product profile of a molecular drug-susceptibility test for use in microscopy centers. J Infect Dis 2015; 211 Suppl 2:S39-49. [PMID: 25765105 DOI: 10.1093/infdis/jiu682] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Current phenotypic testing for drug resistance in patients with tuberculosis is inadequate primarily with respect to turnaround time. Molecular tests hold the promise of an improved time to diagnosis. METHODS A target product profile for a molecular drug-susceptibility test (DST) was developed on the basis of a collaborative effort that included opinions gathered from researchers, clinicians, policy makers, and test developers on optimal clinical and operational characteristics in settings of intended use. In addition, the current diagnostic ecosystem and the diagnostic development landscape were mapped. RESULTS Molecular DSTs for detecting tuberculosis in microscopy centers should ideally evaluate for resistance to rifampin, fluoroquinolones, isoniazid, and pyrazinamide and enable the selection of the most appropriate treatment regimen. Performance characteristics of DSTs need to be optimized, but compromises can be made that depend on the trade-off between a false-positive result and a false-negative result. The operational requirements of a test will vary depending on the site of implementation. However, the most-important considerations pertain to quality control, maintenance and calibration, and the ability to export data. CONCLUSION This target product profile defines the needs as perceived by the tuberculosis stakeholder community and attempts to provide a means of communication with test developers to ensure that fit-for-purpose DSTs are being developed.
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Affiliation(s)
- Claudia M Denkinger
- FIND Division of Infectious Disease, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | - Marco Schito
- Division of AIDS, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | | | - Frank Cobelens
- KNCV Tuberculosis Foundation, the Hague Amsterdam Institute for Global Health and Development, Academic Medical Center, Amsterdam, The Netherlands
| | - Madhukar Pai
- McGill International TB Centre Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Canada
| | | | | | | | | | - Jim Gallarda
- Bill and Melinda Gates Foundation, Seattle, Washington
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Kik SV, Denkinger CM, Jefferson C, Ginnard J, Pai M. Potential market for novel tuberculosis diagnostics: worth the investment? J Infect Dis 2015; 211 Suppl 2:S58-66. [PMID: 25765107 DOI: 10.1093/infdis/jiu817] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The potential available market (PAM) for new diagnostics for tuberculosis that meet the specifications of the high-priority target product profiles (TPPs) is currently unknown. METHODS We estimated the PAM in 2020 in 4 high-burden countries (South Africa, Brazil, China, and India) for tests that meet the specifications outlined in the TPPs. The yearly PAM was estimated for the most likely application of each TPP. RESULTS In 2020 the PAM for all 4 countries together was estimated to be (1) 12M tests/year with a value of 48M-71M USD for a sputum smear-replacement test; (2) 16M tests/year with a value of 65M-97M USD for a biomarker test; (3) 18M tests/year with a value of 18M-35M USD for a triage test; (4) 12M tests/year with a value of 59M-2238M USD for a tuberculosis detection plus drug susceptibility test (DST) all-in-one or 1.5M tests/year for a DST that follows a positive tuberculosis detection test with a corresponding value of 75M-121M for both tuberculosis detection and DST. CONCLUSIONS Although there is a considerable potential market for novel tuberculosis diagnostics that fit the specification of the TPPs in the 4 high-burden countries, the actual market for an individual product remains uncertain.
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Affiliation(s)
- Sandra V Kik
- McGill International TB Centre and Department of Epidemiology and Biostatistics, McGill University
| | - Claudia M Denkinger
- McGill International TB Centre and Department of Epidemiology and Biostatistics, McGill University Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | | | | | - Madhukar Pai
- McGill International TB Centre and Department of Epidemiology and Biostatistics, McGill University
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Denkinger CM, Kik SV, Cirillo DM, Casenghi M, Shinnick T, Weyer K, Gilpin C, Boehme CC, Schito M, Kimerling M, Pai M. Defining the needs for next generation assays for tuberculosis. J Infect Dis 2015; 211 Suppl 2:S29-38. [PMID: 25765104 DOI: 10.1093/infdis/jiu821] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
To accelerate the fight against tuberculosis, major diagnostic challenges need to be addressed urgently. Post-2015 targets are unlikely to be met without the use of novel diagnostics that are more accurate and can be used closer to where patients first seek care in affordable diagnostic algorithms. This article describes the efforts by the stakeholder community that led to the identification of the high-priority diagnostic needs in tuberculosis. Subsequently target product profiles for the high-priority diagnostic needs were developed and reviewed in a World Health Organization (WHO)-led consensus meeting. The high-priority diagnostic needs included (1) a sputum-based replacement test for smear-microscopy; (2) a non-sputum-based biomarker test for all forms of tuberculosis, ideally suitable for use at levels below microscopy centers; (3) a simple, low cost triage test for use by first-contact care providers as a rule-out test, ideally suitable for use by community health workers; and (4) a rapid drug susceptibility test for use at the microscopy center level. The developed target product profiles, along with complimentary work presented in this supplement, will help to facilitate the interaction between the tuberculosis community and the diagnostics industry with the goal to lead the way toward the post-2015 global tuberculosis targets.
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Affiliation(s)
- Claudia M Denkinger
- FIND, Geneva, Switzerland Division of Infectious Disease, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Sandra V Kik
- McGill International TB Centre and Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Canada
| | | | | | - Thomas Shinnick
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Karin Weyer
- World Health Organization, Geneva, Switzerland
| | | | | | - Marco Schito
- HJF-DAIDS, A division of The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland
| | | | - Madhukar Pai
- McGill International TB Centre and Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Canada
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Pantoja A, Kik SV, Denkinger CM. Costs of novel tuberculosis diagnostics--will countries be able to afford it? J Infect Dis 2015; 211 Suppl 2:S67-77. [PMID: 25765108 DOI: 10.1093/infdis/jiu820] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Four priority target product profiles for the development of diagnostic tests for tuberculosis were identified: 1) Rapid sputum-based (RSP), 2) non-sputum Biomarker-based (BMT), 3) triage test followed by confirmatory test (TT), and 4) drug-susceptibility testing (DST). METHODS We assessed the cost of the new tests in suitable strategies and of the conventional diagnosis of tuberculosis as per World Health Organization guidelines, in 36 high tuberculosis and MDR burden countries. Costs were then compared to the available funding for tuberculosis at country level. RESULTS Costs of diagnosing tuberculosis using RSP ranged US$93-187 million/year; if RSP unit cost is of US$2-4 it would be lower/similar cost than conventional strategy with sputum smear microscopy (US$ 119 million/year). Using BMT (with unit cost of US$2-4) would cost US$70-121 million/year and be lower/comparable cost than conventional diagnostics. Using TT with TPP characteristics (unit cost of US$1-2) followed by Xpert would reduce diagnostic costs up to US$36 million/year. Costs of using different novel DST strategies for the diagnosis of drug resistance would be higher compared with conventional diagnosis. CONCLUSIONS Introducing a TT or a biomarker test with optimal characteristics would be affordable from a cost and affordability perspective at the current available funding for tuberculosis. Additional domestic or donor funding would be needed in most countries to achieve affordability for other new diagnostic tests.
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Affiliation(s)
| | - Sandra V Kik
- McGill International TB Centre and Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Canada
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Pai M, Schito M. Tuberculosis diagnostics in 2015: landscape, priorities, needs, and prospects. J Infect Dis 2015; 211 Suppl 2:S21-8. [PMID: 25765103 PMCID: PMC4366576 DOI: 10.1093/infdis/jiu803] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In 2015, tuberculosis remains a major global health problem, and drug-resistant tuberculosis is a growing threat. Although tuberculosis diagnosis in many countries is still reliant on older tools, new diagnostics are changing the landscape. Stimulated, in part, by the success and roll out of Xpert MTB/RIF, there is now considerable interest in new technologies. The landscape looks promising, with a robust pipeline of new tools, particularly molecular diagnostics, and well over 50 companies actively engaged in product development. However, new diagnostics are yet to reach scale, and there needs to be greater convergence between diagnostics development and development of shorter-duration tuberculosis drug regimens. Another concern is the relative absence of non-sputum-based diagnostics in the pipeline for children and of biomarker tests for triage, cure, and progression of latent Mycobacterium tuberculosis infection. Several initiatives, described in this supplement, have been launched to further stimulate product development and policy, including assessment of needs and priorities, development of target product profiles, compilation of data on resistance-associated mutations, and assessment of market size and potential for new diagnostics. Advocacy is needed to increase funding for tuberculosis research and development, and governments in high-burden countries must invest more in tuberculosis control to meet post-2015 targets for care, control, and prevention.
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Affiliation(s)
- Madhukar Pai
- McGill International TB Centre
- McGill Global Health Programs, McGill University, Montreal, Canada
| | - Marco Schito
- Division of AIDS, Henry M. Jackson Foundation for the Advancement of Military Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
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Weyer K. Discovery, Innovation, and New Frontiers in Tuberculosis Diagnostics: Reflections and Expectations. J Infect Dis 2015; 211 Suppl 2:S78-80. [DOI: 10.1093/infdis/jiu822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abstract
In a Guest Editorial on World TB Day, Madhukar Pai and Puneet Dewan identify programmatic and policy changes needed to end TB by 2035.
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Affiliation(s)
- Madhukar Pai
- McGill Global Health Programs & McGill International TB Centre, McGill University, Quebec, Canada
- * E-mail:
| | - Puneet Dewan
- Bill & Melinda Gates Foundation, New Delhi, India
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Köser CU, Javid B, Liddell K, Ellington MJ, Feuerriegel S, Niemann S, Brown NM, Burman WJ, Abubakar I, Ismail NA, Moore D, Peacock SJ, Török ME. Drug-resistance mechanisms and tuberculosis drugs. Lancet 2015; 385:305-7. [PMID: 25706840 PMCID: PMC4374148 DOI: 10.1016/s0140-6736(14)62450-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Claudio U Köser
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QW, UK.
| | - Babak Javid
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QW, UK; School of Medicine, Tsinghua University, Beijing, China
| | | | - Matthew J Ellington
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Silke Feuerriegel
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany; German Centre for Infection Research, Borstel, Germany
| | - Stefan Niemann
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Nicholas M Brown
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | | | - Ibrahim Abubakar
- Tuberculosis Section, Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK; Research Department of Infection and Population Health, University College London, London, UK
| | - Nazir A Ismail
- Centre for Tuberculosis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - David Moore
- TB Centre, London School of Hygiene and Tropical Medicine, London, UK; Laboratorio de Investigación de Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Sharon J Peacock
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QW, UK; Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK; Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - M Estée Török
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QW, UK; Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK; Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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Shinnick TM, Starks AM, Alexander HL, Castro KG. Evaluation of the Cepheid Xpert MTB/RIF assay. Expert Rev Mol Diagn 2014; 15:9-22. [PMID: 25373876 DOI: 10.1586/14737159.2015.976556] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The lack of capacity to provide laboratory confirmation of a diagnosis of tuberculosis disease (TB) is contributing to enormous gaps in the ability to find, treat and follow TB patients. WHO estimates that globally only about 57% of the notified new cases of pulmonary TB in 2012 and about 19% of rifampicin-resistant TB cases were laboratory confirmed. The Cepheid Xpert(®) MTB/RIF assay has been credited with revolutionizing laboratory testing to aid in the diagnosis of TB and rifampicin-resistant TB. This semi-automated test can detect both the causative agent of TB and mutations that confer rifampicin resistance from clinical specimens within 2 h after starting the test. In this article, we review the performance of the test, its pathway to regulatory approval and endorsement, guidelines for its use and lessons learned from the implementation of the test in low-burden, high-resource countries and in high-burden, low-resource countries.
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Affiliation(s)
- Thomas M Shinnick
- Division of Tuberculosis Elimination, National Center for HIV, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA 30333
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Tukvadze N, Bablishvili N, Apsindzelashvili R, Blumberg HM, Kempker RR. Performance of the MTBDRsl assay in Georgia. Int J Tuberc Lung Dis 2014; 18:233-9. [PMID: 24429319 DOI: 10.5588/ijtld.13.0468] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
SETTING The country of Georgia has a high burden of multi- (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB). OBJECTIVE To assess the performance of the GenoType® MTBDRsl assay in the detection of resistance to kanamycin (KM), capreomycin (CPM) and ofloxacin (OFX), and of XDR-TB. DESIGN Consecutive acid-fast bacilli smear-positive sputum specimens identified as MDR-TB using the MTBDRplus test were evaluated with the MTBDRsl assay and conventional second-line drug susceptibility testing (DST). RESULTS Among 159 specimens, amplification was adequate in 154 (97%), including 9 of 9 culture-negative and 2 of 3 contaminated specimens. Second-line DST revealed that 17 (12%) Mycobacterium tuberculosis isolates were XDR-TB. Compared to DST, the MTBDRsl had 41% sensitivity and 98% specificity in detecting XDR-TB and 81% sensitivity and 99% specificity in detecting OFX resistance. Sensitivity was low in detecting resistance to KM (29%) and CPM (57%), while specificity was respectively 99% and 94%. Median times from sputum collection to second-line DST and MTBDRsl results were 70-104 vs. 10 days. CONCLUSION Although the MTBDRsl assay had a rapid turnaround time, detection of second-line drug resistance was poor compared to DST. Further genetic mutations associated with resistance to second-line drugs should be included in the assay to improve test performance and clinical utility.
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Affiliation(s)
- N Tukvadze
- National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - N Bablishvili
- National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | | | - H M Blumberg
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - R R Kempker
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
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den Hertog AL, Menting S, Smienk ET, Werngren J, Hoffner S, Anthony RM. Evaluation of a microcolony growth monitoring method for the rapid determination of ethambutol resistance in Mycobacterium tuberculosis. BMC Infect Dis 2014; 14:380. [PMID: 25011623 PMCID: PMC4227065 DOI: 10.1186/1471-2334-14-380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 07/03/2014] [Indexed: 12/01/2022] Open
Abstract
Background Due to the increasing prevalence of Mycobacterium tuberculosis strains resistant to one or more antibiotics, there is a need for new quantitative culture methods both for drug susceptibility testing and for validation of mutations putatively associated with drug resistance. We previously developed a (myco) bacterial culture method, in which multiple growing microcolonies are monitored individually. Transfer of the growing microcolonies to selective medium allows the effect on the growth rate of each individual colony to be determined. As entire growing colonies are exposed to antibiotics rather than re-subbed, a second lag phase is avoided and results are obtained more rapidly. Here we investigate the performance of the microcolony method to differentiate between ethambutol (EMB) resistant, intermediate and susceptible strains. Methods One week old microcolonies from a reference panel of four strains with known EMB susceptibility were transferred to different concentrations of EMB. Growth rates during the 1st 2 days of exposure were used to set up classification criteria to test and classify a blinded panel of 20 tuberculosis strains with different susceptibilities. Results For 18 strains (90%) reference culture results corresponded to our classifications based on data collected within 9 days of inoculation. A single strain was classified as Intermediate instead of Susceptible, and 1 strain could not be classified due to a contamination. Conclusions Using a microcolony growth monitoring method we were able to classify, within 9 days after inoculation, a panel of strains as EMB susceptible, intermediate or resistant with 90% correlation to the reference methods.
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Affiliation(s)
- Alice L den Hertog
- Royal Tropical Institute, KIT Biomedical Research, Meibergdreef 39, 1105, AZ, Amsterdam, The Netherlands.
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Getting health services to three million people with TB. J Int AIDS Soc 2014; 17:19079. [PMID: 24666595 PMCID: PMC3965710 DOI: 10.7448/ias.17.1.19079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 03/13/2014] [Accepted: 03/13/2014] [Indexed: 11/08/2022] Open
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Lange C, Abubakar I, Alffenaar JWC, Bothamley G, Caminero JA, Carvalho ACC, Chang KC, Codecasa L, Correia A, Crudu V, Davies P, Dedicoat M, Drobniewski F, Duarte R, Ehlers C, Erkens C, Goletti D, Günther G, Ibraim E, Kampmann B, Kuksa L, de Lange W, van Leth F, van Lunzen J, Matteelli A, Menzies D, Monedero I, Richter E, Rüsch-Gerdes S, Sandgren A, Scardigli A, Skrahina A, Tortoli E, Volchenkov G, Wagner D, van der Werf MJ, Williams B, Yew WW, Zellweger JP, Cirillo DM. Management of patients with multidrug-resistant/extensively drug-resistant tuberculosis in Europe: a TBNET consensus statement. Eur Respir J 2014; 44:23-63. [PMID: 24659544 PMCID: PMC4076529 DOI: 10.1183/09031936.00188313] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) substantially challenges TB control, especially in the European Region of the World Health Organization, where the highest prevalence of MDR/XDR cases is reported. The current management of patients with MDR/XDR-TB is extremely complex for medical, social and public health systems. The treatment with currently available anti-TB therapies to achieve relapse-free cure is long and undermined by a high frequency of adverse drug events, suboptimal treatment adherence, high costs and low treatment success rates. Availability of optimal management for patients with MDR/XDR-TB is limited even in the European Region. In the absence of a preventive vaccine, more effective diagnostic tools and novel therapeutic interventions the control of MDR/XDR-TB will be extremely difficult. Despite recent scientific advances in MDR/XDR-TB care, decisions for the management of patients with MDR/XDR-TB and their contacts often rely on expert opinions, rather than on clinical evidence. This document summarises the current knowledge on the prevention, diagnosis and treatment of adults and children with MDR/XDR-TB and their contacts, and provides expert consensus recommendations on questions where scientific evidence is still lacking. TBNET consensus statement on the management of patients with MDR/XDR-TB has been released in theEur Respir Jhttp://ow.ly/uizRD
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Affiliation(s)
- Christoph Lange
- For the authors' affiliations see the Acknowledgements section
| | | | | | | | - Jose A Caminero
- For the authors' affiliations see the Acknowledgements section
| | | | - Kwok-Chiu Chang
- For the authors' affiliations see the Acknowledgements section
| | - Luigi Codecasa
- For the authors' affiliations see the Acknowledgements section
| | - Ana Correia
- For the authors' affiliations see the Acknowledgements section
| | - Valeriu Crudu
- For the authors' affiliations see the Acknowledgements section
| | - Peter Davies
- For the authors' affiliations see the Acknowledgements section
| | - Martin Dedicoat
- For the authors' affiliations see the Acknowledgements section
| | | | - Raquel Duarte
- For the authors' affiliations see the Acknowledgements section
| | - Cordula Ehlers
- For the authors' affiliations see the Acknowledgements section
| | - Connie Erkens
- For the authors' affiliations see the Acknowledgements section
| | - Delia Goletti
- For the authors' affiliations see the Acknowledgements section
| | - Gunar Günther
- For the authors' affiliations see the Acknowledgements section
| | - Elmira Ibraim
- For the authors' affiliations see the Acknowledgements section
| | - Beate Kampmann
- For the authors' affiliations see the Acknowledgements section
| | - Liga Kuksa
- For the authors' affiliations see the Acknowledgements section
| | - Wiel de Lange
- For the authors' affiliations see the Acknowledgements section
| | - Frank van Leth
- For the authors' affiliations see the Acknowledgements section
| | - Jan van Lunzen
- For the authors' affiliations see the Acknowledgements section
| | | | - Dick Menzies
- For the authors' affiliations see the Acknowledgements section
| | | | - Elvira Richter
- For the authors' affiliations see the Acknowledgements section
| | | | | | - Anna Scardigli
- For the authors' affiliations see the Acknowledgements section
| | - Alena Skrahina
- For the authors' affiliations see the Acknowledgements section
| | - Enrico Tortoli
- For the authors' affiliations see the Acknowledgements section
| | | | - Dirk Wagner
- For the authors' affiliations see the Acknowledgements section
| | | | - Bhanu Williams
- For the authors' affiliations see the Acknowledgements section
| | - Wing-Wai Yew
- For the authors' affiliations see the Acknowledgements section
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Esposito S, Giannini A, Biondetti P, Bonelli N, Nosotti M, Bosis S, Calderini E, Principi N. Subcutaneous emphysema as the first relevant clinical sign of complicated tubercular lymph node disease in a child. BMC Infect Dis 2013; 13:461. [PMID: 24094042 PMCID: PMC3851260 DOI: 10.1186/1471-2334-13-461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 10/02/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Children make up a significant proportion of the global tuberculosis (TB) caseload, and experience considerable TB-related morbidity and mortality. Unfortunately, it is not easy to diagnose TB in the first years of life because of the diversity of its clinical presentation and the non-specific nature of most of its symptoms. CASE PRESENTATION A 26-month-old male child was admitted to hospital because of the sudden onset of rapidly increasing swelling of the neck, face and upper trunk a few hours before. Upon admission, his temperature was 36.5°C, pulse rate 120/min, respiratory rate 36/min, and O2 saturation 97% in air. Palpation revealed subcutaneous emphysema (SE) over the swollen skin areas, and an examination of the respiratory system revealed crepitations in the left part of the chest without any significant suggestion of mediastinal shift. Chest radiography showed enlargement of the left lung hilum with pneumomediastinum and diffuse SE. Bronchoscopy was carried out because of the suspicion that the SE may have been due to the inhalation of a peanut. This excluded the presence of a foreign body but showed that the left main bronchus was partially obstructed with caseous material and showed significant signs of granulomatous inflammation on the wall. Contrast-enhanced computed tomography of the lungs confirmed the SE and pneumomediastinum, and revealed bilateral hilum lymph node disease with infiltration of the adjacent anatomical structure and a considerable breach in the left primary bronchus wall conditioning the passage of air in the mediastinum and subcutaneous tissue. As a tuberculin skin test and polymerase chain reaction for Mycobacterium tuberculosis on bronchial material and gastric aspirate were positive, a diagnosis of TB was made and oral anti-TB therapy was started, which led to the elimination of M. tuberculosis and a positive clinical outcome. CONCLUSIONS This is the first case in which SE was the first relevant clinical manifestation of TB and arose from infiltration of the bronchial wall secondary to caseous necrosis of the hilum lymph nodes. Physicians should be aware of the fact that SE is one of the possible initial signs and symptoms of early TB infection, and act accordingly.
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Affiliation(s)
- Susanna Esposito
- Pediatric Clinic 1, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122 Milan, Italy.
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Cobelens FGJ. For whom the bell tolls: isoniazid preventive therapy and tuberculosis drug resistance. Sci Transl Med 2013; 5:180fs12. [PMID: 23576813 DOI: 10.1126/scitranslmed.3006094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The expected increase in drug-resistant tuberculosis due to large-scale preventive treatment in people living with HIV calls for reconsidering the "double use" of isoniazid for prophylaxis and curative treatment (Mills et al., this issue).
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Affiliation(s)
- Frank G J Cobelens
- Department of Global Health and Amsterdam Institute for Global Health and Development, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.
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Zumla A, Kim P, Maeurer M, Schito M. Zero deaths from tuberculosis: progress, reality, and hope. THE LANCET. INFECTIOUS DISEASES 2013; 13:285-7. [DOI: 10.1016/s1473-3099(13)70039-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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