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Li TX, Wang J, Yang YS, Wang PS, Zhou G, Liao CY, Zhang HZ, Luo M, Zeng XG, Yang GQ, Yang LJ, Chen YK. Evaluation of Xpert MTB/RIF assay for the diagnosis of extrapulmonary tuberculosis in Southwest China. PLoS Negl Trop Dis 2023; 17:e0011403. [PMID: 37363913 DOI: 10.1371/journal.pntd.0011403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
The purpose of this study was to determine the diagnostic efficacy of Xpert MTB/RIF assay for rapid diagnosis of Tuberculosis (TB) and detection of rifampicin (RIF) resistance in patients suspected of having EPTB, assessing it against traditional culture and drug susceptibility test (DST) by proportional method, and the ability to predict multidrug resistance TB by Xpert MTB/RIF assay. In this study, the Xpert MTB/RIF assay was applied to 1,614 extrapulmonary specimens. Compared with TB culture and Composite Reference Standard (CRS), the Xpert MTB/RIF assay had a high sensitivity and specificity for detection of EPTB. Depending on the culture method or CRS as the standard, sensitivity of the Xpert MTB/RIF assay for detection of MTB in pleural effusion, cerebrospinal fluid, thoracic drainage fluid and throat swabs specimens were lower than that of other specimens. According to the experimental results, we have reason to believe that Xpert MTB/RIF assay is a rapid and simple technique with high sensitivity and specificity for diagnosing EPTB and detecting drug resistance in variety of specimens. Xpert MTB/RIF assay combined with DST maybe identify more cases of multi-drug resistant tuberculosis (MDR-TB).
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Affiliation(s)
- Tong-Xin Li
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Jing Wang
- Clinical Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Yu-Sheng Yang
- Department of Orthopaedics, Southwest Hospital, the Third Military Medical University, Chongqing, China
| | - Peng-Sen Wang
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Gang Zhou
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Chuan-Yu Liao
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Hui-Zheng Zhang
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Ming Luo
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Xiao-Gang Zeng
- Thoracic Surgery, Chongqing Public Health Medical Center, Chongqing, China
| | - Guo-Qiang Yang
- General Surgery and Orthopedics Department, Chongqing Public Health Medical Center, Chongqing, China
| | - Li-Jun Yang
- General Surgery and Orthopedics Department, Chongqing Public Health Medical Center, Chongqing, China
| | - Yao-Kai Chen
- Department of infectious diseases, Chongqing Public Health Medical Center, Chongqing, China
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2
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Emikoglu Cerit SKB, Tarhan GL, Ceyhan I. Investigation of species distribution of nontuberculosis mycobacteria isolated from sputum samples in patients with suspected pulmonary tuberculosis. Int J Mycobacteriol 2022; 11:145-149. [PMID: 35775546 DOI: 10.4103/ijmy.ijmy_51_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Aims Rapid and accurate identification of mycobacteria is important for the species-specific treatment of the disease. The aim of this study was the identification at the species level of 34 nontuberculous mycobacteria strains isolated from respiratory tract samples and 14 reference strains as by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Materials and Methods Isolates derived from clinical specimens were subcultured in the Lowenstein-Jensen medium. Deoxyribonucleic acid isolation was carried out using the boiling method. PCR amplification was performed using primers specific to the hsp65 gene region. The PCR products were digested BstEII and HaEIII enzymes. All samples were studied comparatively by two different centers. Results In our study, the most common species were found to be Mycobacterium intracellulare in 23.52% (8/34). The performance of the PCR-RFLP method in detecting mycobacteria was found to be 82.35%. Conclusions The PCR-RFLP method is a rapid, cheap, and practical method for the identification of mycobacteria.
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Affiliation(s)
| | - G Lnur Tarhan
- Department of Medical Microbiology, Faculty of Medicine, Adiyaman University, Adiyaman, Turkey
| | - Ismail Ceyhan
- Department of Public Health Nursing, Health Science Faculty, Ankara Yildirim Beyazit University, Ankara, Turkey
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Binjomah AZ, Alnimr AM, Zareah SM, Alharbi SF, Alasmari KS, Aldosari KM, Alduealej IM. The diagnostic impact of implementing a molecular-based algorithm to standard mycobacterial screening at a reference laboratory with an intermediate prevalence for non-respiratory samples. Saudi J Biol Sci 2021; 28:4103-4108. [PMID: 34354388 PMCID: PMC8324989 DOI: 10.1016/j.sjbs.2021.05.080] [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: 03/17/2021] [Revised: 05/29/2021] [Accepted: 05/30/2021] [Indexed: 11/17/2022] Open
Abstract
Rapid, reliable results can be given by molecular, direct detection and identification of the Mycobacterium tuberculosis (MTB/Mtb) complex from clinical samples. The Xpert MTB/RIF assay is an assay that has been availablefor more than a decade for identification of Mycobacterium tuberculosis and resistance to rifampicin. However, there is minimal evidence on its clinical usefulness in paucibacillary, non-respiratory samples. The Xpert MTB/RIF assay clinical utility index, its diagnostic characteristics and the number required to diagnose 2935 non-respiratory specimens submitted for routine mycobacterial work-up in a reference laboratory in an intermediate prevalence setting per specimen form were evaluated. The Xpert MTB/RIF assay showed a variable clinical utility index and number required to diagnose (NND) depending on the type of specimen, which was moderate in tissue biopsies (NND = 1.8) and excellent in pus and urine samples, compared to acid-fast microscopy and culture as a gold standard technique (NND = 1.1 and 1.2). Microscopy, on the other hand, consistently showed a weak to fair index of clinical usefulness in all specimen forms, with in NND of 2.3-12.5. The NND for detecting tuberculous infection in the cerebrospinal fluid by the Xpert MTB/RIF assay was noted to be 1.2, with a moderate clinical utility index of 0.8. The evidence presented indicates that the overall appropriate diagnostic utility of the Xpert MTB/RIF assay is clinically successful in most non-respiratory samples. To check the cost-effectiveness and prognostic effect of integrating this completely automated molecular-based assay into the routine testing algorithm for non-respiratory mycobacterial specimens, further data must be collected.
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Affiliation(s)
- Abdulwahab Z. Binjomah
- Riyadh Regional Laboratory and Blood Bank, Mycobacteriology Reference Laboratory, Imam Abdulaziz Bin Mohammed Bin Saud Street, Ulaishah, 3485, Riyadh 12746, Saudi Arabia
- College of Medicine, Alfaisal University, Takhassusi Street, Riyadh 11533, Saudi Arabia
| | - Amani M. Alnimr
- Department of Microbiology, King Fahad Hospital of the University, College of Medicine, Imam Abdulrahman Bin Faisal University, King Faisal Road, Dammam 34212, Saudi Arabia
| | - Suzan M. Zareah
- Riyadh Regional Laboratory and Blood Bank, Mycobacteriology Reference Laboratory, Imam Abdulaziz Bin Mohammed Bin Saud Street, Ulaishah, 3485, Riyadh 12746, Saudi Arabia
| | - Shafi F. Alharbi
- Riyadh Regional Laboratory and Blood Bank, Mycobacteriology Reference Laboratory, Imam Abdulaziz Bin Mohammed Bin Saud Street, Ulaishah, 3485, Riyadh 12746, Saudi Arabia
| | - Khalid S. Alasmari
- Riyadh Regional Laboratory and Blood Bank, Mycobacteriology Reference Laboratory, Imam Abdulaziz Bin Mohammed Bin Saud Street, Ulaishah, 3485, Riyadh 12746, Saudi Arabia
| | - Kamel M. Aldosari
- Riyadh Regional Laboratory and Blood Bank, Mycobacteriology Reference Laboratory, Imam Abdulaziz Bin Mohammed Bin Saud Street, Ulaishah, 3485, Riyadh 12746, Saudi Arabia
| | - Ibrahim M. Alduealej
- Riyadh Regional Laboratory and Blood Bank, Mycobacteriology Reference Laboratory, Imam Abdulaziz Bin Mohammed Bin Saud Street, Ulaishah, 3485, Riyadh 12746, Saudi Arabia
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4
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Bielsa S, Bernet A, Civit C, Acosta C, Manonelles A, Porcel JM. FluoroType® MTB in pleural fluid for diagnosing tuberculosis. Rev Clin Esp 2021; 221:139-144. [PMID: 32499060 DOI: 10.1016/j.rce.2020.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 03/14/2020] [Accepted: 04/02/2020] [Indexed: 11/29/2022]
Abstract
OBJECTIVES This work aims to investigate the diagnostic accuracy of a nucleic acid amplification test (FluoroType MTB®) in pleural fluid (PF) and sputum to diagnose tuberculous pleural effusion (TPE). We also analyzed the increase in diagnostic accuracy of a second FluoroType MTB® test on a second thoracentesis sample when the first was negative. METHODS We conducted a prospective single-center study that included 207 patients with pleural effusion (31 tuberculous and 176 due to other causes). Of the 31 cases of TPE, 21 (68%) were confirmed histologically or microbiologically; the other cases were considered probable. RESULTS The operational characteristics of FluoroType MTB® in PF for identifying tuberculosis were a sensitivity of 13%, a specificity of 99%, a positive likelihood ratio of 11, and a negative likelihood ratio of 0.9. The diagnostic efficacy data for sputum samples were 21%, 91%, 2.4, and 0.9, respectively. PF and sputum cultures in solid and liquid media had greater sensitivity (36% and 31%, respectively). A second FluoroType MTB® test in PF was negative for 24 patients who had TPE and for whom the first FluoroType MTB® test was also negative. Only two (6.5%) patients with TPE had a confirmed diagnosis based exclusively on the positive results of the FluoroType MTB® in PF. CONCLUSION Due to its low sensitivity, the FluoroType MTB® test in PF has a limited role in diagnosing tuberculous pleurisy.
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Affiliation(s)
- S Bielsa
- Unidad de Medicina Pleural, Servicio de Medicina Interna, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, España
| | - A Bernet
- Servicio de Microbiología, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, España
| | - C Civit
- Unidad de Medicina Pleural, Servicio de Medicina Interna, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, España
| | - C Acosta
- Unidad de Medicina Pleural, Servicio de Medicina Interna, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, España
| | - A Manonelles
- Servicio de Microbiología, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, España
| | - J M Porcel
- Unidad de Medicina Pleural, Servicio de Medicina Interna, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, España.
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5
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Bielsa S, Bernet A, Civit C, Acosta C, Manonelles A, Porcel JM. FluoroType® MTB in pleural fluid for diagnosing tuberculosis. Rev Clin Esp 2021; 221:139-144. [PMID: 33998461 DOI: 10.1016/j.rceng.2020.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/02/2020] [Indexed: 11/24/2022]
Abstract
OBJECTIVES This work aims to investigate the diagnostic accuracy of a nucleic acid amplification test (FluoroType MTB®) in pleural fluid (PF) and sputum to diagnose tuberculous pleural effusion (TPE). We also analyzed the increase in diagnostic accuracy of a second FluoroType MTB® test on a second thoracentesis sample when the first was negative. METHODS We conducted a prospective single-center study that included 207 patients with pleural effusion (31 tuberculous and 176 due to other causes). Of the 31 cases of TPE, 21 (68%) were confirmed histologically or microbiologically; the other cases were considered probable. RESULTS The operational characteristics of FluoroType MTB® in PF for identifying tuberculosis were a sensitivity of 13%, a specificity of 99%, a positive likelihood ratio of 11, and a negative likelihood ratio of 0.9. The diagnostic efficacy data for sputum samples were 21%, 91%, 2.4, and 0.9, respectively. PF and sputum cultures in solid and liquid media had greater sensitivity (36% and 31%, respectively). A second FluoroType MTB® test in PF was negative for 24 patients who had TPE and for whom the first FluoroType MTB® test was also negative. Only two (6.5%) patients with TPE had a confirmed diagnosis based exclusively on the positive results of the FluoroType MTB® in PF. CONCLUSION Due to its low sensitivity, the FluoroType MTB® test in PF has a limited role in diagnosing tuberculous pleurisy.
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Affiliation(s)
- S Bielsa
- Unidad de Medicina Pleural, Servicio de Medicina Interna, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, Spain
| | - A Bernet
- Servicio de Microbiología, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, Spain
| | - C Civit
- Unidad de Medicina Pleural, Servicio de Medicina Interna, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, Spain
| | - C Acosta
- Unidad de Medicina Pleural, Servicio de Medicina Interna, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, Spain
| | - A Manonelles
- Servicio de Microbiología, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, Spain
| | - J M Porcel
- Unidad de Medicina Pleural, Servicio de Medicina Interna, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, Spain.
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Kohli M, Schiller I, Dendukuri N, Yao M, Dheda K, Denkinger CM, Schumacher SG, Steingart KR. Xpert MTB/RIF Ultra and Xpert MTB/RIF assays for extrapulmonary tuberculosis and rifampicin resistance in adults. Cochrane Database Syst Rev 2021; 1:CD012768. [PMID: 33448348 PMCID: PMC8078545 DOI: 10.1002/14651858.cd012768.pub3] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Xpert MTB/RIF Ultra (Xpert Ultra) and Xpert MTB/RIF are World Health Organization (WHO)-recommended rapid nucleic acid amplification tests (NAATs) widely used for simultaneous detection of Mycobacterium tuberculosis complex and rifampicin resistance in sputum. To extend our previous review on extrapulmonary tuberculosis (Kohli 2018), we performed this update to inform updated WHO policy (WHO Consolidated Guidelines (Module 3) 2020). OBJECTIVES To estimate diagnostic accuracy of Xpert Ultra and Xpert MTB/RIF for extrapulmonary tuberculosis and rifampicin resistance in adults with presumptive extrapulmonary tuberculosis. SEARCH METHODS Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, Web of Science, Latin American Caribbean Health Sciences Literature, Scopus, ClinicalTrials.gov, the WHO International Clinical Trials Registry Platform, the International Standard Randomized Controlled Trial Number Registry, and ProQuest, 2 August 2019 and 28 January 2020 (Xpert Ultra studies), without language restriction. SELECTION CRITERIA Cross-sectional and cohort studies using non-respiratory specimens. Forms of extrapulmonary tuberculosis: tuberculous meningitis and pleural, lymph node, bone or joint, genitourinary, peritoneal, pericardial, disseminated tuberculosis. Reference standards were culture and a study-defined composite reference standard (tuberculosis detection); phenotypic drug susceptibility testing and line probe assays (rifampicin resistance detection). DATA COLLECTION AND ANALYSIS Two review authors independently extracted data and assessed risk of bias and applicability using QUADAS-2. For tuberculosis detection, we performed separate analyses by specimen type and reference standard using the bivariate model to estimate pooled sensitivity and specificity with 95% credible intervals (CrIs). We applied a latent class meta-analysis model to three forms of extrapulmonary tuberculosis. We assessed certainty of evidence using GRADE. MAIN RESULTS 69 studies: 67 evaluated Xpert MTB/RIF and 11 evaluated Xpert Ultra, of which nine evaluated both tests. Most studies were conducted in China, India, South Africa, and Uganda. Overall, risk of bias was low for patient selection, index test, and flow and timing domains, and low (49%) or unclear (43%) for the reference standard domain. Applicability for the patient selection domain was unclear for most studies because we were unsure of the clinical settings. Cerebrospinal fluid Xpert Ultra (6 studies) Xpert Ultra pooled sensitivity and specificity (95% CrI) against culture were 89.4% (79.1 to 95.6) (89 participants; low-certainty evidence) and 91.2% (83.2 to 95.7) (386 participants; moderate-certainty evidence). Of 1000 people where 100 have tuberculous meningitis, 168 would be Xpert Ultra-positive: of these, 79 (47%) would not have tuberculosis (false-positives) and 832 would be Xpert Ultra-negative: of these, 11 (1%) would have tuberculosis (false-negatives). Xpert MTB/RIF (30 studies) Xpert MTB/RIF pooled sensitivity and specificity against culture were 71.1% (62.8 to 79.1) (571 participants; moderate-certainty evidence) and 96.9% (95.4 to 98.0) (2824 participants; high-certainty evidence). Of 1000 people where 100 have tuberculous meningitis, 99 would be Xpert MTB/RIF-positive: of these, 28 (28%) would not have tuberculosis; and 901 would be Xpert MTB/RIF-negative: of these, 29 (3%) would have tuberculosis. Pleural fluid Xpert Ultra (4 studies) Xpert Ultra pooled sensitivity and specificity against culture were 75.0% (58.0 to 86.4) (158 participants; very low-certainty evidence) and 87.0% (63.1 to 97.9) (240 participants; very low-certainty evidence). Of 1000 people where 100 have pleural tuberculosis, 192 would be Xpert Ultra-positive: of these, 117 (61%) would not have tuberculosis; and 808 would be Xpert Ultra-negative: of these, 25 (3%) would have tuberculosis. Xpert MTB/RIF (25 studies) Xpert MTB/RIF pooled sensitivity and specificity against culture were 49.5% (39.8 to 59.9) (644 participants; low-certainty evidence) and 98.9% (97.6 to 99.7) (2421 participants; high-certainty evidence). Of 1000 people where 100 have pleural tuberculosis, 60 would be Xpert MTB/RIF-positive: of these, 10 (17%) would not have tuberculosis; and 940 would be Xpert MTB/RIF-negative: of these, 50 (5%) would have tuberculosis. Lymph node aspirate Xpert Ultra (1 study) Xpert Ultra sensitivity and specificity (95% confidence interval) against composite reference standard were 70% (51 to 85) (30 participants; very low-certainty evidence) and 100% (92 to 100) (43 participants; low-certainty evidence). Of 1000 people where 100 have lymph node tuberculosis, 70 would be Xpert Ultra-positive and 0 (0%) would not have tuberculosis; 930 would be Xpert Ultra-negative and 30 (3%) would have tuberculosis. Xpert MTB/RIF (4 studies) Xpert MTB/RIF pooled sensitivity and specificity against composite reference standard were 81.6% (61.9 to 93.3) (377 participants; low-certainty evidence) and 96.4% (91.3 to 98.6) (302 participants; low-certainty evidence). Of 1000 people where 100 have lymph node tuberculosis, 118 would be Xpert MTB/RIF-positive and 37 (31%) would not have tuberculosis; 882 would be Xpert MTB/RIF-negative and 19 (2%) would have tuberculosis. In lymph node aspirate, Xpert MTB/RIF pooled specificity against culture was 86.2% (78.0 to 92.3), lower than that against a composite reference standard. Using the latent class model, Xpert MTB/RIF pooled specificity was 99.5% (99.1 to 99.7), similar to that observed with a composite reference standard. Rifampicin resistance Xpert Ultra (4 studies) Xpert Ultra pooled sensitivity and specificity were 100.0% (95.1 to 100.0), (24 participants; low-certainty evidence) and 100.0% (99.0 to 100.0) (105 participants; moderate-certainty evidence). Of 1000 people where 100 have rifampicin resistance, 100 would be Xpert Ultra-positive (resistant): of these, zero (0%) would not have rifampicin resistance; and 900 would be Xpert Ultra-negative (susceptible): of these, zero (0%) would have rifampicin resistance. Xpert MTB/RIF (19 studies) Xpert MTB/RIF pooled sensitivity and specificity were 96.5% (91.9 to 98.8) (148 participants; high-certainty evidence) and 99.1% (98.0 to 99.7) (822 participants; high-certainty evidence). Of 1000 people where 100 have rifampicin resistance, 105 would be Xpert MTB/RIF-positive (resistant): of these, 8 (8%) would not have rifampicin resistance; and 895 would be Xpert MTB/RIF-negative (susceptible): of these, 3 (0.3%) would have rifampicin resistance. AUTHORS' CONCLUSIONS Xpert Ultra and Xpert MTB/RIF may be helpful in diagnosing extrapulmonary tuberculosis. Sensitivity varies across different extrapulmonary specimens: while for most specimens specificity is high, the tests rarely yield a positive result for people without tuberculosis. For tuberculous meningitis, Xpert Ultra had higher sensitivity and lower specificity than Xpert MTB/RIF against culture. Xpert Ultra and Xpert MTB/RIF had similar sensitivity and specificity for rifampicin resistance. Future research should acknowledge the concern associated with culture as a reference standard in paucibacillary specimens and consider ways to address this limitation.
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MESH Headings
- Adult
- Antibiotics, Antitubercular/therapeutic use
- Bias
- Drug Resistance, Bacterial
- False Negative Reactions
- False Positive Reactions
- Humans
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/isolation & purification
- Nucleic Acid Amplification Techniques/methods
- Nucleic Acid Amplification Techniques/statistics & numerical data
- Reagent Kits, Diagnostic
- Rifampin/therapeutic use
- Sensitivity and Specificity
- Tuberculosis/cerebrospinal fluid
- Tuberculosis/diagnosis
- Tuberculosis/drug therapy
- Tuberculosis, Lymph Node/cerebrospinal fluid
- Tuberculosis, Lymph Node/diagnosis
- Tuberculosis, Lymph Node/drug therapy
- Tuberculosis, Meningeal/cerebrospinal fluid
- Tuberculosis, Meningeal/diagnosis
- Tuberculosis, Meningeal/drug therapy
- Tuberculosis, Multidrug-Resistant/cerebrospinal fluid
- Tuberculosis, Multidrug-Resistant/diagnosis
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Pleural/cerebrospinal fluid
- Tuberculosis, Pleural/diagnosis
- Tuberculosis, Pleural/drug therapy
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Affiliation(s)
- Mikashmi Kohli
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Canada
| | - Ian Schiller
- Centre for Outcomes Research, McGill University Health Centre - Research Institute, Montreal, Canada
| | - Nandini Dendukuri
- Centre for Outcomes Research, McGill University Health Centre - Research Institute, Montreal, Canada
| | - Mandy Yao
- Centre for Outcomes Research, McGill University Health Centre - Research Institute, Montreal, Canada
| | - Keertan Dheda
- Centre for Lung Infection and Immunity Unit, Department of Medicine and UCT Lung Institute, University of Cape Town, Cape Town, South Africa
- Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK
| | - Claudia M Denkinger
- FIND, Geneva , Switzerland
- Division of Tropical Medicine, Centre for Infectious Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Karen R Steingart
- Honorary Research Fellow, Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
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Kohli M, Schiller I, Dendukuri N, Dheda K, Denkinger CM, Schumacher SG, Steingart KR. Xpert ® MTB/RIF assay for extrapulmonary tuberculosis and rifampicin resistance. Cochrane Database Syst Rev 2018; 8:CD012768. [PMID: 30148542 PMCID: PMC6513199 DOI: 10.1002/14651858.cd012768.pub2] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Tuberculosis (TB) is the world's leading infectious cause of death. Extrapulmonary TB accounts for 15% of TB cases, but the proportion is increasing, and over half a million people were newly diagnosed with rifampicin-resistant TB in 2016. Xpert® MTB/RIF (Xpert) is a World Health Organization (WHO)-recommended, rapid, automated, nucleic acid amplification assay that is used widely for simultaneous detection of Mycobacterium tuberculosis complex and rifampicin resistance in sputum specimens. This Cochrane Review assessed the accuracy of Xpert in extrapulmonary specimens. OBJECTIVES To determine the diagnostic accuracy of Xpert a) for extrapulmonary TB by site of disease in people presumed to have extrapulmonary TB; and b) for rifampicin resistance in people presumed to have extrapulmonary TB. SEARCH METHODS We searched the Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, Web of Science, Latin American Caribbean Health Sciences Literature (LILACS), Scopus, ClinicalTrials.gov, the WHO International Clinical Trials Registry Platform, the International Standard Randomized Controlled Trial Number (ISRCTN) Registry, and ProQuest up to 7 August 2017 without language restriction. SELECTION CRITERIA We included diagnostic accuracy studies of Xpert in people presumed to have extrapulmonary TB. We included TB meningitis and pleural, lymph node, bone or joint, genitourinary, peritoneal, pericardial, and disseminated TB. We used culture as the reference standard. For pleural TB, we also included a composite reference standard, which defined a positive result as the presence of granulomatous inflammation or a positive culture result. For rifampicin resistance, we used culture-based drug susceptibility testing or MTBDRplus as the reference standard. DATA COLLECTION AND ANALYSIS Two review authors independently extracted data, assessed risk of bias and applicability using the QUADAS-2 tool. We determined pooled predicted sensitivity and specificity for TB, grouped by type of extrapulmonary specimen, and for rifampicin resistance. For TB detection, we used a bivariate random-effects model. Recognizing that use of culture may lead to misclassification of cases of extrapulmonary TB as 'not TB' owing to the paucibacillary nature of the disease, we adjusted accuracy estimates by applying a latent class meta-analysis model. For rifampicin resistance detection, we performed univariate meta-analyses for sensitivity and specificity separately to include studies in which no rifampicin resistance was detected. We used theoretical populations with an assumed prevalence to provide illustrative numbers of patients with false positive and false negative results. MAIN RESULTS We included 66 unique studies that evaluated 16,213 specimens for detection of extrapulmonary TB and rifampicin resistance. We identified only one study that evaluated the newest test version, Xpert MTB/RIF Ultra (Ultra), for TB meningitis. Fifty studies (76%) took place in low- or middle-income countries. Risk of bias was low for patient selection, index test, and flow and timing domains and was high or unclear for the reference standard domain (most of these studies decontaminated sterile specimens before culture inoculation). Regarding applicability, in the patient selection domain, we scored high or unclear concern for most studies because either patients were evaluated exclusively as inpatients at tertiary care centres, or we were not sure about the clinical settings.Pooled Xpert sensitivity (defined by culture) varied across different types of specimens (31% in pleural tissue to 97% in bone or joint fluid); Xpert sensitivity was > 80% in urine and bone or joint fluid and tissue. Pooled Xpert specificity (defined by culture) varied less than sensitivity (82% in bone or joint tissue to 99% in pleural fluid and urine). Xpert specificity was ≥ 98% in cerebrospinal fluid, pleural fluid, urine, and peritoneal fluid.Xpert testing in cerebrospinal fluidXpert pooled sensitivity and specificity (95% credible interval (CrI)) against culture were 71.1% (60.9% to 80.4%) and 98.0% (97.0% to 98.8%), respectively (29 studies, 3774 specimens; moderate-certainty evidence).For a population of 1000 people where 100 have TB meningitis on culture, 89 would be Xpert-positive: of these, 18 (20%) would not have TB (false-positives); and 911 would be Xpert-negative: of these, 29 (3%) would have TB (false-negatives).For TB meningitis, ultra sensitivity and specificity against culture (95% confidence interval (CI)) were 90% (55% to 100%) and 90% (83% to 95%), respectively (one study, 129 participants).Xpert testing in pleural fluidXpert pooled sensitivity and specificity (95% CrI) against culture were 50.9% (39.7% to 62.8%) and 99.2% (98.2% to 99.7%), respectively (27 studies, 4006 specimens; low-certainty evidence).For a population of 1000 people where 150 have pleural TB on culture, 83 would be Xpert-positive: of these, seven (8%) would not have TB (false-positives); and 917 would be Xpert-negative: of these, 74 (8%) would have TB (false-negatives).Xpert testing in urineXpert pooled sensitivity and specificity (95% CrI) against culture were 82.7% (69.6% to 91.1%) and 98.7% (94.8% to 99.7%), respectively (13 studies, 1199 specimens; moderate-certainty evidence).For a population of 1000 people where 70 have genitourinary TB on culture, 70 would be Xpert-positive: of these, 12 (17%) would not have TB (false-positives); and 930 would be Xpert-negative: of these, 12 (1%) would have TB (false-negatives).Xpert testing for rifampicin resistanceXpert pooled sensitivity (20 studies, 148 specimens) and specificity (39 studies, 1088 specimens) were 95.0% (89.7% to 97.9%) and 98.7% (97.8% to 99.4%), respectively (high-certainty evidence).For a population of 1000 people where 120 have rifampicin-resistant TB, 125 would be positive for rifampicin-resistant TB: of these, 11 (9%) would not have rifampicin resistance (false-positives); and 875 would be negative for rifampicin-resistant TB: of these, 6 (1%) would have rifampicin resistance (false-negatives).For lymph node TB, the accuracy of culture, the reference standard used, presented a greater concern for bias than in other forms of extrapulmonary TB. AUTHORS' CONCLUSIONS In people presumed to have extrapulmonary TB, Xpert may be helpful in confirming the diagnosis. Xpert sensitivity varies across different extrapulmonary specimens, while for most specimens, specificity is high, the test rarely yielding a positive result for people without TB (defined by culture). Xpert is accurate for detection of rifampicin resistance. For people with presumed TB meningitis, treatment should be based on clinical judgement, and not withheld solely on an Xpert result, as is common practice when culture results are negative.
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Affiliation(s)
- Mikashmi Kohli
- McGill UniversityDepartment of Epidemiology, Biostatistics and Occupational HealthMontrealCanada
| | - Ian Schiller
- McGill University Health Centre ‐ Research InstituteDivision of Clinical EpidemiologyMontrealCanada
| | - Nandini Dendukuri
- McGill University Health Centre ‐ Research InstituteDivision of Clinical EpidemiologyMontrealCanada
| | - Keertan Dheda
- University of Cape Town3 Centre for Lung Infection and Immunity Unit, Department of Medicine and UCT Lung InstituteCape TownSouth Africa
| | | | | | - Karen R Steingart
- Department of Clinical Sciences, Liverpool School of Tropical MedicineHonorary Research FellowPembroke PlaceLiverpoolUK
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8
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Abstract
A review of pulmonary infections of all types with diagnostic and morphological features.
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9
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Ansari N, Ghazvini K, Ramezani M, Shahdordizadeh M, Yazdian-Robati R, Abnous K, Taghdisi SM. Selection of DNA aptamers against Mycobacterium tuberculosis Ag85A, and its application in a graphene oxide-based fluorometric assay. Mikrochim Acta 2017; 185:21. [PMID: 29594592 DOI: 10.1007/s00604-017-2550-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/09/2017] [Indexed: 01/08/2023]
Abstract
The Mycobacterium Ag85 complex is the major secretory protein of M. tuberculosis. It is a potential marker for early diagnosis of tuberculosis (TB). The authors have identified specific aptamers for Ag85A (FbpA) via protein SELEX using magnetic beads. After twelve rounds of selection, two aptamers (Apt8 and Apt22) were chosen from different groups, and their binding constants were determined by flow cytometry. Apt22 (labeled with Atto 647N) binds to FbpA with high affinity (Kd = 63 nM) and specificity. A rapid, sensitive, and low-cost fluorescent assay was designed based on the use of Apt22 and graphene oxide, with a limit of detection of 1.5 nM and an analytical range from 5 to 200 nM of FbpA. Graphical abstract Schematic illustration of graphene oxide-based aptasensor for fluorometric determination of FbpA.
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Affiliation(s)
- Najmeh Ansari
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, 91778-99191, Iran
| | - Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Buali Research Institute, Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, 91778-99191, Iran
| | - Mohammad Ramezani
- Nanotechnology Research Center, Mashhad University of Medical Sciences, Mashhad, 91778-99191, Iran
| | - Mahin Shahdordizadeh
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, 91778-99191, Iran
| | - Rezvan Yazdian-Robati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, 91778-99191, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Mashhad University of Medical Sciences, Mashhad, 91778-99191, Iran.
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Mashhad University of Medical Sciences, Mashhad, 91778-99191, Iran.
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10
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Dwivedi S, Purohit P, Misra R, Pareek P, Goel A, Khattri S, Pant KK, Misra S, Sharma P. Diseases and Molecular Diagnostics: A Step Closer to Precision Medicine. Indian J Clin Biochem 2017; 32:374-398. [PMID: 29062170 PMCID: PMC5634985 DOI: 10.1007/s12291-017-0688-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The current advent of molecular technologies together with a multidisciplinary interplay of several fields led to the development of genomics, which concentrates on the detection of pathogenic events at the genome level. The structural and functional genomics approaches have now pinpointed the technical challenge in the exploration of disease-related genes and the recognition of their structural alterations or elucidation of gene function. Various promising technologies and diagnostic applications of structural genomics are currently preparing a large database of disease-genes, genetic alterations etc., by mutation scanning and DNA chip technology. Further the functional genomics also exploring the expression genetics (hybridization-, PCR- and sequence-based technologies), two-hybrid technology, next generation sequencing with Bioinformatics and computational biology. Advances in microarray “chip” technology as microarrays have allowed the parallel analysis of gene expression patterns of thousands of genes simultaneously. Sequence information collected from the genomes of many individuals is leading to the rapid discovery of single nucleotide polymorphisms or SNPs. Further advances of genetic engineering have also revolutionized immunoassay biotechnology via engineering of antibody-encoding genes and the phage display technology. The Biotechnology plays an important role in the development of diagnostic assays in response to an outbreak or critical disease response need. However, there is also need to pinpoint various obstacles and issues related to the commercialization and widespread dispersal of genetic knowledge derived from the exploitation of the biotechnology industry and the development and marketing of diagnostic services. Implementation of genetic criteria for patient selection and individual assessment of the risks and benefits of treatment emerges as a major challenge to the pharmaceutical industry. Thus this field is revolutionizing current era and further it may open new vistas in the field of disease management.
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Affiliation(s)
- Shailendra Dwivedi
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, 342005 India
| | - Purvi Purohit
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, 342005 India
| | - Radhieka Misra
- Era's Lucknow Medical College and Hospital, Lucknow, 226003 India
| | - Puneet Pareek
- Department of Radio-Therapy, All India Institute of Medical Sciences, Jodhpur, 342005 India
| | - Apul Goel
- Department of Urology, King George Medical University, Lucknow, 226003 India
| | - Sanjay Khattri
- Department of Pharmacology and Therapeutics, King George Medical University, Lucknow, 226003 India
| | - Kamlesh Kumar Pant
- Department of Pharmacology and Therapeutics, King George Medical University, Lucknow, 226003 India
| | - Sanjeev Misra
- Department of Surgical Oncology, All India Institute of Medical Sciences, Jodhpur, 342005 India
| | - Praveen Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, 342005 India
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11
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Verza M, Schmid KB, Barcellos RB, Linck N, Bello GL, Scapin D, Sperhacke RD, Silva MSN, Wollheim C, Rivero MGC, Kritski AL, Rezende L, Oliveira MM, Costa ERD, Rossetti MLR. Performance of a molecular assay to detect Mycobacterium tuberculosis complex DNA in clinical specimens: multicenter study in Brazil. Mem Inst Oswaldo Cruz 2017; 112:94-99. [PMID: 28177043 PMCID: PMC5293118 DOI: 10.1590/0074-02760160196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 10/31/2016] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND In high tuberculosis (TB) burden countries, there are few data on the performance of new molecular commercialised assays developed locally. OBJECTIVE To evaluate the performance of a new molecular commercialised assay for TB diagnosis (Detect-TB) in three laboratories. METHODS A total of 302 sputum samples from an equal number of patients with presumptive diagnosis of pulmonary tuberculosis (PTB) were submitted for routine smear microscopy, culture, and Detect-TB assay at three different sites in Brazil (the cities of Caxias do Sul, São Paulo and Canoas). FINDINGS Seventy four (24.7%) TB cases were diagnosed (65 bacteriologically confirmed). When compared to smear microscopy/culture results, the overall sensitivity and specificity of Detect-TB assay was 84.6% (CI 95%; 73.7-91.6) and 93.1% (CI 95%; 89.1-95.8), respectively. When compared to bacteriological and clinical diagnostic criteria, the sensitivity and specificity of Detect-TB assay was 74.3% (CI 95%; 63.3-82.9) and 92.9% (CI 95%; 88.7-95.6), respectively. Among the three sites - Caxias do Sul, São Paulo and Canoas - the sensitivity and specificity were respectively 94.7% and 97.8%; 71.4% and 93.9%, 82.1% and 88.9%. MAIN CONCLUSIONS These findings suggest that the Detect-TB assay could be applied routinely in reference laboratories across different regions in Brazil.
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Affiliation(s)
- Mirela Verza
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, RS, Brasil
| | - Karen Barros Schmid
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, RS, Brasil
| | - Regina Bones Barcellos
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, RS, Brasil.,Rede Brasileira de Pesquisa em Tuberculose, Rio de Janeiro, RJ, Brasil
| | - Natali Linck
- Universidade Luterana do Brasil, Canoas, RS, Brasil
| | | | | | - Rosa Dea Sperhacke
- Universidade de Caxias do Sul, Laboratório de Pesquisa em HIV/AIDS, Caxias do Sul, RS, Brasil
| | | | - Claudia Wollheim
- Universidade de Caxias do Sul, Laboratório de Microbiologia Clínica, Caxias do Sul, RS, Brasil
| | | | - Afrânio Lineu Kritski
- Universidade Federal do Rio de Janeiro, Faculdade de Medicina, Centro de Pesquisa em Tuberculose do Hospital Universitário Clementino Fraga Filho, Laboratório de Genética e Biologia Molecular, Rio de Janeiro, RJ, Brasil.,Rede Brasileira de Pesquisa em Tuberculose, Rio de Janeiro, RJ, Brasil
| | | | - Martha Maria Oliveira
- Universidade Federal do Rio de Janeiro, Faculdade de Medicina, Centro de Pesquisa em Tuberculose do Hospital Universitário Clementino Fraga Filho, Laboratório de Genética e Biologia Molecular, Rio de Janeiro, RJ, Brasil.,Rede Brasileira de Pesquisa em Tuberculose, Rio de Janeiro, RJ, Brasil
| | - Elis Regina Dalla Costa
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, RS, Brasil.,Rede Brasileira de Pesquisa em Tuberculose, Rio de Janeiro, RJ, Brasil
| | - Maria Lucia Rosa Rossetti
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, RS, Brasil.,Universidade Luterana do Brasil, Canoas, RS, Brasil.,Rede Brasileira de Pesquisa em Tuberculose, Rio de Janeiro, RJ, Brasil
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12
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Khanna V, Kumar A, Alexander N, Surendran P. A case report on esophageal tuberculosis - A rare entity. Int J Surg Case Rep 2017; 35:41-43. [PMID: 28437671 PMCID: PMC5403801 DOI: 10.1016/j.ijscr.2017.03.042] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/30/2017] [Accepted: 03/30/2017] [Indexed: 12/14/2022] Open
Abstract
Esophageal Tuberculosis accounts for only 2.8% of all cases of Gastrointestinal Tuberculosis. Upper gastrointestinal endoscopy revealed an ulcerative growth in the distal esophagus. Dysphagia is the commonest presenting feature of esophageal tuberculosis. Histopathology and TB-PCR are the key to confirm the diagnosis.
This is a case report of a rare form of tuberculosis in a patient presenting with dysphagia. Patient was subjected to upper gastrointestinal endoscopy, which revealed an ulcerative growth in the distal esophagus. Histopathology revealed esophageal tuberculosis. Patient was managed conservatively with Anti-Tuberculosis Treatment (ATT). Follow up endoscopy after two months revealed resolution of the growth and patient was symptomatically better. In spite of the rare nature of the disease, it can be managed effectively with ATT to avoid complications (fistula, stricture, and esophageal perforation), which might warrant surgery.
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Affiliation(s)
- Vatsal Khanna
- Sri Ramachandra Medical College, Porur, Chennai 600116, Tamil Nadu, India.
| | - Abhilash Kumar
- Sri Ramachandra Medical College, Porur, Chennai 600116, Tamil Nadu, India.
| | - Naveen Alexander
- Sri Ramachandra Medical College, Porur, Chennai 600116, Tamil Nadu, India.
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13
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Jung D, Lee H, Park S. Mycobacterium tuberculosisDNA Detection and Molecular Drug Susceptibility Test in AFB-stained Sputum Slides. ACTA ACUST UNITED AC 2016. [DOI: 10.15616/bsl.2016.22.1.24] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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14
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Suzana S, Ninan MM, Gowri M, Venkatesh K, Rupali P, Michael JS. Xpert MTB/Rif for the diagnosis of extrapulmonary tuberculosis--an experience from a tertiary care centre in South India. Trop Med Int Health 2016; 21:385-92. [PMID: 26671654 DOI: 10.1111/tmi.12655] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
OBJECTIVE The Xpert MTB/Rif, with a detection limit of 131 CFU/ml, plays a valuable role in the diagnosis of extrapulmonary tuberculosis, both susceptible and resistant. This study aims at evaluating the Xpert MTB/Rif for the same, at a tertiary care centre in south India, assessing it against both culture and a composite gold standard (CGS). METHODS We tested consecutive samples from patients suspected of extrapulmonary tuberculosis with Xpert MTB/Rif, evaluated its sensitivity and specificity against solid and/or liquid culture and CGS. An individual analysis of different sample types (tissue biopsies, fluids, pus, lymph node biopsies and CSF) given an adequate sample size, against both culture and CGS, was also performed. RESULTS In total, 494 samples were analysed against culture. Compared to culture, the sensitivity of Xpert MTB/Rif was 89% (95% CI 0.81-0.94) and its specificity was 74% (95% CI 0.70-0.78). When Xpert MTB/Rif was compared to the CGS, pooled sensitivity was 62% (95% CI 0.56-0.67) and specificity was 100% (95% CI 0.91-1.00). CONCLUSION This assay performs better than the currently available conventional laboratory methods. The rapidity with which results are obtained is an added advantage, and its integration into a routine diagnostic protocol must be considered.
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Affiliation(s)
- Shirly Suzana
- Department of Microbiology, Christian Medical College, Vellore, India
| | - Marilyn M Ninan
- Department of Microbiology, Christian Medical College, Vellore, India
| | - Mahasampath Gowri
- Department of Biostatistics, Christian Medical College, Vellore, India
| | - Krishnan Venkatesh
- Department of Spinal Disorders, Christian Medical College, Vellore, India
| | - Priscilla Rupali
- Department of Infectious Diseases, Christian Medical College, Vellore, India
| | - Joy S Michael
- Department of Microbiology, Christian Medical College, Vellore, India
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15
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Phunpae P, Chanwong S, Tayapiwatana C, Apiratmateekul N, Makeudom A, Kasinrerk W. Rapid diagnosis of tuberculosis by identification of Antigen 85 in mycobacterial culture system. Diagn Microbiol Infect Dis 2014; 78:242-8. [DOI: 10.1016/j.diagmicrobio.2013.11.028] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 11/22/2013] [Accepted: 11/24/2013] [Indexed: 11/17/2022]
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16
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Qin L, Gao S, Wang J, Zheng R, Lu J, Hu Z. The conservation and application of three hypothetical protein coding gene for direct detection of Mycobacterium tuberculosis in sputum specimens. PLoS One 2013; 8:e73955. [PMID: 24058507 PMCID: PMC3772801 DOI: 10.1371/journal.pone.0073955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/24/2013] [Indexed: 11/18/2022] Open
Abstract
Background Accurate and early diagnosis of tuberculosis (TB) is of major importance in the control of TB. One of the most important technical advances in diagnosis of tuberculosis is the development of nucleic acid amplification (NAA) tests. However, the choice of the target sequence remains controversial in NAA tests. Recently, interesting alternatives have been found in hypothetical protein coding sequences from mycobacterial genome. Methodology/Principal Findings To obtain rational biomarker for TB diagnosis, the conservation of three hypothetical genes was firstly evaluated in 714 mycobacterial strains. The results showed that SCAR1 (Sequenced Characterized Amplified Region) based on Rv0264c coding gene showed the highest conservation (99.8%) and SCAR2 based on Rv1508c gene showed the secondary high conservation (99.7%) in M. tuberculosis (MTB) strains. SCAR3 based on Rv2135c gene (3.2%) and IS6110 (8%) showed relatively high deletion rate in MTB strains. Secondly, three SCAR markers were evaluated in 307 clinical sputum from patients in whom TB was suspected or patients with diseases other than TB. The amplification of IS6110 and 16SrRNA sequences together with both clinical and bacteriological identification was as a protocol to evaluate the efficacy of SCAR markers. The sensitivities and specificities, positive predictive value (PPV) and negative predictive value (NPV) of all NAA tests were higher than those of bacteriological detection. In four NAA tests, IS6110 and SCAR3 showed the highest PPV (100%) and low NPV (70% and 68.8%, respectively), and SCAR1 and SCAR2 showed the relatively high PPV and NPV (97% and 82.6%, 95.6% and 88.8%, respectively). Conclusions/Significance Our result indicated that SCAR1 and SCAR2 with a high degree of sequence conservation represent efficient and promising alternatives as NAA test targets in identification of MTB. Moreover, the targets developed from this study may provide more alternative targets for the development of a multisite system to effectively detect MTB in samples.
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Affiliation(s)
- Lianhua Qin
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shihui Gao
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jie Wang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ruijuan Zheng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Junmei Lu
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhongyi Hu
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- * E-mail:
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17
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Abstract
Tuberculosis globally results in almost 2 million human deaths annually, with 1 in 4 deaths from tuberculosis being human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS)-related. Primarily a pathogen of the respiratory system, aerobic Mycobacterium tuberculosis complex (MTBC) infects the lungs via the inhalation of infected aerosol droplets generated by people with pulmonary disease through coughing. This review focuses on M. tuberculosis transmission, epidemiology, detection methods and technologies.
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Affiliation(s)
- Balkis A Talip
- Northern Ireland Centre for Food and Health (NICHE), School of Biomedical Sciences, University of Ulster, Coleraine
| | - Roy D Sleator
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
| | - Colm J Lowery
- Northern Ireland Centre for Food and Health (NICHE), School of Biomedical Sciences, University of Ulster, Coleraine
| | - James S G Dooley
- Northern Ireland Centre for Food and Health (NICHE), School of Biomedical Sciences, University of Ulster, Coleraine
| | - William J Snelling
- Northern Ireland Centre for Food and Health (NICHE), School of Biomedical Sciences, University of Ulster, Coleraine
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18
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Ferrara F, Naranjo LA, Kumar S, Gaiotto T, Mukundan H, Swanson B, Bradbury ARM. Using phage and yeast display to select hundreds of monoclonal antibodies: application to antigen 85, a tuberculosis biomarker. PLoS One 2012; 7:e49535. [PMID: 23166701 PMCID: PMC3498134 DOI: 10.1371/journal.pone.0049535] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 10/10/2012] [Indexed: 11/24/2022] Open
Abstract
Background Current diagnostic methods for tuberculosis (TB), a major global health challenge that kills nearly two million people annually, are time-consuming and inadequate. During infection a number of bacterial molecules that play a role in the infective process are released and have been proposed as biomarkers for early TB diagnosis. Antigen 85 (Ag85) is the most abundant secreted TB protein, and a potential target for this diagnostic approach. One of the bottlenecks in the direct detection of such bacterial targets is the availability of robust, sensitive, specific antibodies. Methods Using Ag85 as a model, we describe a method to select antibodies against any potential target using a novel combination of phage and yeast display that exploits the advantage of each approach. Results The efficiency of this approach was attested to by the 111 specific antibodies identified in initial screens. These were assessed for binding to the different Ag85 subunits, affinity, and activity in sandwich assays. Conclusions The novelty of this approach lies in the possibility of screening the entire output of a phage antibody selection in a single experiment by yeast display. This can be considered analogous to carrying out a million ELISAs. The monoclonal antibodies (mAbs) identified in this way show high binding affinity and selectivity for the antigens and offer an advantage over traditional mAbs produced by relatively expensive and time consuming techniques. This approach has wide applicability, and the affinity of selected antibodies can be significantly improved, if required.
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Affiliation(s)
- Fortunato Ferrara
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Leslie A. Naranjo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Sandeep Kumar
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tiziano Gaiotto
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Harshini Mukundan
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Basil Swanson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Andrew R. M. Bradbury
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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19
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Balasingham SV, Davidsen T, Szpinda I, Frye SA, Tønjum T. Molecular Diagnostics in Tuberculosis. Mol Diagn Ther 2012; 13:137-51. [DOI: 10.1007/bf03256322] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Performance assessment of a novel two-step multiple displacement amplification-PCR assay for detection of Mycobacterium tuberculosis complex in sputum specimens. J Clin Microbiol 2012; 50:1443-5. [PMID: 22259205 DOI: 10.1128/jcm.05787-11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A novel two-step multiple displacement amplification-PCR (MDA-PCR) assay for tuberculosis detection in 200 sputum specimens was evaluated. The MDA-PCR assay indicated a significant increase in sensitivity and specificity compared with those of standard PCR alone.
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21
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Michelon CT, Rosso F, Schmid KB, Sperhacke RD, Oliveira MM, Kritski AL, Rezende L, Costa ERD, Ribeiro AW, Verza M, Cafrune PI, Silva MSN, Kuhleis D, Zaha A, Rossetti MLR. Colorimetric microwell plate reverse-hybridization assay for Mycobacterium tuberculosis detection. Mem Inst Oswaldo Cruz 2011; 106:194-9. [PMID: 21537680 DOI: 10.1590/s0074-02762011000200013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 01/26/2011] [Indexed: 11/22/2022] Open
Abstract
Direct smear examination using Ziehl-Neelsen staining for pulmonary tuberculosis (PTB) diagnosis is inexpensive and easy to use, but has the major limitation of low sensitivity. Rapid molecular methods are becoming more widely available in centralized laboratories, but they depend on timely reporting of results and strict quality assurance obtainable only from costly commercial kits available in high burden nations. This study describes a pre-commercial colorimetric method, Detect-TB, for detecting Mycobacterium tuberculosis DNA in which an oligonucleotide probe is fixed onto wells of microwell plates and hybridized with biotinylated polymerase chain reaction amplification products derived from clinical samples. The probe is capable of hybridising with the IS6110 insertion element and was used to specifically recognise the M. tuberculosis complex. When combined with an improved silica-based DNA extraction method, the sensitivity of the test was 50 colony-forming units of the M. tuberculosis reference strain H37Rv. The results that were in agreement with reference detection methods were observed in 95.2% (453/476) of samples included in the analysis. Sensitivity and specificity for 301 induced sputum samples and 175 spontaneous sputum samples were 85% and 98%, and 94% and 100%, respectively. This colorimetric method showed similar specificity to that described for commercially available kits and may provide an important contribution for PTB diagnosis.
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Affiliation(s)
- Candice Tosi Michelon
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, RS, Brasil
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Runa F, Yasmin M, Hoq MM, Begum J, Rahman ASMM, Ahsan CR. Molecular versus conventional methods: clinical evaluation of different methods for the diagnosis of tuberculosis in Bangladesh. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2011; 44:101-5. [PMID: 21439511 DOI: 10.1016/j.jmii.2010.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Revised: 03/04/2010] [Accepted: 05/27/2010] [Indexed: 11/24/2022]
Abstract
BACKGROUND The diagnosis of tuberculosis (TB) in developing countries, such as Bangladesh, is based mainly on microscopic detection of acid-fast bacilli in smears from clinical specimens. On the other hand, the detection of TB by polymerase chain reaction (PCR) is quite new in Bangladesh. In this study, we compared the molecular method with the conventional diagnosis procedures, where Lowenstein-Jensen medium culture results have been used as the "gold standard." METHODS A total of 135 sputum samples were collected from clinically suspected patients with pulmonary TB. A direct smear was made from each sputum specimen and stained by the Ziehl-Neelsen (Z-N) method. The sputum samples were then processed, and the pellet was used for both Z-N (concentration) and auramine O fluorescence staining or resuspended in phosphate buffered saline to inoculate Lowenstein-Jensen medium or processed for PCR detection of Mycobacterium tuberculosis. RESULTS The direct smear staining yielded 44 (32.6%) sputum samples that were acid-fast positive, which increased after concentration, yielding 60 (44.4%) acid-fast-positive samples. Fluorescence microscopy using auramine O staining further increased the number of positive samples to 67 (49.6%). The biochemical tests showed 75 (55.6%) sputum samples to be culture positive, and the MB/BacT system increased the recovery up to 90 (66.7%) culture positives. On the other hand, PCR yielded 93 (68.9%) positive results, 20 (21.5%) of which were culture-negative sputum specimens. CONCLUSION It is suggested that the Z-N direct microscopy on its own is the best method (with high specificity) for confirming the diagnosis of acid-fast bacilli. Although the PCR diagnosis of TB appears to be a rapid and sensitive method, the results should be interpreted with care in the clinical settings.
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Affiliation(s)
- Farhana Runa
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
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Mixed infection with Beijing and non-Beijing strains and drug resistance pattern of Mycobacterium tuberculosis. J Clin Microbiol 2010; 48:4474-80. [PMID: 20980571 DOI: 10.1128/jcm.00930-10] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mixed infection with Beijing and non-Beijing strains of Mycobacterium tuberculosis has been reported and has been suggested to mediate elevation of the reinfection rate in regions with a high incidence of tuberculosis (TB). To evaluate the prevalence of infection with both Beijing and non-Beijing strains of M. tuberculosis in eastern Taiwan, the region with the highest TB incidence in Taiwan, 185 active pulmonary TB patients were enrolled at Tzu Chi General Hospital from October 2007 to September 2008. A modified multiplex PCR method was developed to distinguish Beijing and non-Beijing strains directly using the sputum of patients. Of the 185 patients, 46.5% were infected with a Beijing strain, 42.2% were infected with a non-Beijing strain, and 11.3% were infected with both strain types. Notably, mixed infection with both strain types was not associated with TB treatment history or the high-incidence race group, aborigines. In addition, the incidence rate of mixed infection before treatment with anti-TB medication was as high as that in patients with a history of anti-TB treatment. Further analysis of antibiotic susceptibility revealed that Beijing strains alone had the highest multidrug resistance rate (17.5%), mixed infection had the highest rate of resistance to at least one drug (23.8%), and non-Beijing strains had the highest rate of sensitivity to all drugs (79.5%), implying that Beijing strains are predominant in the development of drug resistance in tuberculosis.
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Kiraz N, Saglik I, Kiremitci A, Kasifoglu N, Akgun Y. Evaluation of the GenoType Mycobacteria Direct assay for direct detection of the Mycobacterium tuberculosis complex obtained from sputum samples. J Med Microbiol 2010; 59:930-934. [PMID: 20448064 DOI: 10.1099/jmm.0.013490-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An increase in the prevalence of tuberculosis (TB) in recent years has accelerated the search for novel tools for the rapid diagnosis of TB infection. This study evaluated the GenoType Mycobacteria Direct (GTMD) assay (Hain Lifescience) for direct detection of the Mycobacterium tuberculosis complex (MTBC) from sputum samples and compared it with conventional methods. The GTMD test is a commercial assay produced using strip techniques and works based on a nucleic acid sequence-based amplification technique. This test allows 23S rRNA amplification-based detection of MTBC, Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium kansasii and Mycobacterium malmoense directly from decontaminated clinical samples within 6 h. In the present study, 115 sputum samples were processed to detect acid-fast bacilli (AFB) using two microscopy methods (carbol fuchsin and fluorescent staining), two culture methods [Löwenstein-Jensen (LJ) and BACTEC 12B media] and the GTMD test. The results showed that 86 of the samples were positive by direct microscopy, 84 were positive by BACTEC 12B culture, 73 were positive by LJ culture and 95 were positive by the GTMD test. All of the isolates turned out to be MTBC. Moreover, the sensitivity and specificity of the GTMD test for MTBC in patients were 97 and 58 %, respectively, taking the culture combination as the gold standard. When the test was compared with culture of samples from anti-TB-treated patients, the sensitivity and specificity for the test were 100 and 15 %, respectively. Low specificity in treated people might arise from depressed proliferation of AFB. As the two methods target the same living bacilli, the difference is obviously notable. When the culture results and clinical findings of the patients were evaluated together (true-positive specimens), the sensitivity and specificity values of the GTMD test for all patients were 97 and 90 %, respectively. However, both of these values increased to 100 % for the patients receiving anti-TB treatment. These results implied that, to determine whether the patient's sputum contains living AFB, more sensitive techniques should be employed during the follow-up of the patients. These observations suggest that the GTMD method can be useful for early diagnosis of clinically and radiologically suspicious TB cases where smears are negative for Mycobacterium. In addition, the use of a GTMD test in smear-positive cases is helpful and practical in order to identify MTBC quickly. This allows more rapid treatment decisions and infection control precautions.
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Affiliation(s)
- Nuri Kiraz
- Eskisehir Osmangazi University, Faculty of Medicine, Department of Microbiology, Eskisehir, Turkey
| | - Imran Saglik
- Eskisehir Osmangazi University, Faculty of Medicine, Department of Microbiology, Eskisehir, Turkey
| | - Abdurrahman Kiremitci
- Eskisehir Osmangazi University, Faculty of Medicine, Department of Microbiology, Eskisehir, Turkey
| | - Nilgun Kasifoglu
- Eskisehir Osmangazi University, Faculty of Medicine, Department of Microbiology, Eskisehir, Turkey
| | - Yurdanur Akgun
- Eskisehir Osmangazi University, Faculty of Medicine, Department of Microbiology, Eskisehir, Turkey
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Direct detection of mycobacterial species in pulmonary specimens by two rapid amplification tests, the gen-probe amplified mycobacterium tuberculosis direct test and the genotype mycobacteria direct test. J Clin Microbiol 2009; 47:3635-9. [PMID: 19794042 DOI: 10.1128/jcm.00411-09] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nucleic acid amplification tests have improved tuberculosis diagnostics considerably. This study evaluates a new amplification test, the GenoType Mycobacteria Direct (GTMD) test, for detection of the Mycobacterium tuberculosis complex, Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium kansasii, and Mycobacterium malmoense directly in 61 sputum samples. Thirty (49.2%) samples were auramine smear positive, and 31 (50.8%) were smear negative. The GTMD results were compared to the Gen-Probe Amplified M. tuberculosis Direct (MTD) test results, using culturing and sequencing of the 16S rRNA gene as reference methods. The GTMD test could identify 28 of 29 samples containing the M. tuberculosis complex and was negative in a sputum sample containing M. intracellulare. The overall sensitivity and specificity results were 93.3% and 90.0% for the GTMD test, respectively, and 93.1% and 93.5% for the MTD test, respectively. The GTMD test is rapid and can be easily included in routine clinical laboratories for the direct detection of the M. tuberculosis complex in smear-positive sputum samples as an adjunct to microscopy and culture. Further studies are needed to evaluate the performance of the GTMD test for the detection of atypical mycobacteria.
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Sener AG, Kurultay N, Afsar I. Evaluation of the results of Mycobacterium tuberculosis direct test (MTD) and Mycobacterial culture in urine samples. Braz J Microbiol 2008; 39:673-5. [PMID: 24031287 PMCID: PMC3768455 DOI: 10.1590/s1517-838220080004000014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Revised: 04/09/2008] [Accepted: 11/02/2008] [Indexed: 11/22/2022] Open
Abstract
Tuberculosis remains a public health problem in Turkey. Rapid detection of Mycobacterium tuberculosis plays a key role in control of infection. In this article, the Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test (MTD) was evaluated for detection of M. tuberculosis in urine samples. The performance of the MTD was very good and appropriate for routine laboratory diagnosis.
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Affiliation(s)
- Asli Gamze Sener
- Ataturk Training and Research Hospital, Microbiology and Clinical Microbiology Laboratory Izmir/Turkey
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Jarzembowski JA, Young MB. Nontuberculous mycobacterial infections. Arch Pathol Lab Med 2008; 132:1333-41. [PMID: 18684037 DOI: 10.5858/2008-132-1333-nmi] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2008] [Indexed: 11/06/2022]
Abstract
CONTEXT Nontuberculous mycobacteria include numerous acid-fast bacilli species, many of which have only recently been recognized as pathogenic. The diagnosis of mycobacterial disease is based on a combination of clinical features, microbiologic data, radiographic findings, and histopathologic studies. OBJECTIVE To provide an overview of the clinical and pathologic aspects of nontuberculous mycobacteria infection, including diagnostic laboratory methods, classification, epidemiology, clinical presentation, and treatment. DATA SOURCES Review of the pertinent literature and published methodologies. CONCLUSIONS Nontuberculous mycobacteria include numerous acid-fast bacilli species, many of which are potentially pathogenic, and are classified according to the Runyon system based on growth rates and pigment production. Their slow growth hinders cultures, which require special medium and prolonged incubation. Although such methods are still used, newer nucleic acid-based technologies (polymerase chain reaction and hybridization assays) can rapidly detect and speciate some mycobacteria--most notably, distinguishing Mycobacterium tuberculosis from other species. Infections caused by these organisms can present as a variety of clinical syndromes, not only in immunocompromised patients but also in immunocompetent hosts. Most common among these are chronic pulmonary infections, superficial lymphadenitis, soft tissue and osteoarticular infections, and disseminated disease. Treatment of nontuberculous mycobacterial infections is difficult, requiring extended courses of multidrug therapy with or without adjunctive surgical intervention.
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Affiliation(s)
- Jason A Jarzembowski
- Department of Pathology, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53201, USA.
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Kumar G, Dagur PK, Singh M, Yadav VS, Dayal R, Singh HB, Katoch VM, Sengupta U, Joshi B. Diagnostic Potential of Ag85C in Comparison to Various Secretory Antigens for Childhood Tuberculosis. Scand J Immunol 2008; 68:177-83. [DOI: 10.1111/j.1365-3083.2008.02133.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Campos M, Quartin A, Mendes E, Abreu A, Gurevich S, Echarte L, Ferreira T, Cleary T, Hollender E, Ashkin D. Feasibility of Shortening Respiratory Isolation with a Single Sputum Nucleic Acid Amplification Test. Am J Respir Crit Care Med 2008; 178:300-5. [DOI: 10.1164/rccm.200803-381oc] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Djelouadji Z, Raoult D, Daffé M, Drancourt M. A single-step sequencing method for the identification of Mycobacterium tuberculosis complex species. PLoS Negl Trop Dis 2008; 2:e253. [PMID: 18618024 PMCID: PMC2453075 DOI: 10.1371/journal.pntd.0000253] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Accepted: 05/20/2008] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The Mycobacterium tuberculosis complex (MTC) comprises closely related species responsible for strictly human and zoonotic tuberculosis. Accurate species determination is useful for the identification of outbreaks and epidemiological links. Mycobacterium africanum and Mycobacterium canettii are typically restricted to Africa and M. bovis is a re-emerging pathogen. Identification of these species is difficult and expensive. METHODOLOGY/PRINCIPAL FINDINGS The Exact Tandem Repeat D (ETR-D; alias Mycobacterial Interspersed Repetitive Unit 4) was sequenced in MTC species type strains and 110 clinical isolates, in parallel to reference polyphasic identification based on phenotype profiling and sequencing of pncA, oxyR, hsp65, gyrB genes and the major polymorphism tandem repeat. Inclusion of M. tuberculosis isolates in the expanding, antibiotic-resistant Beijing clone was determined by Rv0927c gene sequencing. The ETR-D (780-bp) sequence unambiguously identified MTC species type strain except M. pinnipedii and M. microti thanks to six single nucleotide polymorphisms, variable numbers (1-7 copies) of the tandem repeat and two deletions/insertions. The ETR-D sequencing agreed with phenotypic identification in 107/110 clinical isolates and with reference polyphasic molecular identification in all isolates, comprising 98 M. tuberculosis, 5 M. bovis BCG type, 5 M. canettii, and 2 M. africanum. For M. tuberculosis isolates, the ETR-D sequence was not significantly associated with the Beijing clone. CONCLUSIONS/SIGNIFICANCE ETR-D sequencing allowed accurate, single-step identification of the MTC at the species level. It circumvented the current expensive, time-consuming polyphasic approach. It could be used to depict epidemiology of zoonotic and human tuberculosis, especially in African countries where several MTC species are emerging.
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Affiliation(s)
- Zoheira Djelouadji
- Unité des Rickettsies CNRS UMR6020, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - Didier Raoult
- Unité des Rickettsies CNRS UMR6020, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - Mamadou Daffé
- Département de Mécanismes Moléculaires des Infections Mycobactériennes, Institut de Pharmacologie et Biologie structurale, Toulouse, France
| | - Michel Drancourt
- Unité des Rickettsies CNRS UMR6020, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
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el-Sayed Zaki M, Abou-el Hassan S. Clinical evaluation of Gen-Probe's amplified mycobacterium tuberculosis direct test for rapid diagnosis of Mycobacterium tuberculosis in Egyptian children at risk for infection. Arch Pathol Lab Med 2008; 132:244-7. [PMID: 18251584 DOI: 10.5858/2008-132-244-ceogam] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2007] [Indexed: 11/06/2022]
Abstract
CONTEXT Diagnostic detection of tuberculosis (TB) has improved considerably. Available, standardized, nucleic acid-based amplification techniques have been shown to yield reliable results within 4 to 7 hours of sample processing. OBJECTIVE To study the diagnostic performance of Gen-Probe's technique for direct detection of Mycobacterium tuberculosis in comparison with BACTEC 460 TB culture for both positive and negative Ziehl-Neelsen smears in Egyptian children at risk for TB infection. DESIGN We prospectively evaluated 50 children from families with a positive history of TB. All patients were referred from outpatient clinics of the Mansoura University Children's Hospital, Egypt. The children had a positive tuberculin skin test with an induration diameter of more than 10 mm and had scars from a bacille Calmette-Guérin vaccination within the past 2 years. Three consecutive sputum samples were taken from each patient. The samples were examined to detect M. tuberculosis by means of the Gen-Probe technique, direct smear microscopy, and bacterial culture by BACTEC 460 TB. RESULTS Of the 50 cases, 30 (60%) had sputum samples that were positive for TB by BACTEC 460 TB culture, and 29 cases (58%) were positive by the Gen-Probe technique. Sensitivity and specificity of Ziehl-Neelsen smears was 83.3% and 100%, respectively, with overall accuracy of 90%. Sensitivity and specificity of the Gen-Probe technique were 96.7% and 100%, respectively, with overall accuracy of 98%. CONCLUSIONS The results of this study suggest that the Gen-Probe technique is an accurate method for rapid detection of M. tuberculosis complexes in respiratory samples from children at risk for TB. It can be used for diagnosis of smear-negative cases that are suspect for TB.
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Affiliation(s)
- Maysaa el-Sayed Zaki
- Egypt-Mansoura University, Faculty of Medicine, Department of Clinical Pathology, Mansoura 65 Egypt.
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Ling DI, Flores LL, Riley LW, Pai M. Commercial nucleic-acid amplification tests for diagnosis of pulmonary tuberculosis in respiratory specimens: meta-analysis and meta-regression. PLoS One 2008; 3:e1536. [PMID: 18253484 PMCID: PMC2212137 DOI: 10.1371/journal.pone.0001536] [Citation(s) in RCA: 151] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Accepted: 01/06/2008] [Indexed: 11/22/2022] Open
Abstract
Background Hundreds of studies have evaluated the diagnostic accuracy of nucleic-acid amplification tests (NAATs) for tuberculosis (TB). Commercial tests have been shown to give more consistent results than in-house assays. Previous meta-analyses have found high specificity but low and highly variable estimates of sensitivity. However, reasons for variability in study results have not been adequately explored. We performed a meta-analysis on the accuracy of commercial NAATs to diagnose pulmonary TB and meta-regression to identify factors that are associated with higher accuracy. Methodology/Principal Findings We identified 2948 citations from searching the literature. We found 402 articles that met our eligibility criteria. In the final analysis, 125 separate studies from 105 articles that reported NAAT results from respiratory specimens were included. The pooled sensitivity was 0.85 (range 0.36–1.00) and the pooled specificity was 0.97 (range 0.54–1.00). However, both measures were significantly heterogeneous (p<.001). We performed subgroup and meta-regression analyses to identify sources of heterogeneity. Even after stratifying by type of commercial test, we could not account for the variability. In the meta-regression, the threshold effect was significant (p = .01) and the use of other respiratory specimens besides sputum was associated with higher accuracy. Conclusions/Significance The sensitivity and specificity estimates for commercial NAATs in respiratory specimens were highly variable, with sensitivity lower and more inconsistent than specificity. Thus, summary measures of diagnostic accuracy are not clinically meaningful. The use of different cut-off values and the use of specimens other than sputum could explain some of the observed heterogeneity. Based on these observations, commercial NAATs alone cannot be recommended to replace conventional tests for diagnosing pulmonary TB. Improvements in diagnostic accuracy, particularly sensitivity, need to be made in order for this expensive technology to be worthwhile and beneficial in low-resource countries.
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Affiliation(s)
- Daphne I. Ling
- Division of Epidemiology, School of Public Health, University of California, Berkeley, California, United States of America
| | - Laura L. Flores
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, San Francisco, California, United States of America
| | - Lee W. Riley
- Division of Epidemiology, School of Public Health, University of California, Berkeley, California, United States of America
- Division of Infectious Diseases, School of Public Health, University of California, Berkeley, California, United States of America
| | - Madhukar Pai
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
- * To whom correspondence should be addressed. E-mail:
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Jung CL, Kim MK, Seo DC, Lee MA. Clinical Usefulness of Real-time PCR and Amplicor MTB PCR Assays for Diagnosis of Tuberculosis. ACTA ACUST UNITED AC 2008. [DOI: 10.5145/kjcm.2008.11.1.29] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Chae Lim Jung
- Department of Laboratory Medicine, School of Medicine, Ewha Womans University Mokdong Hospital, Seoul, Korea
| | - Mi Kyung Kim
- Department of Laboratory Medicine, School of Medicine, Ewha Womans University Mokdong Hospital, Seoul, Korea
| | - Dong Chun Seo
- Department of Laboratory Medicine, School of Medicine, Ewha Womans University Mokdong Hospital, Seoul, Korea
| | - Mi Ae Lee
- Department of Laboratory Medicine, School of Medicine, Ewha Womans University Mokdong Hospital, Seoul, Korea
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Guerra RL, Hooper NM, Baker JF, Alborz R, Armstrong DT, Maltas G, Kiehlbauch JA, Dorman SE. Use of the amplified mycobacterium tuberculosis direct test in a public health laboratory: test performance and impact on clinical care. Chest 2007; 132:946-51. [PMID: 17573496 DOI: 10.1378/chest.06-2959] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND The Amplified Mycobacterium tuberculosis Direct Test (MTD; Gen-Probe; San Diego, CA) is a nucleic-acid amplification test for rapid pulmonary tuberculosis (PTB) diagnosis. In a routine public health setting, test accuracy and impact on clinical decisions are unknown. METHODS Retrospectively, we evaluated MTD accuracy and impact on clinical decisions in a public health setting. To estimate MTD accuracy, mycobacterial culture was used as the "gold standard." To evaluate MTD impact on clinical decisions, concordance of clinician presumptive diagnosis (at time of MTD and smear availability) and definitive diagnosis, and duration of nonindicated tuberculosis therapy were determined for smear-positive PTB suspects in a period of MTD availability (MTD group) and a prior period of MTD nonavailability (non-MTD group). RESULTS A total of 1,151 respiratory specimens from 638 PTB suspects were analyzed. MTD sensitivity, specificity, positive predictive value, and negative predictive value were 91.7%, 98.7%, 96.7%, and 96.5% overall, respectively; and 98.7%, 97.8%, 98.7%, and 97.8% for smear-positive patients; and 62.2%, 98.9%, 85.2%, and 96.1% for smear-negative patients. In the MTD group, concordance between definitive and clinician presumptive diagnoses was 78% (95% confidence interval [CI], 64 to 88%), similar to that for the non-MTD group (79%; 95% CI, 68.4 to 89.6%). However, concordance between definitive diagnosis and the MTD test was 98% (95% CI, 94.1 to 100%). Median duration of nonindicated tuberculosis treatment was 6 days for the MTD group vs 31 days for the non-MTD group (p = 0.002). CONCLUSION In this public health setting, MTD was accurate and rapidly detected more than half of the smear-negative PTB cases. For smear-positive PTB suspects, MTD had excellent concordance with definitive diagnosis, but clinicians often inappropriately initiated TB therapy despite a negative MTD result.
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Affiliation(s)
- Renata L Guerra
- School of Medicine, Johns Hopkins University, Room 1M-06, 1550 Orleans St, Baltimore, MD 21231, USA
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Yin MT, Dobkin JF, Grbic JT. Epidemiology, pathogenesis, and management of human immunodeficiency virus infection in patients with periodontal disease. Periodontol 2000 2007; 44:55-81. [PMID: 17474926 DOI: 10.1111/j.1600-0757.2007.00205.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Michael T Yin
- Division of Infectious Diseases, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA
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Garcia EP, Dowding LA, Stanton LW, Slepnev VI. Scalable transcriptional analysis routine--multiplexed quantitative real-time polymerase chain reaction platform for gene expression analysis and molecular diagnostics. J Mol Diagn 2005; 7:444-54. [PMID: 16237214 PMCID: PMC1888488 DOI: 10.1016/s1525-1578(10)60575-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We report the development of a new technology for simultaneous quantitative detection of multiple targets in a single sample. Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. STAR demonstrated similar or better sensitivity and precision compared to two commonly used methods, SYBR Green-based and TaqMan probe-based real-time reverse transcriptase-polymerase chain reaction. STAR can be used as a flexible platform for building a variety of applications to monitor gene expression, from single gene assays to assays analyzing the expression level of multiple genes. Using severe acute respiratory syndrome (SARS) corona virus as a model system, STAR technology detected single copies of the viral genome in a two-gene multiplex. Blinded studies using RNA extracted from various tissues of a SARS-infected individual showed that STAR correctly identified all samples containing SARS virus and yielded negative results for non-SARS control samples. Using alternate priming strategies, STAR technology can be adapted to transcriptional profiling studies without requiring a priori sequence information. Thus, STAR technology offers a flexible platform for development of highly multiplexed assays in gene expression analysis and molecular diagnostics.
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Abstract
Molecular diagnostics in tuberculosis has enabled rapid detection of Mycobacterium tuberculosis complex in clinical specimens, identification of mycobacterial species, detection of drug resistance, and typing for epidemiological investigation. In the laboratory diagnosis of tuberculosis, the nucleic acid amplification (NAA) test is rapid and specific but not as sensitive as culture of mycobacteria. The primary determinant of successful NAA testing for tuberculosis depends on the shedding of mycobacterial DNA in secretions from caseating granulomas and its dissemination into sterile body fluids or tissue biopsies. In multibacillary diseases with a high mycobacterial load, a positive Ziehl-Neelsen smear with a positive NAA test is diagnostic of active tuberculosis, whereas a positive Ziehl-Neelsen smear with a negative NAA test in the absence of inhibitors would indicate nontuberculous mycobacterial disease. The role of the NAA test is more important in paucibacillary diseases with low mycobacterial loads. The presence of polymerase chain reaction (PCR) inhibitors, however, especially in extrapulmonary specimens, may produce false-negative results. Although this problem can be overcome to some extent by extra extraction steps, the additional processing invariably leads to the loss of mycobacterial DNA. To circumvent this problem, a brief culture augmentation step is carried out before the NAA test is performed, which can enhance the mycobacterial load while concomitantly diluting inhibitors, thereby maintaining the sensitivity of the test without excessively increasing turnaround time.
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Affiliation(s)
- V C C Cheng
- Centre of Infection and Immunology, University of Hong Kong, Hong Kong Special Administrative Region, China
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39
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Johansen IS, Lundgren B, Tabak F, Petrini B, Hosoglu S, Saltoglu N, Thomsen VØ. Improved sensitivity of nucleic acid amplification for rapid diagnosis of tuberculous meningitis. J Clin Microbiol 2004; 42:3036-40. [PMID: 15243056 PMCID: PMC446323 DOI: 10.1128/jcm.42.7.3036-3040.2004] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Early diagnosis of tuberculous meningitis (TBM) is essential for a positive outcome; but present microbiological diagnostic techniques are insensitive, slow, or laborious. We evaluated the standard BDProbeTec ET strand displacement amplification method (the standard ProbeTec method) for the detection of Mycobacterium tuberculosis complex organisms in parallel with the ProbeTec method with a modified pretreatment procedure with 101 prospectively collected cerebrospinal fluid specimens from 94 patients with suspected TBM. By the modified method, the sample-washing step was omitted. A definitive diagnosis was attained by culture. Thirteen specimens from 12 patients were culture positive for M. tuberculosis complex organisms; three specimens (23%) were microscopy positive for acid-fast bacilli. Among the culture-positive specimens, the standard ProbeTec method was positive for 8 (61.5%) and the modified assay was positive for 10 (76.9%). The overall specificity by both procedures was 98.8% compared to the results of culture. After discrepancy analysis, conducted by reviewing the patients' previous laboratory data, the specificity increased to 100%. If the cutoff value for respiratory specimens was adjusted from the recommended value of 3,400 to 1,000, the sensitivity of the modified procedure increased to 84.7%, with unchanged specificity. Results were obtained in 3 to 4 h. The new pretreatment procedure with the ProbeTec assay described here provides a rapid, simple, and sensitive tool for the diagnosis of TBM.
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Affiliation(s)
- Isik Somuncu Johansen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen S, Denmark.
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40
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Kivihya-Ndugga L, van Cleeff M, Juma E, Kimwomi J, Githui W, Oskam L, Schuitema A, van Soolingen D, Nganga L, Kibuga D, Odhiambo J, Klatser P. Comparison of PCR with the routine procedure for diagnosis of tuberculosis in a population with high prevalences of tuberculosis and human immunodeficiency virus. J Clin Microbiol 2004; 42:1012-5. [PMID: 15004046 PMCID: PMC356878 DOI: 10.1128/jcm.42.3.1012-1015.2004] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Direct smear examination with Ziehl-Neelsen (ZN) staining for the diagnosis of tuberculosis (TB) as employed in most low-income countries is cheap and easy to use, but its low sensitivity is a major drawback. The low specificity of chest X-rays, used for the diagnosis of smear-negative TB, risks high levels of overdiagnosis. Major advances in molecular techniques, which rapidly identify mycobacterial DNA in sputa, may overcome these obstacles. In this study, the AMPLICOR PCR system was used to diagnose pulmonary TB in a developing country with high prevalences of both TB and human immunodeficiency virus (HIV). The sensitivity and specificity of this technique were compared to those of the usual diagnostic techniques. Sputum specimens were collected from 1,396 TB suspects attending the Rhodes Chest Clinic, Nairobi, Kenya. The specimens were analyzed for the presence of Mycobacterium tuberculosis by PCR; culture on Löwenstein-Jensen medium was used as the "gold standard." All culture-positive samples were genotyped to identify the mycobacterial species. The sensitivity and specificity of PCR were 93 and 84%, respectively. HIV status did not affect the sensitivity of PCR. A total of 99.7% of the true smear-positive and 82.1% of the true smear-negative TB patients were correctly identified by PCR. PCR detected M. tuberculosis in 11.7% of the culture-negative suspects, 60% of which had one or two PCR-positive sputum specimens. Of the 490 positive cultures, 486 were identified as M. tuberculosis. The high sensitivity of Amplicor PCR merits usage in a clinical setting with high TB and HIV burdens. Thus, PCR can be considered as an alternative to ZN staining in combination with chest X-ray for diagnosis of TB; however, cost-effectiveness studies and operational studies are required to support an evidence-based decision of introducing PCR for TB control in high-burden environments.
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Affiliation(s)
- Lydia Kivihya-Ndugga
- Centre for Respiratory Diseases Research, Kenya Medical Research Institute, Nairobi, Kenya
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41
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Piersimoni C, Scarparo C. Relevance of commercial amplification methods for direct detection of Mycobacterium tuberculosis complex in clinical samples. J Clin Microbiol 2004; 41:5355-65. [PMID: 14662911 PMCID: PMC309028 DOI: 10.1128/jcm.41.12.5355-5365.2003] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Claudio Piersimoni
- Department of Clinical Microbiology, General Hospital Umberto I, Ancona, Italy.
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42
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Pai M, Flores LL, Hubbard A, Riley LW, Colford JM. Nucleic acid amplification tests in the diagnosis of tuberculous pleuritis: a systematic review and meta-analysis. BMC Infect Dis 2004; 4:6. [PMID: 15102325 PMCID: PMC387423 DOI: 10.1186/1471-2334-4-6] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2003] [Accepted: 02/23/2004] [Indexed: 11/25/2022] Open
Abstract
Background Conventional tests for tuberculous pleuritis have several limitations. A variety of new, rapid tests such as nucleic acid amplification tests – including polymerase chain reaction – have been evaluated in recent times. We conducted a systematic review to determine the accuracy of nucleic acid amplification (NAA) tests in the diagnosis of tuberculous pleuritis. Methods A systematic review and meta-analysis of 38 English and Spanish articles (with 40 studies), identified via searches of six electronic databases, hand searching of selected journals, and contact with authors, experts, and test manufacturers. Sensitivity, specificity, and other measures of accuracy were pooled using random effects models. Summary receiver operating characteristic curves were used to summarize overall test performance. Heterogeneity in study results was formally explored using subgroup analyses. Results Of the 40 studies included, 26 used in-house ("home-brew") tests, and 14 used commercial tests. Commercial tests had a low overall sensitivity (0.62; 95% confidence interval [CI] 0.43, 0.77), and high specificity (0.98; 95% CI 0.96, 0.98). The positive and negative likelihood ratios for commercial tests were 25.4 (95% CI 16.2, 40.0) and 0.40 (95% CI 0.24, 0.67), respectively. All commercial tests had consistently high specificity estimates; the sensitivity estimates, however, were heterogeneous across studies. With the in-house tests, both sensitivity and specificity estimates were significantly heterogeneous. Clinically meaningful summary estimates could not be determined for in-house tests. Conclusions Our results suggest that commercial NAA tests may have a potential role in confirming (ruling in) tuberculous pleuritis. However, these tests have low and variable sensitivity and, therefore, may not be useful in excluding (ruling out) the disease. NAA test results, therefore, cannot replace conventional tests; they need to be interpreted in parallel with clinical findings and results of conventional tests. The accuracy of in-house nucleic acid amplification tests is poorly defined because of heterogeneity in study results. The clinical applicability of in-house NAA tests remains unclear.
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Affiliation(s)
- Madhukar Pai
- Division of Epidemiology, School of Public Health University of California, Berkeley 140, Warren Hall, Berkeley, CA 94720, USA
| | - Laura L Flores
- Division of Infectious Diseases, School of Public Health University of California, Berkeley 140, Warren Hall, Berkeley, CA 94720, USA
| | - Alan Hubbard
- Division of Biostatistics, School of Public Health University of California, Berkeley 140, Warren Hall, Berkeley, CA 94720, USA
| | - Lee W Riley
- Division of Infectious Diseases, School of Public Health University of California, Berkeley 140, Warren Hall, Berkeley, CA 94720, USA
| | - John M Colford
- Division of Epidemiology, School of Public Health University of California, Berkeley 140, Warren Hall, Berkeley, CA 94720, USA
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43
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Broccolo F, Scarpellini P, Locatelli G, Zingale A, Brambilla AM, Cichero P, Sechi LA, Lazzarin A, Lusso P, Malnati MS. Rapid diagnosis of mycobacterial infections and quantitation of Mycobacterium tuberculosis load by two real-time calibrated PCR assays. J Clin Microbiol 2004; 41:4565-72. [PMID: 14532183 PMCID: PMC254334 DOI: 10.1128/jcm.41.10.4565-4572.2003] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sensitive and specific techniques to detect and identify Mycobacterium tuberculosis directly in clinical specimens are important for the diagnosis and management of patients with tuberculosis (TB). We developed two real-time PCR assays, based on the IS6110 multicopy element and on the senX3-regX3 intergenic region, which provide a rapid method for the diagnosis of mycobacterial infections. The sensitivity and specificity of both assays were established by using purified DNA from 71 clinical isolates and 121 clinical samples collected from 83 patients, 20 of whom were affected by TB. Both assays are accurate, sensitive, and specific, showing a complementary pattern of Mycobacterium recognition: broader for the IS6110-based assay and restricted to the M. tuberculosis complex for the senX3-regX3-based assay. Moreover, the addition of a synthetic DNA calibrator prior to DNA extraction allowed us to measure the efficiency of DNA recovery and to control for the presence of PCR inhibitors. The mycobacterial burden of the clinical samples, as assessed by direct microscopy, correlates with the M. tuberculosis DNA load measured by the senX3-regX3-based assay. In addition, reduced levels of M. tuberculosis DNA load are present in those patients subjected to successful therapy, suggesting a potential use of this assay for monitoring treatment efficacy. Therefore, these assays represent a fully controlled high-throughput system for the evaluation of mycobacterial burden in clinical specimens.
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44
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PCR and Diagnosis of Tuberculosis. Tuberculosis (Edinb) 2004. [DOI: 10.1007/978-3-642-18937-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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45
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Sarmiento OL, Weigle KA, Alexander J, Weber DJ, Miller WC. Assessment by meta-analysis of PCR for diagnosis of smear-negative pulmonary tuberculosis. J Clin Microbiol 2003; 41:3233-40. [PMID: 12843069 PMCID: PMC165327 DOI: 10.1128/jcm.41.7.3233-3240.2003] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We conducted a meta-analysis to assess the performance of PCR for the diagnosis of smear-negative pulmonary tuberculosis (SPT) and to identify factors that account for differences in the diagnostic accuracy of different studies. Studies published before February 2002 were included if sensitivity and specificity of PCR in smear-negative respiratory or gastric-aspirate specimens could be calculated. Analysis was conducted by using summary receiver operating characteristics models. Sensitivity and specificity ranged from 9 to 100% and from 25 to 100%, respectively. Fewer than 40% of the 50 studies reported results by number of patients, reported clinical characteristics of patients, or used as a reference standard combined culture and clinical criteria. Studies that included bronchial specimens showed higher accuracy than studies that evaluated only sputum specimens or included gastric aspirates. Studies that did not report that tests were applied blindly showed higher accuracy than those reporting blind testing. Increased sensitivity due to the use of DNA purification methods was associated with decreased specificity. Studies published after 1995, using Amplicor or dUTP-UNG, were associated with an increase in specificity at the expense of lower sensitivity. We concluded that PCR is not consistently accurate enough to be routinely recommended for the diagnosis of SPT. However, PCR of bronchial specimens could be useful in highly suspicious SPT cases. Studies not reporting blind testing are likely to overestimate accuracy of PCR. Future evaluation of PCR accuracy should be conducted by patient and type of respiratory specimen, blindly, by using a reference standard that combines culture and clinical criteria and addresses the issue of how patient characteristics affect PCR accuracy.
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Affiliation(s)
- Olga L Sarmiento
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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46
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LaRosa JA, Cutaia M. Urban Tuberculosis: The New Face of an Old Problem. Curr Infect Dis Rep 2003; 5:246-253. [PMID: 12760823 DOI: 10.1007/s11908-003-0080-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) persists as a worldwide health crisis. Nearly one third of the world's population is infected with TB and it remains a critical public health issue. In the past two decades, international efforts have focused on improving identification of those infected with TB as well as supporting molecular microbiologists in developing better diagnostic techniques. Furthermore, implementation of programs such as directly observed therapy have assisted more patients in receiving and completing therapy. This review aims to identify some of the more relevant findings in the field of TB over the past few years with a special emphasis on TB in urban communities.
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Affiliation(s)
- Jennifer A. LaRosa
- Chief, Pulmonary & Critical Care, NY Harbor Health Care System, Brooklyn Campus, 800 Poly Place, Brooklyn, NY 11209-7104, USA.
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47
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Murdoch DR. Nucleic acid amplification tests for the diagnosis of pneumonia. Clin Infect Dis 2003; 36:1162-70. [PMID: 12715312 DOI: 10.1086/374559] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2002] [Accepted: 01/22/2003] [Indexed: 11/03/2022] Open
Abstract
Molecular diagnostic techniques, such as polymerase chain reaction (PCR), are promising tools for the rapid etiological diagnosis of pneumonia. PCR offers potential advantages over conventional tests for the detection of Mycoplasma pneumoniae, Legionella species, and Chlamydia pneumoniae. For pneumococcal pneumonia in adults, PCR adds little to existing diagnostic tests and is unable to distinguish pneumococcal colonization from infection when testing respiratory samples. Although PCR is probably more sensitive than are conventional microscopy-based methods for diagnosing Pneumocystis carinii pneumonia, the specificity is uncertain, because P. carinii can occasionally be detected in the absence of clinical symptoms. PCR is useful for the diagnosis of viral pneumonia in immunocompromised patients. Further work is required to better characterize the role of PCR versus the role of other tests for diagnosing pneumonia and to develop standard PCR assays that can be readily adopted by routine diagnostic laboratories.
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Affiliation(s)
- David R Murdoch
- Microbiology Unit, Canterbury Health Laboratories, and Department of Pathology, Christchurch School of Medicine and Health Sciences, Christchurch, New Zealand.
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48
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Saves I, Lewis LA, Westrelin F, Warren R, Daffé M, Masson JM. Specificities and functions of the recA and pps1 intein genes of Mycobacterium tuberculosis and application for diagnosis of tuberculosis. J Clin Microbiol 2002; 40:943-50. [PMID: 11880421 PMCID: PMC120251 DOI: 10.1128/jcm.40.3.943-950.2002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The worldwide recrudescence of tuberculosis and the widespread appearance of antibiotic resistance have strengthened the need for rapid and specific diagnostic tools. The prevailing microbiological identification of Mycobacterium tuberculosis, the causative agent of tuberculosis, which implies the use of in vitro cultures and acid-fast staining microscopy, is time-consuming. Detection of M. tuberculosis directly in clinical samples through PCR amplification of mycobacterium-specific genes, designed to shorten diagnostic delay, demonstrated reliability and high sensitivity. However, the quality of the diagnosis depends on the specificity of the target sequence for M. tuberculosis complex strains. In the present study, we demonstrated the specificity of recA and pps1 inteins for this complex and thus the feasibility of using intein-coding sequences as a new target for PCR diagnosis. Indeed, the recA and pps1 genes of 36 clinical isolates of M. tuberculosis and 10 field strains of M. bovis were found to be interrupted by an intein sequence at the RecA-a and Pps1-b sites, respectively, while a large number of nontuberculous mycobacterial species failed to demonstrate these insertions. Besides, the MtuPps1, which was cloned and expressed in Escherichia coli, was shown to possess an endonuclease activity. The intein cleaves the 40-bp sequence spanning the intein insertion site Pps1-b in the inteinless pps1 gene. In addition to the PCR amplification of recA and pps1 intein genes as a tool for diagnosis, the specific endonuclease activity could represent a new molecular approach to identify M. tuberculosis.
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Affiliation(s)
- Isabelle Saves
- Institut de Pharmacologie et Biologie Structurale (UMR5089), CNRS/Université Paul Sabatier Toulouse III, France.
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49
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Landowski CP, Godfrey HP, Bentley-Hibbert SI, Liu X, Huang Z, Sepulveda R, Huygen K, Gennaro ML, Moy FH, Lesley SA, Haak-Frendscho M. Combinatorial use of antibodies to secreted mycobacterial proteins in a host immune system-independent test for tuberculosis. J Clin Microbiol 2001; 39:2418-24. [PMID: 11427548 PMCID: PMC88164 DOI: 10.1128/jcm.39.7.2418-2424.2001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Laboratory diagnosis of tuberculosis is often difficult. Immunodetection of circulating Mycobacterium tuberculosis proteins shed during active infection would not depend on an intact host immune response and could take advantage of the speed and low costs afforded by antibody-based assays. We previously showed that patients with active tuberculosis had increased levels of circulating antigen 85 (Ag85) proteins independent of their tuberculin skin test status (S. I. Bentley-Hibbert, X. Quan, T. Newman, K. Huygen, and H. P. Godfrey, Infect. Immun. 67:581-588, 1999). To extend these observations to a Mycobacterium bovis BCG-vaccinated population and to another secreted mycobacterial protein, Ag85 and PstS-1 (protein antigen B, p38 antigen) were quantified in sera from 97 Chilean tuberculosis patients and healthy controls (many of whom had received BCG as children) using dot immunobinding, mouse monoclonal anti-BCG Ag85 complex antibody, and chicken antipeptide antibodies reactive with M. tuberculosis Ag85B and PstS-1. The latter antibodies had been raised to peptide-derived immunogens expressed on a novel proprietary protein carrier in Escherichia coli. Median serum Ag85 levels measured by using either anti-Ag85 antibody were significantly higher in patients with active tuberculosis than in healthy controls (P, <0.001 to 0.01); the median serum PstS-1 levels were similar in patients and controls. The sensitivity of significantly elevated circulating Ag85 levels in patients with pulmonary tuberculosis measured by anti-Ag85 complex or anti-Ag85B antibodies was 60 and 55%, respectively, but increased to 77% when results obtained with both anti-Ag85 antibodies were considered jointly (P < 0.02). The corresponding specificities for individual and joint consideration were 95, 85, and 80%, respectively. These results indicate that elevated Ag85 levels can be detected in patients with active tuberculosis even after BCG vaccination and suggest that combinatorial use of antibodies directed at different epitopes of this protein could provide a viable strategy for developing new host immune response-independent diagnostic tests for tuberculosis.
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Affiliation(s)
- C P Landowski
- Immunology and Neurobiology R & D, Promega Corporation, Madison, Wisconsin 53711, USA
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50
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Abstract
AbstractTuberculosis is one of the leading infectious diseases in the world and is responsible for more than 2 million deaths and 8 million new cases annually. Because of the slow growth rate of the causative agent Mycobacterium tuberculosis, isolation, identification, and drug susceptibility testing of this organism and other clinically important mycobacteria can take several weeks or longer. During the past several years, many molecular methods have been developed for direct detection, species identification, and drug susceptibility testing of mycobacteria. These methods can potentially reduce the diagnostic time from weeks to days. Currently, two nucleic acid amplification methods, the Enhanced Mycobacterium tuberculosis Direct Test (Gen-Probe) and the Amplicor Mycobacterium tuberculosis Test (Roche Diagnostic Systems), have been approved by the Food and Drug Administration for direct detection of M. tuberculosis from clinical specimens. PCR-based sequencing has become commonly used to identify many mycobacterial species. DNA probes have been widely used for species determination of the most commonly encountered mycobacteria. High-density oligonucleotide arrays (DNA microarrays) also have been applied to simultaneous species identification and detection of mutations that confer rifampin resistance in mycobacteria.
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Affiliation(s)
- Hanna Soini
- Department of Pathology, Baylor College of Medicine, Houston, TX 77030
- Mycobacterial Reference Laboratory, National Public Health Institute, Kiinamyllynkatu 13, 20520 Turku, Finland
| | - James M Musser
- Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4th St., Hamilton, MT 59840
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