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Kim CH, Woo H, Hyun IG, Kim C, Choi JH, Jang SH, Park SM, Kim DG, Lee MG, Jung KS, Hyun J, Kim HS. A comparison between the efficiency of the Xpert MTB/RIF assay and nested PCR in identifying Mycobacterium tuberculosis during routine clinical practice. J Thorac Dis 2014; 6:625-31. [PMID: 24976983 DOI: 10.3978/j.issn.2072-1439.2014.04.12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/02/2014] [Indexed: 11/14/2022]
Abstract
OBJECTIVES Polymerase chain reaction (PCR) for the detection of Mycobacterium tuberculosis (MTB) is more sensitive, specific, and rapid than the conventional methods of acid-fast bacilli (AFB) smear and culture. The aim of this study was to determine if the Xpert MTB/rifampicin (RIF) assay had additional advantages over nested PCR for the detection of MTB in a geographical area with intermediate tuberculosis (TB) incidence. METHODS Between February and December 2013, the Xpert MTB/RIF assay and MTB nested PCR, as well as AFB smear and culture, were simultaneously performed on 198 clinical samples (160 pulmonary and 38 non-pulmonary specimens) collected from 171 patients hospitalized at Hallym University Medical Center for possible TB. The accuracy of the diagnosis of MTB culture-positive TB and the turnaround time of reporting laboratory results were calculated and compared. Rifampin resistance by the Xpert MTB/RIF assay was reviewed with that of conventional drug susceptibility testing (DST). RESULTS The sensitivity, specificity, and positive and negative predictive values of the Xpert MTB/RIF assay and MTB nested PCR for diagnosis of MTB culture-positive pulmonary TB were 86.1% vs. 69.4% (P=0.1563), 97.8% vs. 94.1% (P=0.2173), 91.2% vs. 75.8% (P=0.1695), and 96.4% vs. 92.0% (P=0.2032), respectively. The median turnaround times of the Xpert MTB/RIF assay and MTB nested PCR were 0 [0-4] days and 4 [1-11] days, respectively (P<0.001). Two cases of rifampin resistance, as determined by the Xpert MTB/RIF assay, were found to be multi-drug resistant (MDR) pulmonary TB by DST. CONCLUSIONS The Xpert MTB/RIF assay seemed to be sensitive, specific, and comparable to nested PCR for identifying MTB among clinically suspected TB patients, and the assay can be valuable in giving a timely identification of resistance to rifampin.
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Affiliation(s)
- Cheol-Hong Kim
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Heungjeong Woo
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - In Gyu Hyun
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Changhwan Kim
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Jeong-Hee Choi
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Seung-Hun Jang
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Sang Myeon Park
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Dong-Gyu Kim
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Myung Goo Lee
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Ki-Suck Jung
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Jeongwon Hyun
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Hyun Soo Kim
- 1 Department of Internal Medicine, 2 Lung Research Institute, 3 Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
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Luo RF, Banaei N. Molecular approaches and biomarkers for detection of Mycobacterium tuberculosis. Clin Lab Med 2014; 33:553-66. [PMID: 23931838 DOI: 10.1016/j.cll.2013.03.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Tuberculosis (TB) continues to be a public health emergency, compounded by the lack of adequate diagnostic testing in many regions of the world. New advances in the molecular detection of Mycobacterium tuberculosis, including faster and simpler nucleic acid amplification tests, have resulted in rapid and cost-effective methods to diagnose TB and test for drug resistance. Ongoing research on biomarkers for TB infection may lead to new tests for blood, urine, breath, and sputum. Sustained investment in the development and dissemination of diagnostic tests for TB is critical for increasing TB case finding, placing patients on appropriate treatment, and reducing transmission.
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Affiliation(s)
- Robert F Luo
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, L235, Stanford, CA 94305, USA.
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Potential for use of the Seegene Anyplex MTB/NTM real-time detection assay in a regional reference laboratory. J Clin Microbiol 2014; 52:1708-10. [PMID: 24554748 DOI: 10.1128/jcm.03585-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Requests for direct molecular diagnosis of mycobacterial disease are increasingly warranted. The Anyplex MTB/NTM assay demonstrates sensitivities, specificities, and positive and negative predictive values of 1.00, 0.96, 0.93, and 1.00 for Mycobacterium tuberculosis complex (MTBC) and 1.00, 0.97, 0.75, and 1.00 for nontuberculous mycobacteria (NTM) detection, respectively, making it a suitable screening test for mycobacterial detection.
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Abstract
Microscopic examination of sputum smears (search for acid-fast bacilli or AFB) is the most rapid procedure for diagnosis of contagious tuberculosis. Gene amplification is not yet reliable for direct detection of M. tuberculosis in clinical specimens that are AFB smear-negative. Culture (3 to 8 weeks on Lowenstein-Jensen medium or 1 to 4 weeks in liquid media) remains essential to identify AFB and conduct antibiotic susceptibility testing. AFB from culture can be identified in a few hours by molecular approaches with specific DNA probes. Results of susceptibility testing, even in liquid media, are not available until 2 to 4 weeks after the recovery of specimens, although mutations of the rpoB and katG 315 genes, which confer resistance to rifampin and isoniazid, can be detected within hours by molecular hybridization with specific probes fixed on strips. Immunologic tests that measure the interferon gamma produced by sensitized lymphocytes are promising tools for the diagnosis of latent tuberculosis.
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Affiliation(s)
- Chantal Truffot-Pernot
- Laboratoire de bactériologie-hygiène, Centre national de référence mycobactéries et résistance des mycobactéries aux antituberculeux, Paris (75).
| | - Nicolas Véziris
- Laboratoire de bactériologie-hygiène, Centre national de référence mycobactéries et résistance des mycobactéries aux antituberculeux, Paris (75)
| | - Wladimir Sougakoff
- Laboratoire de bactériologie-hygiène, Centre national de référence mycobactéries et résistance des mycobactéries aux antituberculeux, Paris (75)
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Greco S, Girardi E, Navarra A, Saltini C. Current evidence on diagnostic accuracy of commercially based nucleic acid amplification tests for the diagnosis of pulmonary tuberculosis. Thorax 2006; 61:783-90. [PMID: 16738037 PMCID: PMC2117107 DOI: 10.1136/thx.2005.054908] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Even though commercial nucleic acid amplification tests (NAATs) have become the most frequently used molecular tests for laboratory diagnosis of pulmonary tuberculosis (TB), published studies report variable estimates of their diagnostic accuracy. We analysed the accuracy of commercial NAATs for the diagnosis of pulmonary TB in smear positive and smear negative respiratory samples using culture as a reference standard. METHODS English language studies reporting data sufficient for calculating sensitivity and specificity of commercial NAATs on smear positive and/or smear negative respiratory samples were included. Meta-regression was used to analyse associations with reference test quality, the prevalence of TB, sample and test type. Predictive values for different levels of pre-test probability were quantified using Bayes' approach. RESULTS Sixty three journal articles published between 1995 and 2004 met the inclusion criteria. Pooled sensitivity and specificity were 0.96 and 0.85 among smear positive samples and 0.66 and 0.98 among smear negative samples. The number of culture media used as reference test, the inclusion of bronchial samples, and the TB prevalence were found to influence the reported accuracy. The test type had no effect on the diagnostic odds ratio but seemed to be correlated with sensitivity or specificity, probably via a threshold effect. CONCLUSIONS Commercial NAATs can be confidently used to exclude TB in patients with smear positive samples in which environmental mycobacteria infection is suspected and to confirm TB in a proportion of smear negative cases. The methodological characteristics of primary studies have a considerable effect on the reported diagnostic accuracy.
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Affiliation(s)
- S Greco
- Dipartimento di Malattie Polmonari, Azienda Ospedaliera San Camillo-Forlanini, Rome, Italy.
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Piersimoni C, Nista D, Zallocco D, Galassi M, Cimarelli ME, Tubaldi A. Clinical suspicion as a primary guidance to use commercial amplification tests for rapid diagnosis of pulmonary tuberculosis. Diagn Microbiol Infect Dis 2005; 53:195-200. [PMID: 16249062 DOI: 10.1016/j.diagmicrobio.2005.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The Abbott LCx (Abbott Park, IL) Mycobacterium tuberculosis complex is a commercial amplification assay discontinued from the European market in 2002. A prospective clinical study was carried out to evaluate the clinical utility of the above test as applied by specialists for the rapid diagnosis of active pulmonary tuberculosis (PTB). According to the physician's clinical judgment, patients were classified into 3 groups (low, intermediate, and high) aiming to estimate the probability of active disease. The gold standard for final diagnosis was based on microbiologic and clinical information including data from a 6-month follow-up period. Sensitivities and specificities of rapid microbiologic tests were compared with those based on an integrated approach including clinical evaluation plus the above tests. The incidence of PTB in 214 patients was 13.1%. The basis for initial treatment of PTB was smear-positive results in 46%, positive LCx results in 29%, and clinical suspicion in 18%. For the remaining 7%, therapy was started upon receipt of culture results. The sensitivity, specificity, and positive and negative predictive values of the LCx assay were 68%, 99%, 95%, and 95%, respectively. In comparison, they were 93%, 99%, 96%, and 99%, respectively, for the combination of clinical evaluation plus the LCx test. It is concluded that in patients with high-to-moderate pretest probabilities, the combination of clinical judgment and amplification results strongly enhances a rapid and correct diagnosis of PTB.
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Affiliation(s)
- Claudio Piersimoni
- Department of Clinical Microbiology, United Hospitals, I-60020 Ancona, Italy.
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Chakravorty S, Tyagi JS. Novel multipurpose methodology for detection of mycobacteria in pulmonary and extrapulmonary specimens by smear microscopy, culture, and PCR. J Clin Microbiol 2005; 43:2697-702. [PMID: 15956385 PMCID: PMC1151876 DOI: 10.1128/jcm.43.6.2697-2702.2005] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel, robust, reproducible, and multipurpose universal sample processing (USP) methodology for highly sensitive smear microscopy, culturing on solid and liquid media, and inhibition-free PCR which is suitable for the laboratory diagnosis of both pulmonary and extrapulmonary tuberculosis (TB) has been developed. This method exploits the chaotropic properties of guanidinium hydrochloride for sample processing and involves incubating the specimen with USP solution, concentrating bacilli by centrifugation, and using the processed specimen for smear microscopy, culture, and PCR. The detection limit for acid-fast bacilli in spiked sputum by smear microscopy is approximately 300 bacilli per ml of specimen. USP solution-treated specimens are fully compatible with culturing on solid and liquid media. High-quality, PCR-amplifiable mycobacterial DNA can be isolated from all types of clinical specimens processed with USP solution. The method has been extensively validated with both pulmonary and extrapulmonary specimens. Furthermore, the USP method is also compatible with smear microscopy, culture, and PCR of mycobacteria other than tubercle bacilli. In summary, the USP method provides smear microscopy, culture, and nucleic acid amplification technologies with a single sample-processing platform and, to the best of our knowledge, is the only method of its kind described to date. It is expected to be useful for the laboratory diagnosis of TB and other mycobacterial diseases by conventional and modern methods.
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Affiliation(s)
- Soumitesh Chakravorty
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
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Lemaître N, Armand S, Vachée A, Capilliez O, Dumoulin C, Courcol RJ. Comparison of the real-time PCR method and the Gen-Probe amplified Mycobacterium tuberculosis direct test for detection of Mycobacterium tuberculosis in pulmonary and nonpulmonary specimens. J Clin Microbiol 2004; 42:4307-9. [PMID: 15365029 PMCID: PMC516309 DOI: 10.1128/jcm.42.9.4307-4309.2004] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Real-time PCR was compared to Amplified Mycobacterium tuberculosis Direct Test (AMTDII) for 100 clinical specimens. The overall sensitivities of the real-time PCR method and AMTDII were similar for respiratory and nonrespiratory specimens. However, real-time PCR seemed to be less susceptible to amplification inhibitors than AMTDII.
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Affiliation(s)
- Nadine Lemaître
- Laboratoire de Bactériologie-Hygiène, Centre Hospitalier Régional Universitaire de Lille, France.
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Jarlier V, Cambau E, Sougakoff W. [What are the new diagnostic tools in tuberculosis? What is their role in disease management and what are their indications? Gene amplification tests]. Rev Mal Respir 2004; 21:S36-43. [PMID: 15344268 DOI: 10.1016/s0761-8425(04)71383-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- V Jarlier
- Laboratoire de Bactériologie-Hygiène, Groupe Hospitalier Pitié-Salpêtrière et Centre National de Référence de la Résistance des Mycobactéries aux Antituberculeux, Paris, France.
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Patzina RA, de Andrade HF, de Brito T, Filho HC, Kauffman MR, Pagliari C, Lucena A, Ribeiro da Matta VL, Seixas Duarte MI. Molecular and standard approaches to the diagnosis of mycobacterial granulomatous lymphadenitis in paraffin-embedded tissue. J Transl Med 2002; 82:1095-7. [PMID: 12177248 DOI: 10.1097/01.lab.0000024364.02049.b7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Rosely Antunes Patzina
- Departamento de Patologia da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brazil.
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Lim TK, Gough A, Chin NK, Kumarasinghe G. Relationship between estimated pretest probability and accuracy of automated Mycobacterium tuberculosis assay in smear-negative pulmonary tuberculosis. Chest 2000; 118:641-7. [PMID: 10988184 DOI: 10.1378/chest.118.3.641] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND The AMPLICOR assay (Roche; Branchburg, NJ), a rapid direct amplification test for Mycobacterium tuberculosis, has only been licensed for use in smear-positive respiratory specimens. However, many patients with pulmonary tuberculosis (PTB) have smear-negative disease. The clinical utility of this test in patients with smear-negative PTB is unknown. OBJECTIVE To evaluate the effect of pretest probability of PTB estimated by chest physicians on the accuracy of the AMPLICOR assay in patients with smear-negative PTB. DESIGN AND METHODS A prospective study of consecutive patients suspected of having smear-negative PTB. Two chest physicians estimated the pretest probability of active disease (high, intermediate, and low categories). Respiratory specimens were examined with radiometric broth medium cultures and with the AMPLICOR assay for M tuberculosis. The decision on a final diagnosis of PTB was blinded to the AMPLICOR results. RESULTS Active PTB was diagnosed in 25 of 441 patients (5.7%). The AMPLICOR assay had an overall sensitivity of 44% and a specificity of 99%. Results of the assay were negative in seven patients with culture-negative PTB. The proportions of patients in the high, intermediate, and low pretest groups were 4.5%, 19.7%, and 75.7%, respectively. The incidence of PTB for each group was 95%, 3.4%, and 0.9%, respectively. The sensitivities of the AMPLICOR assay in the three groups of patients were 47%, 33%, and 33%, respectively, while the specificities were 100%, 98%, and 99%, respectively. CONCLUSIONS In patients suspected of having smear-negative PTB, the following conclusions were drawn: (1) the incidence of active PTB was low; (2) pretest estimates accurately discriminated between patients with high and low risk of PTB; (3) the risk of PTB was overestimated in the intermediate group; and (4) the utility of the AMPLICOR assay in the intermediate-risk group may be limited by the overestimation of disease prevalence and low test sensitivity. Further studies are needed on the role of the AMPLICOR assay in better selected patients with an intermediate risk of having smear-negative PTB.
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Affiliation(s)
- T K Lim
- Department of Medicine, National University Hospital, Lower Kent Ridge Road, Singapore.
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Cambau E, Wichlacz C, Truffot-Pernot C, Jarlier V. Evaluation of the new MB redox system for detection of growth of mycobacteria. J Clin Microbiol 1999; 37:2013-5. [PMID: 10325366 PMCID: PMC85013 DOI: 10.1128/jcm.37.6.2013-2015.1999] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We evaluated a new mycobacterial culture system, MB Redox, for recovery rate and time to detection of mycobacteria from 742 consecutive respiratory specimens and compared the results to those found with Löwenstein-Jensen (LJ) medium. Twenty specimens (2.7%) were positive for M. tuberculosis: 17 on LJ medium and 19 in MB Redox, with 16 specimens positive in both media. In addition, 24 specimens (3.2%) were positive for nontuberculous mycobacteria (NTM), 20 on LJ medium, 18 in MB Redox, and 14 in both media. For M. tuberculosis, the mean times to detection were 28.9 days on LJ medium and 23.6 days in MB Redox, and for NTM, the mean times to detection were 40.6 days on LJ medium and 32.3 days in MB Redox.
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Affiliation(s)
- E Cambau
- Laboratoire de Bactériologie-Hygiène, Groupe Hospitalier Pitié-Salpêtrière, 75651 Paris Cedex 13, France.
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