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Baudel JL, Tankovic J, Dahoumane R, Carrat F, Galbois A, Ait-Oufella H, Offenstadt G, Guidet B, Maury E. Multiplex PCR performed of bronchoalveolar lavage fluid increases pathogen identification rate in critically ill patients with pneumonia: a pilot study. Ann Intensive Care 2014; 4:35. [PMID: 25593751 PMCID: PMC4273674 DOI: 10.1186/s13613-014-0035-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 10/31/2014] [Indexed: 12/31/2022] Open
Abstract
Background In critically ill patients with pneumonia, accurate microorganism identification allows appropriate antibiotic treatment. In patients undergoing bronchoalveolar lavage (BAL), direct examination of the fluid using Gram staining provides prompt information but pathogen identification accuracy is low. Culture of BAL fluid is actually the reference, but it is not available before 24 to 48 h. In addition, pathogen identification rate observed with direct examination and culture is decreased when antibiotic therapy has been given prior to sampling. We therefore assessed, in critically ill patients with suspected pneumonia, the performance of a multiplex PCR (MPCR) to identify pathogens in BAL fluid. This study is a prospective pilot observation. Methods We used a MPCR detecting 20 types of microorganisms. Direct examination, culture, and MPCR were performed on BAL fluid of critically ill patients with pneumonia suspicion. The final diagnosis of infective pneumonia was retained after the medical chart was reviewed by two experts. Pathogen identification rate of direct examination, culture, and MPCR in patients with confirmed pneumonia was compared. Results Among the 65 patients with pneumonia suspicion, the diagnosis of pneumonia was finally retained in 53 cases. Twenty nine (55%) were community-acquired pneumonia and 24 (45%) were hospital acquired. Pathogen identification rate with MPCR (66%) was greater than with culture (40%) and direct examination (23%) (p =0.01 and p <0.001, respectively). When considering only the microorganisms included in the MPCR panel, the pathogen identification rate provided by MPCR reached 82% and was still higher than with culture (35%, p <0.001) and direct examination (21%, p <0.001). Pathogen identification rate provided by MPCR was not modified in the case of previous antibiotic treatment (66% vs. 64%, NS) and was still better than with culture (23%, p <0.001). Conclusions The results of this pilot study suggest that in critically ill patients, MPCR performed on BAL fluid could provide higher identification rate of pathogens involved in pneumonia than direct examination and culture, especially in patients having received antimicrobial treatment.
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Affiliation(s)
- Jean-Luc Baudel
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Saint-Antoine, Service de Réanimation Médicale, Paris 75012, France
| | - Jacques Tankovic
- AP-HP, Hôpital Saint-Antoine, Service de Microbiologie, Paris 75012, France
| | - Redouane Dahoumane
- AP-HP, Hôpital Saint-Antoine, Service de Microbiologie, Paris 75012, France
| | - Fabrice Carrat
- Inserm, UMR 707, Paris 75012, France ; UPMC - Université Paris 06, Paris 75012, France
| | - Arnaud Galbois
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Saint-Antoine, Service de Réanimation Médicale, Paris 75012, France
| | - Hafid Ait-Oufella
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Saint-Antoine, Service de Réanimation Médicale, Paris 75012, France ; UPMC - Université Paris 06, Paris 75012, France
| | - Georges Offenstadt
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Saint-Antoine, Service de Réanimation Médicale, Paris 75012, France ; Inserm, UMR 707, Paris 75012, France ; UPMC - Université Paris 06, Paris 75012, France
| | - Bertrand Guidet
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Saint-Antoine, Service de Réanimation Médicale, Paris 75012, France ; Inserm, UMR 707, Paris 75012, France ; UPMC - Université Paris 06, Paris 75012, France
| | - Eric Maury
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Saint-Antoine, Service de Réanimation Médicale, Paris 75012, France ; Inserm, UMR 707, Paris 75012, France ; UPMC - Université Paris 06, Paris 75012, France
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Shinnick TM, Starks AM, Alexander HL, Castro KG. Evaluation of the Cepheid Xpert MTB/RIF assay. Expert Rev Mol Diagn 2014; 15:9-22. [PMID: 25373876 DOI: 10.1586/14737159.2015.976556] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The lack of capacity to provide laboratory confirmation of a diagnosis of tuberculosis disease (TB) is contributing to enormous gaps in the ability to find, treat and follow TB patients. WHO estimates that globally only about 57% of the notified new cases of pulmonary TB in 2012 and about 19% of rifampicin-resistant TB cases were laboratory confirmed. The Cepheid Xpert(®) MTB/RIF assay has been credited with revolutionizing laboratory testing to aid in the diagnosis of TB and rifampicin-resistant TB. This semi-automated test can detect both the causative agent of TB and mutations that confer rifampicin resistance from clinical specimens within 2 h after starting the test. In this article, we review the performance of the test, its pathway to regulatory approval and endorsement, guidelines for its use and lessons learned from the implementation of the test in low-burden, high-resource countries and in high-burden, low-resource countries.
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Affiliation(s)
- Thomas M Shinnick
- Division of Tuberculosis Elimination, National Center for HIV, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA 30333
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Tzeng A, Tzeng TH, Vasdev S, Korth K, Healey T, Parvizi J, Saleh KJ. Treating periprosthetic joint infections as biofilms: key diagnosis and management strategies. Diagn Microbiol Infect Dis 2014; 81:192-200. [PMID: 25586931 DOI: 10.1016/j.diagmicrobio.2014.08.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 08/19/2014] [Accepted: 08/22/2014] [Indexed: 12/23/2022]
Abstract
Considerable evidence suggests that microbial biofilms play an important role in periprosthetic joint infection (PJI) pathogenesis. Compared to free-floating planktonic bacteria, biofilm bacteria are more difficult to culture and possess additional immune-evasive and antibiotic resistance mechanisms, making infections harder to detect and eradicate. This article reviews cutting-edge advances in biofilm-associated infection diagnosis and treatment in the context of current PJI guidelines and highlights emerging technologies that may improve the efficacy and reduce costs associated with PJI. Promising PJI diagnostic tools include culture-independent methods based on sequence comparisons of the bacterial 16S ribosomal RNA gene, which offer higher throughput and greater sensitivity than culture-based methods. For therapy, novel methods based on disrupting biofilm-specific properties include quorum quenchers, bacteriophages, and ultrasound/electrotherapy. Since biofilm infections are not easily detected or treated by conventional approaches, molecular diagnostic techniques and next-generation antibiofilm treatments should be integrated into PJI clinical practice guidelines in the near future.
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Affiliation(s)
- Alice Tzeng
- Koch Institute for Integrative Cancer Research, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tony H Tzeng
- Division of Orthopaedics and Rehabilitation, Department of Surgery, Southern Illinois University School of Medicine, Springfield, IL 62794-9679, USA
| | - Sonia Vasdev
- Division of Orthopaedics and Rehabilitation, Department of Surgery, Southern Illinois University School of Medicine, Springfield, IL 62794-9679, USA
| | - Kyle Korth
- Rush University Medical College, Chicago, IL 60612, USA
| | - Travis Healey
- Division of Orthopaedics and Rehabilitation, Department of Surgery, Southern Illinois University School of Medicine, Springfield, IL 62794-9679, USA
| | - Javad Parvizi
- Department of Orthopaedics, Rothman Institute, Thomas Jefferson University Hospital, Philadelphia, PA 19107, USA
| | - Khaled J Saleh
- Division of Orthopaedics and Rehabilitation, Department of Surgery, Southern Illinois University School of Medicine, Springfield, IL 62794-9679, USA.
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Diagnostic value of GeneChip for detection of resistant Mycobacterium tuberculosis in patients with differing treatment histories. J Clin Microbiol 2014; 53:131-5. [PMID: 25355771 DOI: 10.1128/jcm.02283-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The increasing burden of drug-resistant tuberculosis (TB) poses an escalating threat to national TB control programs. To assist appropriate treatment for TB patients, accurate and rapid detection of drug resistance is critical. The GeneChip test is a novel molecular tool for the diagnosis of TB drug resistance. Performance-related data on GeneChip are limited, and evaluation in new and previously treated TB cases has never been performed. We evaluated the diagnostic performance of GeneChip in detecting resistance to rifampin (RMP) and isoniazid (INH) and in detecting multidrug-resistant tuberculosis (MDR-TB) in comparison with standard drug susceptibility testing (DST) and compared the results in a group of previously treated and newly detected TB patients in an urban area in southeastern China. One thousand one hundred seventy-three (83.8%) new cases and 227 (16.2%) previously treated cases were collected between January 2011 and September 2013. The GeneChip showed a specificity of 97.8% and a sensitivity of 94.8% for detection of RMP resistance and 97.3% and 70.9%, respectively, for INH resistance in new cases. For previously treated cases, the overall sensitivity, specificity, and agreement rate are 94.6%, 91.3%, and 92.1%, respectively, for detection of RMP resistance and 69.7%, 95.4%, and 86.8%, respectively, for INH resistance. The sensitivity and specificity of MDR-TB were 81.8% and 99.0% in new cases and 77.8% and 93.4% in previously treated cases, respectively. The GeneChip system provides a simple, rapid, reliable, and accurate clinical assay for the detection of TB drug resistance, and it is a potentially important diagnostic tool in a high-prevalence area.
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Clinical utility of a novel molecular assay in various combination strategies with existing methods for diagnosis of HIV-related tuberculosis in Uganda. PLoS One 2014; 9:e107595. [PMID: 25222866 PMCID: PMC4164637 DOI: 10.1371/journal.pone.0107595] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 08/14/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Low income, high-tuberculosis burden, countries are considering selective deployment of Xpert MTB/RIF assay (Xpert) due to high cost per test. We compared the diagnostic gain of the Xpert add-on strategy with Xpert replacement strategy for pulmonary tuberculosis diagnosis among HIV-infected adults to inform its implementation. METHODS The first diagnostic sputum sample of 424 HIV-infected adults (67% with CD4 counts ≤200/mm3) suspected for tuberculosis was tested by direct Ziehl-Neelsen (DZN) and direct fluorescent microscopy (DFM); concentrated fluorescent microscopy (CFM); Lowenstein-Jensen (LJ) and Mycobacterial Growth Indicator Tube (MGIT) culture; and Xpert. Overall diagnostic yield and sensitivity were calculated using MGIT as reference comparator. The sensitivity of Xpert in an add-on strategy was calculated as the number of smear negative but Xpert positive participants among MGIT positive participants. RESULTS A total of 123 (29.0%) participants were MGIT culture positive for Mycobacterium tuberculosis. The sensitivity (95% confidence interval) was 31.7% (23.6-40.7%) for DZN, 35.0% (26.5-44.0%) for DFM, 43.9% (34.9-53.1%) for CFM, 76.4% (67.9-83.6) for Xpert and 81.3% (73.2-87.7%) for LJ culture. Add-on strategy Xpert showed an incremental sensitivity of 44.7% (35.7-53.9%) when added to DZN, 42.3% (33.4-51.5%) to DFM and 35.0% (26.5-44.0%) to CFM. This translated to an overall sensitivity of 76.4%, 77.3% and 79.0% for add-on strategies based on DZN, DFM and CFM, respectively, compared to 76.4% for Xpert done independently. From replacement to add-on strategy, the number of Xpert cartridges needed was reduced by approximately 10%. CONCLUSIONS Among HIV-infected TB suspects, doing smear microscopy prior to Xpert assay in add-on fashion only identifies a few additional TB cases.
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Mboowa G, Namaganda C, Ssengooba W. Rifampicin resistance mutations in the 81 bp RRDR of rpoB gene in Mycobacterium tuberculosis clinical isolates using Xpert® MTB/RIF in Kampala, Uganda: a retrospective study. BMC Infect Dis 2014; 14:481. [PMID: 25190040 PMCID: PMC4164707 DOI: 10.1186/1471-2334-14-481] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 09/02/2014] [Indexed: 11/15/2022] Open
Abstract
Background Introduction of Xpert® MTB/RIF assay has revolutionalised the diagnosis of tuberculosis (TB) by simultaneously detecting the bacteria and resistance to rifampicin (rif), a surrogate marker for multi-drug resistant TB (MDR-TB) as well as one of the principal first-line anti-tuberculosis drugs. In general, rpoB mutations can be found in 96.1% of rif-resistant Mycobacterium tuberculosis (MTB) strains worldwide and these mutations usually are located in a region at the 507-533rd amino acid residuals (81 bp) in the MTB rpoB gene, which is referred to as Rifampicin-resistance-determining region (RRDR). In this study, we determined the frequency of MDR-TB in Kampala using Xpert® MTB/RIF in comparison with the agar proportion method using Middlebrook 7H11and further determined the frequency of probes for different rpoB gene mutations using Xpert® MTB/RIF assay in the 81 bp RRDR. Methods A total of 1501 specimens received at Mycobacteriology laboratory, Makerere University for Xpert testing between May 2011 and May 2014 were analysed by Xpert® MTB/RIF assay. Specimens that were positive for both MTB and rifampicin resistance were further subjected to a complete first line anti-mycobacterial drug susceptibility testing using Middlebrook 7H11 agar proportion method (APM). Results Xpert® MTB/RIF assay detected 313 MTB positive specimens and out of which 12 specimens had both MTB and rifampicin- resistance conferred by four different rpoB gene mutations in the 81 bp-RRDR of MTB, further one (1/12), specimen was found to be rifampicin mono-resistant on APM while the 11 were found to be MDR-TB. Probes associated with the observed rif- resistance were as follows: E (7/12), B (3/12), A (1/12), D (1/12) and no rif-resistance was associated with probe C. No specimen yielded rif-resistance associated with more than one probe failure (mutation combinations). Probe D was associated with rifampicin mono-resistant. Conclusions MDR-TB was at 3.5% in the studied population. Mutations associated with Probe E (58%) also known as codons 531and 533 are the commonest rpoB gene mutation identified by Xpert® MTB/RIF assay in this setting and mutations identified by probe E of the assay, turned out to be MDR-TB strains by agar proportion method antimicrobial susceptibility testing. No mutation was detected in the codon 522. Electronic supplementary material The online version of this article (doi:10.1186/1471-2334-14-481) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gerald Mboowa
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, P,O Box 7072, Kampala, Uganda.
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Le Palud P, Cattoir V, Malbruny B, Magnier R, Campbell K, Oulkhouir Y, Zalcman G, Bergot E. Retrospective observational study of diagnostic accuracy of the Xpert® MTB/RIF assay on fiberoptic bronchoscopy sampling for early diagnosis of smear-negative or sputum-scarce patients with suspected tuberculosis. BMC Pulm Med 2014; 14:137. [PMID: 25115239 PMCID: PMC4137109 DOI: 10.1186/1471-2466-14-137] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 07/01/2014] [Indexed: 01/22/2023] Open
Abstract
Background Fiberoptic bronchoscopy (FOB) is a useful diagnosis tool in low-burden countries for patients with suspected pulmonary tuberculosis (TB) who are smear-negative or sputum-scarce. This study sought to determine the accuracy of the Xpert® MTB/RIF (XP) assay using FOB samples. Methods We retrospectively reviewed clinical, radiological, and microbiological characteristics of 175 TB-suspected patients requiring diagnostic FOB (bronchial aspirate or bronchoalveolar lavage) with XP assay. Polymerase chain reaction (PCR) and smear microscopy (SM) performances were first compared to culture, then to the final diagnosis, established based on clinical or radiological evolution when cultures were negative. Results Of the total 162 included patients, 30 (18.5%) had a final diagnosis of pulmonary TB, with positive cultures reported in 23. As compared to culture, sensitivity and specificity values were 80.0% and 98.6% for the XP assay, and 25.0% and 95.8% for SM, respectively. As compared to final diagnosis, the corresponding performance values were 60.0% and 100.0% for the XP assay, and 16.7% and 95.5% for SM, respectively. The sensitivity of the XP assay was significantly higher than that of SM in both cases (p = 0.003 and p = 0.001). Concerning the final diagnosis, both XP assay and culture sensitivities were similar (60% vs. 66.7%). PCR assay enabled pulmonary TB to be diagnosed earlier in 13 more cases, compared to SM. Conclusion Our study has confirmed the clinical benefits provided by XP assay compared to SM for the early diagnosis of suspected pulmonary TB cases requiring FOB, on per procedure samples, especially in a low TB-burden country.
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Affiliation(s)
| | | | | | | | | | | | | | - Emmanuel Bergot
- CHU de Caen, Service de Pneumologie et Oncologie thoracique, Caen, F-14000, France.
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Barletta F, Vandelannoote K, Collantes J, Evans CA, Arévalo J, Rigouts L. Standardization of a TaqMan-based real-time PCR for the detection of Mycobacterium tuberculosis-complex in human sputum. Am J Trop Med Hyg 2014; 91:709-14. [PMID: 25114009 DOI: 10.4269/ajtmh.13-0603] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Real-time polymerase chain reaction (qPCR) was optimized for detecting Mycobacterium tuberculosis in sputum. Sputum was collected from patients (N = 112) with suspected pulmonary tuberculosis, tested by smear microscopy, decontaminated, and split into equal aliquots that were cultured in Löwenstein-Jensen medium and tested by qPCR for the small mobile genetic element IS6110. The human ERV3 sequence was used as an internal control. 3 of 112 (3%) qPCR failed. For the remaining 109 samples, qPCR diagnosed tuberculosis in 79 of 84 patients with culture-proven tuberculosis, and sensitivity was greater than microscopy (94% versus 76%, respectively, P < 0.05). The qPCR sensitivity was similar (P = 0.9) for smear-positive (94%, 60 of 64) and smear-negative (95%, 19 of 20) samples. The qPCR was negative for 24 of 25 of the sputa with negative microscopy and culture (diagnostic specificity 96%). The qPCR had 99.5% sensitivity and specificity for 211 quality control samples including 84 non-tuberculosis mycobacteria. The qPCR cost ∼5US$ per sample and provided same-day results compared with 2-6 weeks for culture.
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Affiliation(s)
- Francesca Barletta
- Instituto de Medicina Tropical Alexander von Humboldt, Lima, Peru; Universidad Peruana Cayetano Heredia, Lima, Perú; Infectious Diseases and Immunity, Imperial College London, and Wellcome Trust Imperial College Centre for Global Health, London,United Kingdom; IFHAD: Innovation For Health And Development, London, United Kingdom; Institute of Tropical Medicine, Antwerp-Belgium; University of Antwerp, Belgium
| | - Koen Vandelannoote
- Instituto de Medicina Tropical Alexander von Humboldt, Lima, Peru; Universidad Peruana Cayetano Heredia, Lima, Perú; Infectious Diseases and Immunity, Imperial College London, and Wellcome Trust Imperial College Centre for Global Health, London,United Kingdom; IFHAD: Innovation For Health And Development, London, United Kingdom; Institute of Tropical Medicine, Antwerp-Belgium; University of Antwerp, Belgium
| | - Jimena Collantes
- Instituto de Medicina Tropical Alexander von Humboldt, Lima, Peru; Universidad Peruana Cayetano Heredia, Lima, Perú; Infectious Diseases and Immunity, Imperial College London, and Wellcome Trust Imperial College Centre for Global Health, London,United Kingdom; IFHAD: Innovation For Health And Development, London, United Kingdom; Institute of Tropical Medicine, Antwerp-Belgium; University of Antwerp, Belgium
| | - Carlton A Evans
- Instituto de Medicina Tropical Alexander von Humboldt, Lima, Peru; Universidad Peruana Cayetano Heredia, Lima, Perú; Infectious Diseases and Immunity, Imperial College London, and Wellcome Trust Imperial College Centre for Global Health, London,United Kingdom; IFHAD: Innovation For Health And Development, London, United Kingdom; Institute of Tropical Medicine, Antwerp-Belgium; University of Antwerp, Belgium
| | - Jorge Arévalo
- Instituto de Medicina Tropical Alexander von Humboldt, Lima, Peru; Universidad Peruana Cayetano Heredia, Lima, Perú; Infectious Diseases and Immunity, Imperial College London, and Wellcome Trust Imperial College Centre for Global Health, London,United Kingdom; IFHAD: Innovation For Health And Development, London, United Kingdom; Institute of Tropical Medicine, Antwerp-Belgium; University of Antwerp, Belgium
| | - Leen Rigouts
- Instituto de Medicina Tropical Alexander von Humboldt, Lima, Peru; Universidad Peruana Cayetano Heredia, Lima, Perú; Infectious Diseases and Immunity, Imperial College London, and Wellcome Trust Imperial College Centre for Global Health, London,United Kingdom; IFHAD: Innovation For Health And Development, London, United Kingdom; Institute of Tropical Medicine, Antwerp-Belgium; University of Antwerp, Belgium
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Theron G, Peter J, Calligaro G, Meldau R, Hanrahan C, Khalfey H, Matinyenya B, Muchinga T, Smith L, Pandie S, Lenders L, Patel V, Mayosi BM, Dheda K. Determinants of PCR performance (Xpert MTB/RIF), including bacterial load and inhibition, for TB diagnosis using specimens from different body compartments. Sci Rep 2014; 4:5658. [PMID: 25014250 PMCID: PMC5375978 DOI: 10.1038/srep05658] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 06/16/2014] [Indexed: 11/09/2022] Open
Abstract
The determinants of Xpert MTB/RIF sensitivity, a widely used PCR test for the diagnosis of tuberculosis (TB) are poorly understood. We compared culture time-to-positivity (TTP; a surrogate of bacterial load), MTB/RIF TB-specific and internal positive control (IPC)-specific C(T) values, and clinical characteristics in patients with suspected TB who provided expectorated (n = 438) or induced sputum (n = 128), tracheal aspirates (n = 71), bronchoalveolar lavage fluid (n = 152), pleural fluid (n = 76), cerebral spinal fluid (CSF; n = 152), pericardial fluid (n = 131), or urine (n = 173) specimens. Median bacterial load (TTP in days) was the strongest associate of MTB/RIF positivity in each fluid. TTP correlated with C(T) values in pulmonary specimens but not extrapulmonary specimens (Spearman's coefficient 0.5043 versus 0.1437; p = 0.030). Inhibition affected a greater proportion of pulmonary specimens than extrapulmonary specimens (IPC C(T) > 34: 6% (47/731) versus 1% (4/381; p < 0.0001). Pulmonary specimens had greater load than extrapulmonary specimens [TTPs (interquartile range) of 11 (7-16) versus 22 (18-33.5) days; p < 0.0001]. HIV-infection was associated with a decreased likelihood of MTB/RIF-positivity in pulmonary specimens but an increased likelihood in extrapulmonary specimens. Mycobacterial load, which displays significant variation across different body compartments, is the main determinant of MTB/RIF-positivity rather than PCR inhibition. MTB/RIF C(T) is a poor surrogate of load in extrapulmonary specimens.
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Affiliation(s)
- Grant Theron
- Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Jonny Peter
- Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Greg Calligaro
- Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Richard Meldau
- Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Colleen Hanrahan
- Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, MD, USA
| | - Hoosain Khalfey
- Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Brian Matinyenya
- Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Tapuwa Muchinga
- Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Liezel Smith
- Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Shaheen Pandie
- Division of Cardiology, Department of Medicine, Groote Schuur Hospital and University of Cape Town, South Africa
| | - Laura Lenders
- Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Vinod Patel
- Department of Neurology, University of KwaZulu Natal, South Africa
| | - Bongani M. Mayosi
- Division of Cardiology, Department of Medicine, Groote Schuur Hospital and University of Cape Town, South Africa
| | - Keertan Dheda
- Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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Patil N, Saba H, Marco A, Samant R, Mukasa L. Initial experience with GeneXpert MTB/RIF assay in the Arkansas Tuberculosis Control Program. Australas Med J 2014; 7:203-7. [PMID: 24944716 PMCID: PMC4052441 DOI: 10.4066/amj.2014.1905] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Mycobacterium tuberculosis remains one of the most significant causes of death from an infectious agent. Rapid and accurate diagnosis of pulmonary and extra-pulmonary tuberculosis (TB) is still a great challenge. The GeneXpert MTB/RIF assay is a novel integrated diagnostic system for the diagnosis of tuberculosis and rapid detection of Rifampin (RIF) resistance in clinical specimens. In 2012, the Arkansas Tuberculosis Control Program introduced GeneXpert MTB/RIF assay to replace the labour-intensive Mycobacterium Tuberculosis Direct (MTD) assay. AIMS To rapidly diagnose TB within two hours and to simultaneously detect RIF resistance. OBJECTIVES Describe the procedure used to introduce GeneXpert MTB/RIF assay in the Arkansas Tuberculosis Control Program.Characterise the current gap in rapid M. tuberculosis diagnosis in Arkansas.Assess factors that predict acid fast bacilli (AFB) smearnegative but culture-positive cases in Arkansas.Illustrate, with two case reports, the role of GeneXpert MTB/RIF assay in reduction of time to confirmation of M. tuberculosis diagnosis in the first year of implementation. METHOD Between June 2012 and June 2013, all AFB sputum smearpositive cases and any others, on request by the physician, had GeneXpert MTB/RIF assay performed as well as traditional M. tuberculosis culture and susceptibilities using Mycobacteria Growth Indicator Tube (MGIT) 960 and Löwenstein-Jensen (LJ) slants. Surveillance data for January 2009-June 2013 was analysed to characterise sputum smear-negative but culture-positive cases. RESULTS Seventy-one TB cases were reported from June 2012- June 2013. GeneXpert MTB/RIF assay identified all culture-positive cases as well as three cases that were negative on culture. Also, this rapid assay identified all six smear-negative but M. tuberculosis culture-positive cases; two of these cases are described as case reports. CONCLUSION GeneXpert MTB/RIF assay has made rapid TB diagnosis possible, with tremendous potential in determining isolation of TB suspects on one hand, and quickly ruling out TB whenever suspected.
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Affiliation(s)
- Naveen Patil
- Arkansas Department of Health
- University of Arkansas for Medical Sciences
| | | | | | | | - Leonard Mukasa
- Arkansas Department of Health
- University of Arkansas for Medical Sciences
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Real time PCR quantification of viable Mycobacterium tuberculosis from sputum samples treated with propidium monoazide. Tuberculosis (Edinb) 2014; 94:421-7. [PMID: 24863654 DOI: 10.1016/j.tube.2014.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/22/2014] [Accepted: 04/27/2014] [Indexed: 11/21/2022]
Abstract
Diagnostic methods of TB, nowadays, are prone to delay in diagnosis, increased false negative results and are not sensitive to many forms of paucibacillary disease. The aims of this study were to implement a quantitative nucleic acid-based diagnostic test for paucibacillary tuberculosis, enabling the identification and quantification of viable Mycobacterium tuberculosis bacilli by quantitative Real-Time PCR (qRT-PCR). The intergenic region of the single-copy inhA-mabA gene was chosen as the target region for design of primers and probes conjugated with fluorophores. The construction of synthetic DNA flanking the target region served as standards for absolute quantification of nucleic acids. Using the intercaling dye, propidium monoazide, we were able to discriminate between viable and dead cells of M. tuberculosis. The diagnosis method showed a broad sensitivity (96.1%) when only compared to samples of smear-positive sputum and ROC analyses shows that our approach performed well and yielded a specificity of 84.6% and a sensitivity of 84.6% when compared to M. tuberculosis colony-forming units counting.
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Steingart KR, Schiller I, Horne DJ, Pai M, Boehme CC, Dendukuri N. Xpert® MTB/RIF assay for pulmonary tuberculosis and rifampicin resistance in adults. Cochrane Database Syst Rev 2014; 2014:CD009593. [PMID: 24448973 PMCID: PMC4470349 DOI: 10.1002/14651858.cd009593.pub3] [Citation(s) in RCA: 440] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND Accurate, rapid detection of tuberculosis (TB) and TB drug resistance is critical for improving patient care and decreasing TB transmission. Xpert® MTB/RIF assay is an automated test that can detect both TB and rifampicin resistance, generally within two hours after starting the test, with minimal hands-on technical time. The World Health Organization (WHO) issued initial recommendations on Xpert® MTB/RIF in early 2011. A Cochrane Review on the diagnostic accuracy of Xpert® MTB/RIF for pulmonary TB and rifampicin resistance was published January 2013. We performed this updated Cochrane Review as part of a WHO process to develop updated guidelines on the use of the test. OBJECTIVES To assess the diagnostic accuracy of Xpert® MTB/RIF for pulmonary TB (TB detection), where Xpert® MTB/RIF was used as both an initial test replacing microscopy and an add-on test following a negative smear microscopy result.To assess the diagnostic accuracy of Xpert® MTB/RIF for rifampicin resistance detection, where Xpert® MTB/RIF was used as the initial test replacing culture-based drug susceptibility testing (DST).The populations of interest were adults presumed to have pulmonary, rifampicin-resistant or multidrug-resistant TB (MDR-TB), with or without HIV infection. The settings of interest were intermediate- and peripheral-level laboratories. The latter may be associated with primary health care facilities. SEARCH METHODS We searched for publications in any language up to 7 February 2013 in the following databases: Cochrane Infectious Diseases Group Specialized Register; MEDLINE; EMBASE; ISI Web of Knowledge; MEDION; LILACS; BIOSIS; and SCOPUS. We also searched the metaRegister of Controlled Trials (mRCT) and the search portal of the WHO International Clinical Trials Registry Platform to identify ongoing trials. SELECTION CRITERIA We included randomized controlled trials, cross-sectional studies, and cohort studies using respiratory specimens that allowed for extraction of data evaluating Xpert® MTB/RIF against the reference standard. We excluded gastric fluid specimens. The reference standard for TB was culture and for rifampicin resistance was phenotypic culture-based DST. DATA COLLECTION AND ANALYSIS For each study, two review authors independently extracted data using a standardized form. When possible, we extracted data for subgroups by smear and HIV status. We assessed the quality of studies using QUADAS-2 and carried out meta-analyses to estimate pooled sensitivity and specificity of Xpert® MTB/RIF separately for TB detection and rifampicin resistance detection. For TB detection, we performed the majority of analyses using a bivariate random-effects model and compared the sensitivity of Xpert® MTB/RIF and smear microscopy against culture as reference standard. For rifampicin resistance detection, we undertook univariate meta-analyses for sensitivity and specificity separately to include studies in which no rifampicin resistance was detected. MAIN RESULTS We included 27 unique studies (integrating nine new studies) involving 9557 participants. Sixteen studies (59%) were performed in low- or middle-income countries. For all QUADAS-2 domains, most studies were at low risk of bias and low concern regarding applicability.As an initial test replacing smear microscopy, Xpert® MTB/RIF pooled sensitivity was 89% [95% Credible Interval (CrI) 85% to 92%] and pooled specificity 99% (95% CrI 98% to 99%), (22 studies, 8998 participants: 2953 confirmed TB, 6045 non-TB).As an add-on test following a negative smear microscopy result, Xpert®MTB/RIF pooled sensitivity was 67% (95% CrI 60% to 74%) and pooled specificity 99% (95% CrI 98% to 99%; 21 studies, 6950 participants).For smear-positive, culture-positive TB, Xpert® MTB/RIF pooled sensitivity was 98% (95% CrI 97% to 99%; 21 studies, 1936 participants).For people with HIV infection, Xpert® MTB/RIF pooled sensitivity was 79% (95% CrI 70% to 86%; 7 studies, 1789 participants), and for people without HIV infection, it was 86% (95% CrI 76% to 92%; 7 studies, 1470 participants). Comparison with smear microscopy In comparison with smear microscopy, Xpert® MTB/RIF increased TB detection among culture-confirmed cases by 23% (95% CrI 15% to 32%; 21 studies, 8880 participants).For TB detection, if pooled sensitivity estimates for Xpert® MTB/RIF and smear microscopy are applied to a hypothetical cohort of 1000 patients where 10% of those with symptoms have TB, Xpert® MTB/RIF will diagnose 88 cases and miss 12 cases, whereas sputum microscopy will diagnose 65 cases and miss 35 cases. Rifampicin resistance For rifampicin resistance detection, Xpert® MTB/RIF pooled sensitivity was 95% (95% CrI 90% to 97%; 17 studies, 555 rifampicin resistance positives) and pooled specificity was 98% (95% CrI 97% to 99%; 24 studies, 2411 rifampicin resistance negatives). Among 180 specimens with nontuberculous mycobacteria (NTM), Xpert® MTB/RIF was positive in only one specimen that grew NTM (14 studies, 2626 participants).For rifampicin resistance detection, if the pooled accuracy estimates for Xpert® MTB/RIF are applied to a hypothetical cohort of 1000 individuals where 15% of those with symptoms are rifampicin resistant, Xpert® MTB/RIF would correctly identify 143 individuals as rifampicin resistant and miss eight cases, and correctly identify 833 individuals as rifampicin susceptible and misclassify 17 individuals as resistant. Where 5% of those with symptoms are rifampicin resistant, Xpert® MTB/RIF would correctly identify 48 individuals as rifampicin resistant and miss three cases and correctly identify 931 individuals as rifampicin susceptible and misclassify 19 individuals as resistant. AUTHORS' CONCLUSIONS In adults thought to have TB, with or without HIV infection, Xpert® MTB/RIF is sensitive and specific. Compared with smear microscopy, Xpert® MTB/RIF substantially increases TB detection among culture-confirmed cases. Xpert® MTB/RIF has higher sensitivity for TB detection in smear-positive than smear-negative patients. Nonetheless, this test may be valuable as an add-on test following smear microscopy in patients previously found to be smear-negative. For rifampicin resistance detection, Xpert® MTB/RIF provides accurate results and can allow rapid initiation of MDR-TB treatment, pending results from conventional culture and DST. The tests are expensive, so current research evaluating the use of Xpert® MTB/RIF in TB programmes in high TB burden settings will help evaluate how this investment may help start treatment promptly and improve outcomes.
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Affiliation(s)
- Karen R Steingart
- Liverpool School of Tropical MedicineCochrane Infectious Diseases GroupPembroke PlaceLiverpoolUK
| | - Ian Schiller
- McGill University Health CentreDepartment of Clinical EpidemiologyMcGill UniversityMontrealCanada
| | - David J Horne
- University of WashingtonDivision of Pulmonary and Critical Care MedicineSeattleUSA
| | - Madhukar Pai
- McGill UniversityDepartment of Epidemiology, Biostatistics and Occupational HealthPurvis Hall, Room 501020 Pine Avenue WestMontrealCanadaH3A 1A2
| | - Catharina C Boehme
- Foundation for Innovative New Diagnostics (FIND)16, Av de BudéGenevaSwitzerland
| | - Nandini Dendukuri
- McGill UniversityDepartment of Epidemiology, Biostatistics and Occupational HealthPurvis Hall, Room 501020 Pine Avenue WestMontrealCanadaH3A 1A2
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Steingart KR, Schiller I, Horne DJ, Pai M, Boehme CC, Dendukuri N. Xpert® MTB/RIF assay for pulmonary tuberculosis and rifampicin resistance in adults. Cochrane Database Syst Rev 2014; 2014:CD009593. [PMID: 24448973 DOI: 10.1002/14651858.cd009593.pub3/pdf/standard] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
BACKGROUND Accurate, rapid detection of tuberculosis (TB) and TB drug resistance is critical for improving patient care and decreasing TB transmission. Xpert® MTB/RIF assay is an automated test that can detect both TB and rifampicin resistance, generally within two hours after starting the test, with minimal hands-on technical time. The World Health Organization (WHO) issued initial recommendations on Xpert® MTB/RIF in early 2011. A Cochrane Review on the diagnostic accuracy of Xpert® MTB/RIF for pulmonary TB and rifampicin resistance was published January 2013. We performed this updated Cochrane Review as part of a WHO process to develop updated guidelines on the use of the test. OBJECTIVES To assess the diagnostic accuracy of Xpert® MTB/RIF for pulmonary TB (TB detection), where Xpert® MTB/RIF was used as both an initial test replacing microscopy and an add-on test following a negative smear microscopy result.To assess the diagnostic accuracy of Xpert® MTB/RIF for rifampicin resistance detection, where Xpert® MTB/RIF was used as the initial test replacing culture-based drug susceptibility testing (DST).The populations of interest were adults presumed to have pulmonary, rifampicin-resistant or multidrug-resistant TB (MDR-TB), with or without HIV infection. The settings of interest were intermediate- and peripheral-level laboratories. The latter may be associated with primary health care facilities. SEARCH METHODS We searched for publications in any language up to 7 February 2013 in the following databases: Cochrane Infectious Diseases Group Specialized Register; MEDLINE; EMBASE; ISI Web of Knowledge; MEDION; LILACS; BIOSIS; and SCOPUS. We also searched the metaRegister of Controlled Trials (mRCT) and the search portal of the WHO International Clinical Trials Registry Platform to identify ongoing trials. SELECTION CRITERIA We included randomized controlled trials, cross-sectional studies, and cohort studies using respiratory specimens that allowed for extraction of data evaluating Xpert® MTB/RIF against the reference standard. We excluded gastric fluid specimens. The reference standard for TB was culture and for rifampicin resistance was phenotypic culture-based DST. DATA COLLECTION AND ANALYSIS For each study, two review authors independently extracted data using a standardized form. When possible, we extracted data for subgroups by smear and HIV status. We assessed the quality of studies using QUADAS-2 and carried out meta-analyses to estimate pooled sensitivity and specificity of Xpert® MTB/RIF separately for TB detection and rifampicin resistance detection. For TB detection, we performed the majority of analyses using a bivariate random-effects model and compared the sensitivity of Xpert® MTB/RIF and smear microscopy against culture as reference standard. For rifampicin resistance detection, we undertook univariate meta-analyses for sensitivity and specificity separately to include studies in which no rifampicin resistance was detected. MAIN RESULTS We included 27 unique studies (integrating nine new studies) involving 9557 participants. Sixteen studies (59%) were performed in low- or middle-income countries. For all QUADAS-2 domains, most studies were at low risk of bias and low concern regarding applicability.As an initial test replacing smear microscopy, Xpert® MTB/RIF pooled sensitivity was 89% [95% Credible Interval (CrI) 85% to 92%] and pooled specificity 99% (95% CrI 98% to 99%), (22 studies, 8998 participants: 2953 confirmed TB, 6045 non-TB).As an add-on test following a negative smear microscopy result, Xpert®MTB/RIF pooled sensitivity was 67% (95% CrI 60% to 74%) and pooled specificity 99% (95% CrI 98% to 99%; 21 studies, 6950 participants).For smear-positive, culture-positive TB, Xpert® MTB/RIF pooled sensitivity was 98% (95% CrI 97% to 99%; 21 studies, 1936 participants).For people with HIV infection, Xpert® MTB/RIF pooled sensitivity was 79% (95% CrI 70% to 86%; 7 studies, 1789 participants), and for people without HIV infection, it was 86% (95% CrI 76% to 92%; 7 studies, 1470 participants). Comparison with smear microscopy In comparison with smear microscopy, Xpert® MTB/RIF increased TB detection among culture-confirmed cases by 23% (95% CrI 15% to 32%; 21 studies, 8880 participants).For TB detection, if pooled sensitivity estimates for Xpert® MTB/RIF and smear microscopy are applied to a hypothetical cohort of 1000 patients where 10% of those with symptoms have TB, Xpert® MTB/RIF will diagnose 88 cases and miss 12 cases, whereas sputum microscopy will diagnose 65 cases and miss 35 cases. Rifampicin resistance For rifampicin resistance detection, Xpert® MTB/RIF pooled sensitivity was 95% (95% CrI 90% to 97%; 17 studies, 555 rifampicin resistance positives) and pooled specificity was 98% (95% CrI 97% to 99%; 24 studies, 2411 rifampicin resistance negatives). Among 180 specimens with nontuberculous mycobacteria (NTM), Xpert® MTB/RIF was positive in only one specimen that grew NTM (14 studies, 2626 participants).For rifampicin resistance detection, if the pooled accuracy estimates for Xpert® MTB/RIF are applied to a hypothetical cohort of 1000 individuals where 15% of those with symptoms are rifampicin resistant, Xpert® MTB/RIF would correctly identify 143 individuals as rifampicin resistant and miss eight cases, and correctly identify 833 individuals as rifampicin susceptible and misclassify 17 individuals as resistant. Where 5% of those with symptoms are rifampicin resistant, Xpert® MTB/RIF would correctly identify 48 individuals as rifampicin resistant and miss three cases and correctly identify 931 individuals as rifampicin susceptible and misclassify 19 individuals as resistant. AUTHORS' CONCLUSIONS In adults thought to have TB, with or without HIV infection, Xpert® MTB/RIF is sensitive and specific. Compared with smear microscopy, Xpert® MTB/RIF substantially increases TB detection among culture-confirmed cases. Xpert® MTB/RIF has higher sensitivity for TB detection in smear-positive than smear-negative patients. Nonetheless, this test may be valuable as an add-on test following smear microscopy in patients previously found to be smear-negative. For rifampicin resistance detection, Xpert® MTB/RIF provides accurate results and can allow rapid initiation of MDR-TB treatment, pending results from conventional culture and DST. The tests are expensive, so current research evaluating the use of Xpert® MTB/RIF in TB programmes in high TB burden settings will help evaluate how this investment may help start treatment promptly and improve outcomes.
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Affiliation(s)
- Karen R Steingart
- Cochrane Infectious Diseases Group, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
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Jeong JY, Lee SH, Jang S. A Systematic Review on the Effectiveness of Detection of M. tuberculosisand Rifampin Resistance Using Xpert MTB/RIF. ANNALS OF CLINICAL MICROBIOLOGY 2014. [DOI: 10.5145/acm.2014.17.2.42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Ji-Young Jeong
- Health Technology Assessment Department, National Evidence-based Healthcare Collaborating Agency, Seoul, Korea
| | - Seon-Heui Lee
- Health Technology Assessment Department, National Evidence-based Healthcare Collaborating Agency, Seoul, Korea
| | - Sunyoung Jang
- Department of Nursing, Hanseo University, Seosan, Korea
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Sanjuan-Jimenez R, Morata P, Bermúdez P, Bravo MJ, Colmenero JD. Comparative clinical study of different multiplex real time PCR strategies for the simultaneous differential diagnosis between extrapulmonary tuberculosis and focal complications of brucellosis. PLoS Negl Trop Dis 2013; 7:e2593. [PMID: 24349599 PMCID: PMC3861180 DOI: 10.1371/journal.pntd.0002593] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 11/01/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Both brucellosis and tuberculosis are chronic-debilitating systemic granulomatous diseases with a high incidence in many countries in Africa, Central and South America, the Middle East and the Indian subcontinent. Certain focal complications of brucellosis and extrapulmonary tuberculosis are very difficult to differentiate clinically, biologically and radiologically. As the conventional microbiological methods for the diagnosis of the two diseases have many limitations, as well as being time-consuming, multiplex real time PCR (M RT-PCR) could be a promising and practical approach to hasten the differential diagnosis and improve prognosis. METHODOLOGY/PRINCIPAL FINDINGS We designed a SYBR Green single-tube multiplex real-time PCR protocol targeting bcsp31 and the IS711 sequence detecting all pathogenic species and biovars of Brucella genus, the IS6110 sequence detecting Mycobacterium genus, and the intergenic region senX3-regX3 specifically detecting Mycobacterium tuberculosis complex. The diagnostic yield of the M RT-PCR with the three pairs of resultant amplicons was then analyzed in 91 clinical samples corresponding to 30 patients with focal complications of brucellosis, 24 patients with extrapulmonary tuberculosis, and 36 patients (Control Group) with different infectious, autoimmune or neoplastic diseases. Thirty-five patients had vertebral osteomyelitis, 21 subacute or chronic meningitis or meningoencephalitis, 13 liver or splenic abscess, eight orchiepididymitis, seven subacute or chronic arthritis, and the remaining seven samples were from different locations. Of the three pairs of amplicons (senX3-regX3+ bcsp3, senX3-regX3+ IS711 and IS6110+ IS711) only senX3-regX3+ IS711 was 100% specific for both the Brucella genus and M. tuberculosis complex. For all the clinical samples studied, the overall sensitivity, specificity, and positive and negative predictive values of the M RT-PCR assay were 89.1%, 100%, 85.7% and 100%, respectively, with an accuracy of 93.4%, (95% CI, 88.3-96.5%). CONCLUSIONS/SIGNIFICANCE In this study, a M RT-PCR strategy with species-specific primers based on senX3-regX3+IS711 sequences proved to be a sensitive and specific test, useful for the highly efficient detection of M. tuberculosis and Brucella spp in very different clinical samples. It thus represents an advance in the differential diagnosis between some forms of extrapulmonary tuberculosis and focal complications of brucellosis.
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Affiliation(s)
- Rocio Sanjuan-Jimenez
- Biochemistry, Molecular Biology and Immunology Department, Faculty of Medicine, University of Malaga, Malaga, Spain
| | - Pilar Morata
- Biochemistry, Molecular Biology and Immunology Department, Faculty of Medicine, University of Malaga, Malaga, Spain
| | - Pilar Bermúdez
- Microbiology Service, Carlos Haya University Hospital, Malaga, Spain
| | - M. José Bravo
- Biochemistry, Molecular Biology and Immunology Department, Faculty of Medicine, University of Malaga, Malaga, Spain
| | - Juan D. Colmenero
- Infectious Diseases Service, Carlos Haya University Hospital, Malaga, Spain
- * E-mail:
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66
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Evaluation of GeneXpert MTB/RIF for the detection of Mycobacterium tuberculosis and resistance to rifampin in clinical specimens. J Infect 2013; 68:338-43. [PMID: 24296493 DOI: 10.1016/j.jinf.2013.11.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 11/19/2013] [Accepted: 11/21/2013] [Indexed: 11/22/2022]
Abstract
OBJECTIVES GeneXpert (GX) is a novel real-time polymerase chain reaction assay for the simultaneous detection of Mycobacterium tuberculosis (MTB) and resistance to rifampin (RIF). We evaluated the performance of GX for direct detection of MTB in respiratory and non-respiratory specimens and assessed the ability of the assay to detect resistance to RIF in non-tuberculosis (TB) endemic country. METHODS We analyzed 595 clinical samples in a 1550-bed tertiary hospital in Madrid, Spain. Specimens were processed using GX, auramine smear, conventional culture, and drug phenotypic susceptibility testing (DST) with MGIT SIRE (BD). RESULTS Of the 595 clinical samples, 305 (51.3%) were non-respiratory and 290 (48.7%) were respiratory. In total, MTB was isolated in 81 specimens, 71 of which were positive with GX. The sensitivity, specificity, PPV, and NPV of the GX were: 97.1%, 98.6%, 95.7% and 99.1% for respiratory samples and 33.3%, 99.7%, 80.0% and 97.3% for non-respiratory. GX detected 8 RIF-resistant samples, but only 5 were confirmed by DST. CONCLUSIONS GX is an accurate, easy-to-apply and rapid test to detect MTB, especially in smear-positive respiratory samples. Although is a useful tool for the rapid identification of RIF-resistant MTB strains, the rifampin resistant results should be confirmed by DST.
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Walusimbi S, Bwanga F, De Costa A, Haile M, Joloba M, Hoffner S. Meta-analysis to compare the accuracy of GeneXpert, MODS and the WHO 2007 algorithm for diagnosis of smear-negative pulmonary tuberculosis. BMC Infect Dis 2013; 13:507. [PMID: 24172543 PMCID: PMC3833313 DOI: 10.1186/1471-2334-13-507] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 10/17/2013] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Smear-negative pulmonary tuberculosis (SN-PTB), which is common in HIV-infected patients, is difficult to diagnose using smear microscopy alone. In 2007, the WHO developed an algorithm to improve the diagnosis and management of smear-negative tuberculosis in HIV prevalent and resource constrained settings. Implementation of the algorithm required individuals with presumptive TB to be initially evaluated using two sputum microscopy examinations followed by clinical diagnosis that may include chest X-ray and antibiotic treatment in smear-negative individuals. Since that time, the WHO has endorsed several new tests for diagnosis of tuberculosis. However, it is unclear how the new tests perform when compared to the WHO 2007 algorithm in diagnosis of SN-PTB. Using meta-analysis study design, we summarized and compared the accuracy of Xpert® MTB/Rif assay (GeneXpert) and Microscopic Observation Drug Susceptibility assay (MODS), with the WHO 2007 algorithm in the diagnosis of SN-PTB. METHODS A systematic review and meta-analysis of publications on GeneXpert, or MODS, or the WHO 2007 algorithm for diagnosis of SN-PTB, using culture as reference test was performed. Meta-Disc software was used to obtain pooled sensitivity and specificity of the diagnostic methods. Heterogeneity in the accuracy estimates was tested by reviewing the generated forest plots, sROC curves and the Spearman correlation coefficient of the logit of true positive rate versus the logit of false positive rate. RESULTS Twenty-four publications on all three diagnostic methods were meta-analyzed. The pooled sensitivity and specificity for detection of smear-negative pulmonary tuberculosis were 67% and 98% for GeneXpert, 73% and 91% for MODS, and 61% and 69% for WHO 2007 algorithm, respectively. The sensitivity of GeneXpert reduced from 67% to 54% when sub-group analysis of studies with patient HIV prevalence ≥ 30% was performed. CONCLUSION The GeneXpert, MODS, and the WHO algorithm have moderate to high accuracy for the diagnosis of SN-PTB. However, the accuracy of the tests is extremely variable. The setting and context under which the tests are conducted in addition to several other factors could explain this variability. There is therefore need to investigate these factors further. The information from these studies would inform the adoption and placement of these new tests.
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Affiliation(s)
| | | | | | - Melles Haile
- Department of Public Health Sciences, Karolinska Institute, Stockholm, Sweden.
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Drobniewski F, Nikolayevskyy V, Maxeiner H, Balabanova Y, Casali N, Kontsevaya I, Ignatyeva O. Rapid diagnostics of tuberculosis and drug resistance in the industrialized world: clinical and public health benefits and barriers to implementation. BMC Med 2013; 11:190. [PMID: 23987891 PMCID: PMC3765611 DOI: 10.1186/1741-7015-11-190] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 08/02/2013] [Indexed: 02/06/2023] Open
Abstract
In this article, we give an overview of new technologies for the diagnosis of tuberculosis (TB) and drug resistance, consider their advantages over existing methodologies, broad issues of cost, cost-effectiveness and programmatic implementation, and their clinical as well as public health impact, focusing on the industrialized world. Molecular nucleic-acid amplification diagnostic systems have high specificity for TB diagnosis (and rifampicin resistance) but sensitivity for TB detection is more variable. Nevertheless, it is possible to diagnose TB and rifampicin resistance within a day and commercial automated systems make this possible with minimal training. Although studies are limited, these systems appear to be cost-effective. Most of these tools are of value clinically and for public health use. For example, whole genome sequencing of Mycobacterium tuberculosis offers a powerful new approach to the identification of drug resistance and to map transmission at a community and population level.
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Affiliation(s)
- Francis Drobniewski
- Public Health England National Mycobacterium Reference Laboratory, 2 Newark Street, London E1 2AT, UK.
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69
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Walusimbi S, Bwanga F, Costa AD, Haile M, Hoffner S, Joloba M. Evaluation of the Xpert® MTB/Rif test, microscopic observation drug susceptibility test and nitrate reductase assay, for rapid and accurate diagnosis of smear-negative tuberculosis in HIV patients. Int J Mycobacteriol 2013; 2:148-55. [PMID: 26785983 DOI: 10.1016/j.ijmyco.2013.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 06/23/2013] [Indexed: 10/26/2022] Open
Abstract
Diagnosis of smear-negative tuberculosis (TB), which is frequently seen in HIV-infected patients, is a challenge without conventional culture methods. Since 2007, the WHO (World Health Organization) has endorsed new or improved tests for increased and rapid diagnosis of TB. This study was undertaken in an effort to evaluate the accuracy of two rapid culture methods: the Microscopic Observation Drug Susceptibility assay (MODS) and Nitrate Reductase Assay (NRA), and the molecular based test Xpert® MTB/Rif (Xpert), for diagnosis of smear-negative TB in HIV patients using the mycobacteria growth indicator tube (MGIT) in the BACTEC(TM) MGIT(TM) 960 system as the reference test. 430 smear-negative patients with presumptive TB were enrolled in a cross-sectional study at a tertiary care facility in Uganda. Their sputum was tested on MODS, NRA, Xpert and MGIT. Of the 430 patients, 373 had complete results to compute test accuracy. Mycobacterium tuberculosis (MTB) was detected in 43 patients by MGIT. The sensitivity and specificity were 24.4% and 98.1% for MODS, 41.5% and 92% for NRA, 48.8% and 95.1% for Xpert, respectively. The low sensitivity of the tests implies that additional diagnostics such as chest X-ray and conventional liquid culture methods might still be needed to detect TB in smear-negative HIV patients. The high specificity of the tests is useful to confirm TB in HIV patients with symptoms suggestive of TB.
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Affiliation(s)
- Simon Walusimbi
- Department of Medical Microbiology, Makerere University, College of Health Sciences, Kampala, Uganda; Department of Public Health Sciences, Karolinska Institute, Stockholm, Sweden
| | - Freddie Bwanga
- Department of Medical Microbiology, Makerere University, College of Health Sciences, Kampala, Uganda
| | - Ayesha De Costa
- Department of Public Health Sciences, Karolinska Institute, Stockholm, Sweden
| | - Melles Haile
- Department of Public Health Sciences, Karolinska Institute, Stockholm, Sweden; Department of Diagnostics and Vaccinology, Swedish Institute for Communicable Disease Control, Solna, Sweden.
| | - Sven Hoffner
- Department of Diagnostics and Vaccinology, Swedish Institute for Communicable Disease Control, Solna, Sweden; Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institute, Stockholm, Sweden
| | - Moses Joloba
- Department of Medical Microbiology, Makerere University, College of Health Sciences, Kampala, Uganda
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Theron G, Peter J, Meldau R, Khalfey H, Gina P, Matinyena B, Lenders L, Calligaro G, Allwood B, Symons G, Govender U, Setshedi M, Dheda K. Accuracy and impact of Xpert MTB/RIF for the diagnosis of smear-negative or sputum-scarce tuberculosis using bronchoalveolar lavage fluid. Thorax 2013; 68:1043-51. [PMID: 23811536 DOI: 10.1136/thoraxjnl-2013-203485] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
RATIONALE The accuracy and impact of new tuberculosis (TB) tests, such as Xpert MTB/RIF, when performed on bronchoalveolar lavage fluid (BALF) obtained from patients with sputum-scarce or smear-negative TB is unclear. METHODS South African patients with suspected pulmonary TB (n=160) who were sputum-scarce or smear-negative underwent bronchoscopy. MTB/RIF was performed on uncentrifuged BALF (1 ml) and/or a resuspended pellet of centrifuged BALF (∼10 ml). Time to TB detection and anti-TB treatment initiation were compared between phase one, when MTB/RIF was performed as a research tool, and phase two, when it was used for patient management. RESULTS 27 of 154 patients with complete data had culture-confirmed TB. Of these, a significantly lower proportion were detected by smear microscopy compared with MTB/RIF (58%, 95% CI 39% to 75% versus 93%, 77% to 98%; p<0.001). Of the 127 patients who were culture negative, 96% (91% to 98%) were MTB/RIF negative. When phase two was compared with phase one, MTB/RIF reduced the median days to TB detection (29 (18-41) to 0 (0-0); p<0.001). However, more patients initiated empirical therapy (absence of a positive test in those commencing treatment) in phase one versus phase two (79% (11/14) versus 28% (10/25); p=0.026). Consequently, there was no detectable difference in the overall proportion of patients initiating treatment (26% (17/67; 17% to 37%) versus 36% (26/73; 26% to 47%); p=0.196) or the days to treatment initiation (10 (1-49) versus 7 (0-21); p=0.330). BALF centrifugation, HIV coinfection and a second MTB/RIF did not result in detectable changes in accuracy. CONCLUSIONS MTB/RIF detected TB cases more accurately and more rapidly than smear microscopy and significantly reduced the rate of empirical treatment.
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Affiliation(s)
- Grant Theron
- Department of Medicine, Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, University of Cape Town, , Cape Town, Western Cape, South Africa
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71
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Antonenka U, Hofmann-Thiel S, Turaev L, Esenalieva A, Abdulloeva M, Sahalchyk E, Alnour T, Hoffmann H. Comparison of Xpert MTB/RIF with ProbeTec ET DTB and COBAS TaqMan MTB for direct detection of M. tuberculosis complex in respiratory specimens. BMC Infect Dis 2013; 13:280. [PMID: 23786563 PMCID: PMC3699374 DOI: 10.1186/1471-2334-13-280] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 06/10/2013] [Indexed: 01/29/2023] Open
Abstract
Background Nucleic acid amplification assays allow for the rapid and accurate detection of Mycobacterium tuberculosis (MTB) directly in clinical specimens thereby facilitating diagnosis of tuberculosis (TB). With the fully automated Xpert MTB/RIF system (Cepheid) an innovative solution of TB diagnostics has been launched. We performed a direct head-to-head comparison of Xpert MTB/RIF with two widely used commercial assays, ProbeTec ET DTB (DTB) (Becton-Dickinson) and COBAS TaqMan MTB (CTM-MTB) (Roche). Methods 121 pre-characterized respiratory specimens (68 culture-positive for MTB complex, 24 culture-positive for non-tuberculous mycobacteria and 29 culture-negative) taken from our frozen specimen bank were tested for the presence of MTB complex by the three assays. Results Among culture-positive samples (n = 68), overall sensitivity for detection of MTB complex was 74.6%, 73.8%, and 79.1% for Xpert MTB/RIF, CTM-MTB, and DTB, respectively. Within the subgroup of smear-negative TB samples (n = 51) sensitivity was 68% for Xpert MTB/RIF and CTM-MTB and 72% for DTB. Among smear-positive TB samples (n = 17), all (100%) were detected by DTB and 94.1% and 93.3% by Xpert MTB/RIF and CTM-MTB, respectively. Specificity was best for CTM-MTB (100%) and lowest for Xpert MTB/RIF (96.2%) due to misidentification of two NTM samples as MTB complex. CTM-MTB yielded the highest rate of invalid results (4.1%) (0.8% by Xpert MTB/RIF and DTB, respectively). Conclusions The direct comparison of Xpert MTB/RIF with CTM-MTB and DTB yielded similar overall performance data. Whereas DTB was slightly superior to Xpert MTB/RIF in terms of sensitivity, at least in the sample collection tested here, CTM-MTB performed best in terms of specificity.
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Affiliation(s)
- Uladzimir Antonenka
- IML red, Supranational Reference Laboratory of Tuberculosis, Gauting, Germany
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72
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Wassie L, Abebe M, Aseffa A, Bobosha K, Zewdie M, Chanyalew M, Yamuah LK, Cortés A, González JR, Delgado JM, Ceyhan I, Rosenkrands I, Weldingh K, Andersen P, Doherty TM. Development of a proof of concept immunochromatographic lateral flow assay for point of care diagnosis of Mycobacterium tuberculosis. BMC Res Notes 2013; 6:202. [PMID: 23688126 PMCID: PMC3680158 DOI: 10.1186/1756-0500-6-202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 05/15/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Despite major public health initiatives and the existence of efficacious treatment regimes, tuberculosis (TB) remains a threat, particularly in resource-limited settings. A significant part of the problem is the difficulty of rapidly identifying infected individuals, and as a result, there has been renewed interest in developing better diagnostics for infection or disease caused by Mycobacterium tuberculosis. Many of the existing tools, however, have limitations such as poor sensitivity or specificity, or the need for well-equipped laboratories to function effectively. Serodiagnostic approaches in particular have long drawn attention, due to their potential utility in large field studies, particularly in resource-poor settings. Unfortunately none of the serodiagnostic approaches have so far proven useful under field conditions. RESULTS We screened a large panel of antigens with serodiagnostic potential by ELISA and selected a subpanel that was strongly and broadly recognised by TB patients, but not by controls. These antigens were then formulated into a simple immuno-chromatographic lateral flow assay format, suitable for field use, and tested against panels of plasma and blood samples from individuals with different clinical status (confirmed TB patients, household contacts, and apparently healthy community controls), recruited from Ethiopia (a highly TB-endemic country) and Turkey (a TB meso-endemic country). While specificity was good (97-100% in non TB-endemic controls), the sensitivity was not as high as expected (46-54% in pulmonary TB, 25-29% in extra-pulmonary TB). CONCLUSIONS Though below the level of sensitivity the consortium had set for commercial development, the assay specifically identified M. tuberculosis-infected individuals, and provides a valuable proof of concept.
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Affiliation(s)
- Liya Wassie
- Armauer Hansen Research Institute, P.O. Box: 1005, Jimma Road, Addis Ababa, Ethiopia.
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73
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Integrating the Xpert MTB/RIF assay into a diagnostic workflow for rapid detection of Mycobacterium tuberculosis in a low-prevalence area. J Clin Microbiol 2013; 51:2396-9. [PMID: 23616455 DOI: 10.1128/jcm.00151-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The Xpert MTB/RIF assay is a rapid and fully automated real-time PCR assay. The performance of the Xpert MTB/RIF assay as a primary screening test for urgent clinical specimens was evaluated during a 2-year period. The results showed that replacing smear microscopy with the Xpert MTB/RIF assay facilitates laboratory handling and improves the sensitivity and specificity of Mycobacterium tuberculosis detection.
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74
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Abstract
In recent years, quantitative real-time PCR tests have been extensively developed in clinical microbiology laboratories for routine diagnosis of infectious diseases, particularly bacterial diseases. This molecular tool is well-suited for the rapid detection of bacteria directly in clinical specimens, allowing early, sensitive and specific laboratory confirmation of related diseases. It is particularly suitable for the diagnosis of infections caused by fastidious growth species, and the number of these pathogens has increased recently. This method also allows a rapid assessment of the presence of antibiotic resistance genes or gene mutations. Although this genetic approach is not always predictive of phenotypic resistances, in specific situations it may help to optimize the therapeutic management of patients. Finally, an approach combining the detection of pathogens, their mechanisms of antibiotic resistance, their virulence factors and bacterial load in clinical samples could lead to profound changes in the care of these infected patients.
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Affiliation(s)
- Max Maurin
- Laboratoire de Bactériologie, Département des Agents Infectieux, Institut de Biologie et Pathologie, CHU de Grenoble, Université Joseph Fourier Grenoble 1, France.
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Steingart KR, Sohn H, Schiller I, Kloda LA, Boehme CC, Pai M, Dendukuri N. Xpert® MTB/RIF assay for pulmonary tuberculosis and rifampicin resistance in adults. Cochrane Database Syst Rev 2013:CD009593. [PMID: 23440842 PMCID: PMC4470352 DOI: 10.1002/14651858.cd009593.pub2] [Citation(s) in RCA: 253] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND Accurate and rapid detection of tuberculosis (TB) and drug resistance are critical for improving patient care and decreasing the spread of TB. Xpert® MTB/RIF assay (Xpert) is a rapid, automated test that can detect both TB and rifampicin resistance, within two hours after starting the test, with minimal hands-on technical time, but is more expensive than conventional sputum microscopy. OBJECTIVES To assess the diagnostic accuracy of Xpert for pulmonary TB (TB detection), both where Xpert was used as an initial test replacing microscopy, and where Xpert was used as an add-on test following a negative smear microscopy result.To assess the diagnostic accuracy of Xpert for rifampicin resistance detection where Xpert was used as the initial test, replacing conventional culture-based drug susceptibility testing.The population of interest was adults suspected of having pulmonary TB or multidrug-resistant TB (MDR-TB), with or without HIV infection. SEARCH METHODS We performed a comprehensive search of the following databases: Cochrane Infectious Diseases Group Specialized Register; MEDLINE; EMBASE; ISI Web of Knowledge; MEDION; LILACS; BIOSIS; and SCOPUS. We also searched the metaRegister of Controlled Trials (mRCT) and the search portal of the WHO International Clinical Trials Registry Platform to identify ongoing trials. We performed searches on 25 September 2011 and we repeated them on 15 December 2011, without language restriction. SELECTION CRITERIA We included randomized controlled trials, cross-sectional, and cohort studies that used respiratory specimens to compare Xpert with culture for detecting TB and Xpert with conventional phenotypic drug susceptibility testing for detecting rifampicin resistance. DATA COLLECTION AND ANALYSIS For each study, two review authors independently extracted a set of data using a standardized data extraction form. When possible, we extracted data for subgroups by smear and HIV status. We assessed the quality of studies using the QUADAS-2 tool. We carried out meta-analyses to estimate the pooled sensitivity and specificity of Xpert separately for TB detection and rifampicin resistance detection using a bivariate random-effects model. We estimated the median pooled sensitivity and specificity and their 95% credible intervals (CrI). MAIN RESULTS We identified 18 unique studies as eligible for this review, including two multicentre international studies, one with five and the other with six distinct study centres. The majority of studies (55.6%) were performed in low-income and middle-income countries. In 17 of the 18 studies, Xpert was performed by trained technicians in reference laboratories.When used as an initial test replacing smear microscopy (15 studies, 7517 participants), Xpert achieved a pooled sensitivity of 88% (95% CrI 83% to 92%) and pooled specificity of 98% (95% CrI 97% to 99%). As an add-on test following a negative smear microscopy result (14 studies, 5719 participants), Xpert yielded a pooled sensitivity of 67% (95% CrI 58% to 74%) and pooled specificity of 98% (95% CrI 97% to 99%). In clinical subgroups, we found the following accuracy estimates: the pooled sensitivity was 98% (95% CrI 97% to 99%) for smear-positive, culture-positive TB and 68% (95% CrI 59% to 75%) for smear-negative, culture-positive TB (15 studies); the pooled sensitivity was 80% (95% CrI 67% to 88%) in people living with HIV and 89% (95% CrI 81% to 94%) in people without HIV infection (four studies). For rifampicin resistance detection (11 studies, 2340 participants), Xpert achieved a pooled sensitivity of 94% (95% CrI 87% to 97%) and pooled specificity of 98% (95% CrI 97% to 99%). In a separate analysis, Xpert could distinguish between TB and nontuberculous mycobacteria (NTM) in clinical samples with high accuracy: among 139 specimens with NTM, Xpert was positive in only one specimen that grew NTM.In a hypothetical cohort of 1000 individuals suspected of having rifampicin resistance (a proxy for MDR-TB), where the prevalence of rifampicin resistance is 30%, we estimated that on average Xpert would wrongly identify 14 patients as being rifampicin resistant. In comparison, where the prevalence of rifampicin resistance is only 2%, we estimated that the number of individuals wrongly identified as rifampicin resistant would increase to 20, an increase of 43%. AUTHORS' CONCLUSIONS This review shows that Xpert used as an initial diagnostic test for TB detection and rifampicin resistance detection in patients suspected of having TB, MDR-TB, or HIV-associated TB is sensitive and specific. Xpert may also be valuable as an add-on test following microscopy for patients who have previously been found to be smear-negative. An Xpert result that is positive for rifampicin resistance should be carefully interpreted and take into consideration the risk of MDR-TB in a given patient and the expected prevalence of MDR-TB in a given setting.Studies in this review mainly assessed sensitivity and specificity of the test when used in reference laboratories in research investigations. Most studies were performed in high TB burden countries. Ongoing use of Xpert in high TB burden countries will contribute to the evidence base on the diagnostic accuracy and clinical impact of Xpert in routine programmatic and peripheral health care settings, including settings where the test is performed at the point of care.
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Affiliation(s)
- Karen R Steingart
- Department of Health Services, University of Washington, School of Public Health, Seattle, Washington, USA.
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Muñoz L, Moure R, Porta N, Gonzalez L, Guerra R, Alcaide F, Santin M. GeneXpert® for smear-negative pulmonary tuberculosis: does it play a role in low-burden countries? Diagn Microbiol Infect Dis 2012; 75:325-6. [PMID: 23276773 DOI: 10.1016/j.diagmicrobio.2012.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 11/25/2012] [Indexed: 10/27/2022]
Abstract
We performed a retrospective analysis of costs and time to treatment (TT) of 150 culture-confirmed TB cases: 100 sputum smear (SS) (+) and 50 SS(-). This group underwent GeneXpert® (GX) assay. Expenditures and TT of SS(-)/GX(+) cases were inferred from the SS(+) group. GX detected 68% of SS(-) cases.
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Affiliation(s)
- Laura Muñoz
- Department of Infectious Diseases at Bellvitge University Hospital-IDIBELL, Barcelona, Spain.
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77
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Yoon C, Cattamanchi A, Davis JL, Worodria W, den Boon S, Kalema N, Katagira W, Kaswabuli S, Miller C, Andama A, Albert H, Nabeta P, Gray C, Ayakaka I, Huang L. Impact of Xpert MTB/RIF testing on tuberculosis management and outcomes in hospitalized patients in Uganda. PLoS One 2012; 7:e48599. [PMID: 23139799 PMCID: PMC3490868 DOI: 10.1371/journal.pone.0048599] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 09/27/2012] [Indexed: 02/07/2023] Open
Abstract
RATIONALE The clinical impact of Xpert MTB/RIF for tuberculosis (TB) diagnosis in high HIV-prevalence settings is unknown. OBJECTIVE To determine the diagnostic accuracy and impact of Xpert MTB/RIF among high-risk TB suspects. METHODS WE PROSPECTIVELY ENROLLED CONSECUTIVE, HOSPITALIZED, UGANDAN TB SUSPECTS IN TWO PHASES: baseline phase in which Xpert MTB/RIF results were not reported to clinicians and an implementation phase in which results were reported. We determined the diagnostic accuracy of Xpert MTB/RIF in reference to culture (solid and liquid) and compared patient outcomes by study phase. RESULTS 477 patients were included (baseline phase 287, implementation phase 190). Xpert MTB/RIF had high sensitivity (187/237, 79%, 95% CI: 73-84%) and specificity (190/199, 96%, 95% CI: 92-98%) for culture-positive TB overall, but sensitivity was lower (34/81, 42%, 95% CI: 31-54%) among smear-negative TB cases. Xpert MTB/RIF reduced median days-to-TB detection for all TB cases (1 [IQR 0-26] vs. 0 [IQR 0-1], p<0.001), and for smear-negative TB (35 [IQR 22-55] vs. 22 [IQR 0-33], p=0.001). However, median days-to-TB treatment was similar for all TB cases (1 [IQR 0-5] vs. 0 [IQR 0-2], p=0.06) and for smear-negative TB (7 [IQR 3-53] vs. 6 [IQR 1-61], p=0.78). Two-month mortality was also similar between study phases among 252 TB cases (17% vs. 14%, difference +3%, 95% CI: -21% to +27%, p=0.80), and among 87 smear-negative TB cases (28% vs. 22%, difference +6%, 95% CI: -34 to +46%, p=0.77). CONCLUSIONS Xpert MTB/RIF facilitated more accurate and earlier TB diagnosis, leading to a higher proportion of TB suspects with a confirmed TB diagnosis prior to hospital discharge in a high HIV/low MDR TB prevalence setting. However, our study did not detect a decrease in two-month mortality following implementation of Xpert MTB/RIF possibly because of insufficient powering, differences in empiric TB treatment rates, and disease severity between study phases.
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Affiliation(s)
- Christina Yoon
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - Adithya Cattamanchi
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
- Curry International Tuberculosis Center, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
| | - J. Lucian Davis
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
- Curry International Tuberculosis Center, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - William Worodria
- Department of Medicine, Faculty of Medicine, Makerere University, Kampala, Uganda
- Uganda Ministry of Health, Kampala, Uganda
| | - Saskia den Boon
- Makerere University-University of California San Francisco Research Collaboration, Kampala, Uganda
| | - Nelson Kalema
- Makerere University-University of California San Francisco Research Collaboration, Kampala, Uganda
| | - Winceslaus Katagira
- Makerere University-University of California San Francisco Research Collaboration, Kampala, Uganda
| | - Sylvia Kaswabuli
- Makerere University-University of California San Francisco Research Collaboration, Kampala, Uganda
| | - Cecily Miller
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - Alfred Andama
- Department of Medicine, Faculty of Medicine, Makerere University, Kampala, Uganda
| | - Heidi Albert
- Foundation for Innovative New Diagnostics, Kampala, Uganda
| | - Pamela Nabeta
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Christen Gray
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Irene Ayakaka
- Makerere University-University of California San Francisco Research Collaboration, Kampala, Uganda
| | - Laurence Huang
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
- HIV/AIDS Division, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
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A diagnostic accuracy study of Xpert®MTB/RIF in HIV-positive patients with high clinical suspicion of pulmonary tuberculosis in Lima, Peru. PLoS One 2012; 7:e44626. [PMID: 22970271 PMCID: PMC3436871 DOI: 10.1371/journal.pone.0044626] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 08/06/2012] [Indexed: 01/31/2023] Open
Abstract
Background Diagnosis of pulmonary tuberculosis (TB) among human immunodeficiency virus (HIV) patients remains complex and demands easy to perform and accurate tests. Xpert®MTB/RIF (MTB/RIF) is a molecular TB diagnostic test which is rapid and convenient; the test requires minimal human resources and reports results within two hours. The majority of performance studies of MTB/RIF have been performed in high HIV burden settings, thus TB diagnostic studies among HIV patients in low HIV prevalence settings such as Peru are still needed. Methodology/Principal Findings From April 2010 to May 2011, HIV-positive patients with high clinical suspicion of TB were enrolled from two tertiary hospitals in Lima, Peru. Detection of TB by MTB/RIF was compared to a composite reference standard Löwenstein-Jensen (LJ) and liquid culture. Detection of rifampicin resistance was compared to the LJ proportion method. We included 131 patients, the median CD4 cell count was 154.5 cells/mm3 and 45 (34.4%) had TB. For TB detection among HIV patients, sensitivity of MTB/RIF was 97.8% (95% CI 88.4–99.6) (44/45); specificity was 97.7% (95% CI 91.9–99.4) (84/86); the positive predictive value was 95.7% (95% CI 85.5–98.8) (44/46); and the negative predictive value, 98.8% (95% CI 93.6–99.8) (84/85). MTB/RIF detected 13/14 smear-negative TB cases, outperforming smear microscopy [97.8% (44/45) vs. 68.9% (31/45); p = 0.0002]. For rifampicin resistance detection, sensitivity of MTB/RIF was 100% (95% CI 61.0–100.0) (6/6); specificity was 91.0% (95% CI 76.4–96.9) (30/33); the positive predictive value was 66.7% (95% CI 35.4–87.9) (6/9); and the negative predictive value was 100% (95% CI 88.7 –100.0) (30/30). Conclusions/Significance In HIV patients in our population with a high clinical suspicion of TB, MTB/RIF performed well for TB diagnosis and outperformed smear microscopy.
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79
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Rapid detection of the Mycobacterium tuberculosis complex by use of quenching probe PCR (geneCube). J Clin Microbiol 2012; 50:3604-8. [PMID: 22933602 DOI: 10.1128/jcm.01654-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Early detection of tuberculosis (TB) is essential for infection control. The geneCube (Toyobo) is a novel fully automated gene analyzer that can amplify target DNAs within 60 min. In this study, we evaluated the ability of the geneCube to directly detect Mycobacterium tuberculosis complex (MTBC) and Mycobacterium avium complex (MAC) in clinical specimens. The results were then compared with those obtained using conventional culture, microscopy, and the Cobas Amplicor assay (Roche). We examined a total of 516 frozen samples from 69 patients who showed culture-positive infection (73 samples; 39 MTBC, 32 MAC, and 2 mixed infections) and from 354 patients who were culture negative (443 samples). Assays using the geneCube had a sensitivity of 85.4% and a specificity of 99.8% for detection of MTBC and a sensitivity of 85.3% and a specificity of 99.8% for detection of MAC. These results are similar to those obtained using the Amplicor system but were obtained much more rapidly (1 h with the geneCube versus 5.5 h with the Amplicor system). The geneCube thus enables a significant shortening of the assay time with no loss of sensitivity or specificity.
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80
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Peter JG, Theron G, Muchinga TE, Govender U, Dheda K. The diagnostic accuracy of urine-based Xpert MTB/RIF in HIV-infected hospitalized patients who are smear-negative or sputum scarce. PLoS One 2012; 7:e39966. [PMID: 22815718 PMCID: PMC3392260 DOI: 10.1371/journal.pone.0039966] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 06/05/2012] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Hospitals in sub-Saharan Africa are inundated with HIV-infected patients and tuberculosis (TB) is the commonest opportunistic infection in this sub-group. Up to one third of TB-HIV co-infected patients fail to produce a sputum sample (sputum scarce) and diagnosis is thus often delayed or missed. We investigated the sensitivity of urine-based methods (Xpert MTB/RIF, LAM strip test and LAM ELISA) in such patients. METHODOLOGY/PRINCIPAL FINDINGS 281 HIV-infected hospitalised patients with clinically suspected TB provided a spot urine sample. The reference standard was culture positivity for Mycobacterium tuberculosis on ≥1 sputum or extra-pulmonary sample. MTB/RIF was performed using 1 ml of both unprocessed and, when possible, concentrated urine. Each unconcentrated urine sample was also tested using the Clearview LAM ELISA and Alere LAM strip test. 42% (116/242) of patients had culture-proven TB. 18% (20/54) were sputum scarce. In sputum-scarce patients, the sensitivity of urine MTB/RIF and LAM ELISA was 40% (95%CI: 22-61) and 60% (95%CI: 39-78), respectively. Urine MTB/RIF specificity was 98% (95%CI: 95-100). Combined sensitivity of urine LAM ELISA and MTB/RIF was better than MTB/RIF alone [MTB/RIF and LAM: 70% (95%CI: 48-85) vs. MTB/RIF: 40% (95%CI: 22-61), p = 0.03]. Significant predictors of urine MTB/RIF positivity were CD4<50 cells/ml (p = 0.001), elevated protein-to-creatinine ratio (p<0.001) and LAM ELISA positivity (p<0.001). Urine centrifugation and pelleting significantly increased the sensitivity of MTB/RIF over unprocessed urine in paired samples [42% (95%CI: 26-58) vs. 8% (95%CI: 0-16), p<0.001]. Urine MTB/RIF-generated C(T) values correlated poorly with markers of bacillary burden (smear grade and time-to-positivity). CONCLUSIONS/SIGNIFICANCE This preliminary study indicates that urine-based MTB/RIF, alone or in combination with LAM antigen detection, may potentially aid the diagnosis of TB in HIV-infected patients with advanced immunosuppression when sputum-based diagnosis is not possible. Concentration of urine prior to MTB/RIF-testing significantly improves sensitivity.
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Affiliation(s)
- Jonathan G. Peter
- Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Grant Theron
- Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Tapuwa E. Muchinga
- Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Ureshnie Govender
- Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Keertan Dheda
- Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Infection, University College London Medical School, London, United Kingdom
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81
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Lawn SD, Zumla AI. Diagnosis of extrapulmonary tuberculosis using the Xpert(®) MTB/RIF assay. Expert Rev Anti Infect Ther 2012; 10:631-5. [PMID: 22734954 PMCID: PMC3605769 DOI: 10.1586/eri.12.43] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Evaluation of: Tortoli E, Russo C, Piersimoni C et al. Clinical validation of Xpert MTB/RIF for the diagnosis of extrapulmonary tuberculosis. Eur. Respir. J. doi:10.1183/09031936.00176311 (2012) (Epub ahead of print). The Xpert® MTB/RIF assay has been CE-marked for rapid molecular diagnosis of TB in Europe and has been endorsed by the WHO as a replacement for sputum smear microscopy for diagnosis of pulmonary TB in low- and middle-income countries. However, few data are available to inform recommendations for use of the assay for testing nonsputum clinical samples when investigating suspected extrapulmonary TB (EPTB). We review and discuss the findings of Tortoli and colleagues, who evaluated the assay used for this purpose in a large study of adults and children in Italy. They provide a per-sample analysis of 268 diagnoses of EPTB at a range of anatomic sites (sensitivity: 81.3%; 95% CI: 76.2-85.8) and data for 1206 samples in which EPTB was excluded (specificity: 99.8%; 95% CI: 99.4-100). We discuss how this paper forms an important addition to the growing body of literature demonstrating the utility of Xpert MTB/RIF for EPTB diagnosis when applied to diverse types of clinical samples
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Affiliation(s)
- Stephen D Lawn
- The Desmond Tutu HIV Centre, Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa.
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82
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Theron G, Peter J, Lenders L, van Zyl-Smit R, Meldau R, Govender U, Dheda K. Correlation of mycobacterium tuberculosis specific and non-specific quantitative Th1 T-cell responses with bacillary load in a high burden setting. PLoS One 2012; 7:e37436. [PMID: 22629395 PMCID: PMC3358317 DOI: 10.1371/journal.pone.0037436] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 04/23/2012] [Indexed: 12/21/2022] Open
Abstract
Background Measures of bacillary load in patients with tuberculosis (TB) may be useful for predicting and monitoring response to treatment. The relationship between quantitative T-cell responses and mycobacterial load remains unclear. We hypothesised that, in a HIV-prevalent high burden setting, the magnitude of mycobacterial antigen-specific and non-specific T-cell IFN-γ responses would correlate with (a) bacterial load and (b) culture conversion in patients undergoing treatment. Methods We compared baseline (n = 147), 2 (n = 35) and 6 month (n = 13) purified-protein-derivative (PPD) and RD1-specific (TSPOT.TB and QFT-GIT) blood RD1-specific (TSPOT.TB; QFT-GIT) responses with associates of sputum bacillary load in patients with culture-confirmed TB in Cape Town, South Africa. Results IFN-γ responses were not associated with liquid culture time-to-positivity, smear-grade, Xpert MTB/RIF-generated cycle threshold values or the presence of cavities on the chest radiograph in patients with culture-confirmed TB and irrespective of HIV-status. 2-month IGRA conversion rates (positive-to-negative) were negligible [<11% for TSPOT.TB (3/28) and QFT-GIT (1/29)] and lower compared to culture [60% (21/35); p<0.01]. Conclusions In a high burden HIV-prevalent setting T-cell IFN-γ responses to M. tuberculosis-specific and non-specific antigens do not correlate with bacillary load, including Xpert MTB/RIF-generated CT values, and are therefore poorly suited for monitoring treatment and prognostication.
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Affiliation(s)
- Grant Theron
- Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Jonny Peter
- Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Laura Lenders
- Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Richard van Zyl-Smit
- Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Richard Meldau
- Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Ureshnie Govender
- Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Keertan Dheda
- Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- * E-mail:
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83
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Can a simple flotation method lower the limit of detection of Mycobacterium tuberculosis in extrapulmonary samples analyzed by the GeneXpert MTB/RIF assay? J Clin Microbiol 2012; 50:2272-6. [PMID: 22553234 DOI: 10.1128/jcm.01012-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rapid and accurate diagnosis of tuberculosis (TB) in children and extrapulmonary TB in adults continues to be a challenge. In this study, we determined the lower limit of detection (LOD) of the GeneXpert MTB/RIF assay with nonrespiratory specimens and investigated the utility of flotation procedures for concentrating the bacilli. Clinical specimens (9 cerebrospinal fluid [CSF], 13 gastric aspirate, 8 tissue, and 17 stool) were spiked with single-celled Mycobacterium tuberculosis, and the LOD of the GeneXpert assay was determined. Flotation studies were conducted with sucrose and NaCl, and the cycle thresholds of the MTB/RIF assay were compared between treated and untreated samples. There was no significant difference between the LODs of the GeneXpert assay with saline solution (median, 33 CFU/ml) and CSF (median, 25 CFU/ml) (P > 0.05) or gastric aspirate samples (median, 58 CFU/ml) (P > 0.05). The LOD with spiked tissue (median, 1,525 CFU/ml) and stool samples (median, 6,800 CFU/ml) was significantly elevated compared to that determined with saline solution (P ≤ 0.05 and ≤ 0.0005, respectively). Flotation studies with sucrose or NaCl did not consistently result in lowered cycle thresholds in stool or gastric aspirates, but a cycle reduction of >10 was achieved in two of the three pooled CSF samples. Unlike the results seen with tissue and stool samples, there was no significant PCR inhibition in the MTB/RIF assay with CSF and gastric aspirates. Although preconcentration of CSF samples with sucrose and NaCl may enhance detection of M. tuberculosis by PCR, further advances are needed to concentrate the bacilli and eliminate PCR inhibitors in paucibacillary nonrespiratory samples.
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84
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Performance of the Roche LightCycler real-time PCR assay for diagnosing extrapulmonary tuberculosis. J Clin Microbiol 2012; 50:2100-3. [PMID: 22495565 DOI: 10.1128/jcm.00252-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Roche LightCycler mycobacterium detection molecular assay for Mycobacterium tuberculosis, M. avium, and M. kansasii, was applied to tissue specimens. It performed well on lymph node and cerebrospinal fluid specimens and less well on lung, liver, and bone marrow core biopsy specimens, but used in conjunction with a clinical suspicion of tuberculosis, it could augment patient management.
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85
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Gessoni G, Valverde S, Manoni F. Evaluation of the GeneXpert assay in the detection of Factor V Leiden and prothrombin 20210 in stored, previously classified samples. Clin Chim Acta 2012; 413:814-6. [PMID: 22285776 DOI: 10.1016/j.cca.2012.01.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Revised: 12/23/2011] [Accepted: 01/15/2012] [Indexed: 11/25/2022]
Abstract
BACKGROUND In this study, we evaluated the GeneXpert HemosIL Factor II and Factor V assay, an innovative assay for the detection of Factor V Leiden (FVL) and prothrombin G20210A mutation (GPRO). PATIENTS AND METHODS We evaluated 132 patients that were previously classified (with a concordant result) using two commercial real-time PCR assays supplied, by Applied Biosystems and Roche Molecular Biochemicals. The cohort comprised 75 normal subjects, 10 FVL homozygous, 35 FVL heterozygous, 7 GPRO heterozygous, 2 GPRO homozygous and 3 double heterozygous FVL and GPRO subjects. All of the samples were evaluated using the GeneXpert HemosIL Factor II and Factor V assay. RESULTS All of the samples were correctly identified using the GeneXpert HemosIL Factor II and Factor V assay; therefore, in this patient series, the specificity and sensitivity of the test under evaluation was 1.00. DISCUSSION We have shown that the GeneXpert HemosIL Factor II and Factor V assay, a rapid fully automated assay, can accurately characterise the presence of FV G1691A and FII G20210A polymorphisms with specificity and sensitivity that are comparable to other current real-time PCR-based methods. The theoretical advantages of such an assay include improved standardisation across varying healthcare environments, more thorough sample manipulation and reduced human error.
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Affiliation(s)
- G Gessoni
- Service of Laboratory Medicine, Chioggia, Venice, Italy.
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86
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Direct detection of Mycobacterium tuberculosis complex in clinical samples by a molecular method based on GenoQuick technology. J Clin Microbiol 2012; 50:2089-91. [PMID: 22422848 DOI: 10.1128/jcm.00567-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several molecular systems for direct detection of Mycobacterium tuberculosis complex (MTBC) have recently been developed. The GenoQuick MTB assay (GQ-MTB) used in this study detected 82 of the 96 (85.4%) samples with MTBC, including 50 of 64 (78.1%) samples with negative acid-fast bacillus smears. Fifteen samples containing nontuberculous mycobacteria were also studied: 13 were GQ-MTB negative, one was positive, and one was indeterminate. GQ-MTB showed good effectiveness for the direct detection of MTBC from clinical samples.
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87
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Doblas A, Alcaide F, Benito N, Gurguí M, Torre-Cisneros J. Tuberculosis in solid organ transplant patients. Enferm Infecc Microbiol Clin 2012; 30 Suppl 2:34-9. [PMID: 22542033 DOI: 10.1016/s0213-005x(12)70080-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Tuberculosis is an opportunistic infection with high morbidity and mortality in solid organ transplant patients. The reasons for this high morbidity and mortality lie mostly in diagnostic difficulties, which cause delays in starting treatment, and associated pharmaceutical toxicity. There are still major issues and difficulties in managing tuberculosis in solid organ transplant patients. These include problems due to interactions between antituberculosis and immunosuppressant drugs, the high risk of toxicity of antituberculosis drugs (particularly in liver transplant patients) and the absence of clear indications for the treatment of latent tuberculous infection. This article updates current understanding of tuberculosis in solid organ transplant patients.
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Affiliation(s)
- Antonio Doblas
- Department of Internal Medicine, Hospital de Alta Resolución Valle del Guadiato, Peñarroya-Pueblonuevo, Córdoba, Spain.
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88
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Chang K, Lu W, Wang J, Zhang K, Jia S, Li F, Deng S, Chen M. Rapid and effective diagnosis of tuberculosis and rifampicin resistance with Xpert MTB/RIF assay: a meta-analysis. J Infect 2012; 64:580-8. [PMID: 22381459 DOI: 10.1016/j.jinf.2012.02.012] [Citation(s) in RCA: 168] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 02/13/2012] [Accepted: 02/21/2012] [Indexed: 10/28/2022]
Abstract
OBJECTIVES Xpert MTB/RIF (Cepheid) assay has been introduced for the diagnosis of tuberculosis (TB) and RIF-resistance. The meta-analysis was used to establish the overall accuracy of Xpert MTB/RIF assay for diagnosing TB and RIF-resistance. METHODS Based on comprehensive searches of the Pubmed and Embase, we identified outcome data from all articles estimating diagnostic accuracy with Xpert MTB/RIF assay. A summary estimation for sensitivity, specificity, diagnostic odds ratios (DOR) and the area under the summary ROC curve (AUC) was calculated by using the bivariate random-effects approach. RESULTS The meta-analysis included 18 studies (10,224 suspected specimens). The summary estimate was 90.4% (95%CI 89.2%-91.4%) for sensitivity, 98.4% (95%CI 98.0%-98.7%) for specificity and 328.3/0.9822 for DOR/AUC in pulmonary tuberculosis (PTB). The sensitivity, specificity and DOR/AUC of detecting RIF-resistance were 94.1%, 97.0% and 177.8/0.9832, respectively. For extrapulmonary tuberculosis, the overall pooled sensitivity was 80.4% and specificity was 86.1%. The findings in subgroup analysis were as follows: the accuracy of Xpert MTB/RIF assay is higher in smear-positive specimens and the sensitivity of diagnosing PTB in adults was higher than that in children (90.8% versus 74.3%). CONCLUSIONS TB and RIF-resistance can be rapidly and effectively diagnosed with Xpert MTB/RIF assay.
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Affiliation(s)
- Kai Chang
- Department of Clinical Laboratory Medicine, Institute of Surgery Research, Daping Hospital, The Third Military Medical University, Chongqing, China
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89
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Silent mutation in rpoB detected from clinical samples with rifampin-susceptible Mycobacterium tuberculosis. J Clin Microbiol 2012; 49:3722. [PMID: 21960703 DOI: 10.1128/jcm.05314-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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90
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Sohn H, Pai M, Dendukuri N, Kloda LA, Boehme CC, Steingart KR. Xpert MTB/RIF test for detection of pulmonary tuberculosis and rifampicin resistance. THE COCHRANE DATABASE OF SYSTEMATIC REVIEWS 2012. [DOI: 10.1002/14651858.cd009593] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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91
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Mi X, He F, Xiang M, Lian Y, Yi S. Novel Phage Amplified Multichannel Series Piezoelectric Quartz Crystal Sensor for Rapid and Sensitive Detection of Mycobacterium tuberculosis. Anal Chem 2011; 84:939-46. [DOI: 10.1021/ac2020728] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xianwen Mi
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, China, 410082
- Huaihua Medical College, Huaihua, Hunan Province, China, 418000
| | - Fengjiao He
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, China, 410082
| | - Meiyu Xiang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, China, 410082
| | - Yan Lian
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, China, 410082
| | - Songlin Yi
- Hunan Institute of Tuberculosis Control, Changsha, China, 410006
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92
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Effectiveness of an integrated real-time PCR method for detection of the Mycobacterium tuberculosis complex in smear-negative extrapulmonary samples in an area of low tuberculosis prevalence. J Clin Microbiol 2011; 50:513-5. [PMID: 22162564 DOI: 10.1128/jcm.06467-11] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Early extrapulmonary tuberculosis (EPTB) diagnosis is particularly difficult. Among 108 smear-negative extrapulmonary samples showing a positive culture for Mycobacterium tuberculosis complex (43 body fluids and 65 nonliquid specimens), 63 (58.3%) were positive with the Xpert MTB/RIF assay (GX). GX sensitivity was quite low for samples from sterile locations (especially for pleural fluids: 26.9%) but high for some nonliquid samples, like abscess aspirates (76.5%). In summary, GX may be a useful tool to be considered for EPTB diagnosis.
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93
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Abstract
This article was based on a presentation given at the 26th International Pediatric Association Conference of Pediatrics, Johannesburg, South Africa, 4-9 August 2010. In 2009, there were 9.4 million new cases of tuberculosis (TB) globally, and, of these, approximately 1 million were pediatric cases. Drug-resistant TB makes up a relatively small proportion of new TB cases, but is much more likely in previously treated cases. Pediatric TB remains difficult to diagnose microbiologically, with the result that detection of drug-resistant TB in children is an ongoing challenge. Since children diagnosed with TB predominantly represent recently acquired TB infection, they provide an important indication of drug-resistant TB prevalence and transmission within their communities. Drug-resistant TB is essentially a man-made problem, which consumes large amounts of healthcare resources. Recent technologic advances may pave the way to more rapid and accurate diagnosis of TB in children. Similarly, these advances are likely to result in improved detection of drug-resistant pediatric TB isolates. The treatment of pediatric drug-resistant TB requires prolonged courses of expensive and potentially toxic drugs, many of which are not available in child-friendly formulations. New anti-TB drugs are at various stages of pre-clinical development and will hopefully allow for shorter, more effective treatment regimens in the not too distant future. HIV-infected children are at extremely high risk for TB acquisition and subsequent progression to symptomatic disease; therefore, many cases of pediatric drug-resistant TB occur in HIV-infected children. This often results in complicated pharmacologic regimens (including anti-TB and antiretroviral drugs) that are difficult to comply with and may have unpredictable interactions. There are limited reports of long-term clinical outcomes of children diagnosed with drug-resistant TB, but improvements in the diagnosis and pharmacologic management of these cases have the potential to improve the quality of care offered to these children.
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Affiliation(s)
- Gary Reubenson
- Department of Paediatrics and Child Health, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Gauteng, South Africa.
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94
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Nicol MP, Workman L, Isaacs W, Munro J, Black F, Eley B, Boehme CC, Zemanay W, Zar HJ. Accuracy of the Xpert MTB/RIF test for the diagnosis of pulmonary tuberculosis in children admitted to hospital in Cape Town, South Africa: a descriptive study. THE LANCET. INFECTIOUS DISEASES 2011; 11:819-24. [PMID: 21764384 PMCID: PMC4202386 DOI: 10.1016/s1473-3099(11)70167-0] [Citation(s) in RCA: 226] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
BACKGROUND WHO recommends that Xpert MTB/RIF replaces smear microscopy for initial diagnosis of suspected HIV-associated tuberculosis or multidrug-resistant pulmonary tuberculosis, but no data exist for its use in children. We aimed to assess the accuracy of the test for the diagnosis of pulmonary tuberculosis in children in an area with high tuberculosis and HIV prevalences. METHODS In this prospective, descriptive study, we enrolled children aged 15 years or younger who had been admitted to one of two hospitals in Cape Town, South Africa, with suspected pulmonary tuberculosis between Feb 19, 2009, and Nov 30, 2010. We compared the diagnostic accuracy of MTB/RIF and concentrated, fluorescent acid-fast smear with a reference standard of liquid culture from two sequential induced sputum specimens (primary analysis). RESULTS 452 children (median age 19·4 months, IQR 11·1-46·2) had at least one induced sputum specimen; 108 children (24%) had HIV infection. 27 children (6%) had a positive smear result, 70 (16%) had a positive culture result, and 58 (13%) had a positive MTB/RIF test result. With mycobacterial culture as the reference standard, MTB/RIF tests when done on two induced sputum samples detected twice as many cases (75·9%, 95% CI 64·5-87·2) as did smear microscopy (37·9%, 25·1-50·8), detecting all of 22 smear-positive cases and 22 of 36 (61·1%, 44·4-77·8) smear-negative cases. For smear-negative cases, the incremental increase in sensitivity from testing a second specimen was 27·8% for MTB/RIF, compared with 13·8% for culture. The specificity of MTB/RIF was 98·8% (97·6-99·9). MTB/RIF results were available in median 1 day (IQR 0-4) compared with median 12 days (9-17) for culture (p<0·0001). INTERPRETATION MTB/RIF testing of two induced sputum specimens is warranted as the first-line diagnostic test for children with suspected pulmonary tuberculosis. FUNDING National Institutes of Health, the National Health Laboratory Service Research Trust, the Medical Research Council of South Africa, and Wellcome Trust.
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Affiliation(s)
- Mark P Nicol
- Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
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95
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Blakemore R, Nabeta P, Davidow AL, Vadwai V, Tahirli R, Munsamy V, Nicol M, Jones M, Persing DH, Hillemann D, Ruesch-Gerdes S, Leisegang F, Zamudio C, Rodrigues C, Boehme CC, Perkins MD, Alland D. A multisite assessment of the quantitative capabilities of the Xpert MTB/RIF assay. Am J Respir Crit Care Med 2011; 184:1076-84. [PMID: 21836139 PMCID: PMC3208646 DOI: 10.1164/rccm.201103-0536oc] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 08/02/2011] [Indexed: 01/29/2023] Open
Abstract
RATIONALE The Xpert MTB/RIF is an automated molecular test for Mycobacterium tuberculosis that estimates bacterial burden by measuring the threshold-cycle (Ct) of its M. tuberculosis-specific real-time polymerase chain reaction. Bacterial burden is an important biomarker for disease severity, infection control risk, and response to therapy. OBJECTIVES Evaluate bacterial load quantitation by Xpert MTB/RIF compared with conventional quantitative methods. METHODS Xpert MTB/RIF results were compared with smear-microscopy, semiquantiative solid culture, and time-to-detection in liquid culture for 741 patients and 2,008 samples tested in a multisite clinical trial. An internal control real-time polymerase chain reaction was evaluated for its ability to identify inaccurate quantitative Xpert MTB/RIF results. MEASUREMENTS AND MAIN RESULTS Assays with an internal control Ct greater than 34 were likely to be inaccurately quantitated; this represented 15% of M. tuberculosis-positive tests. Excluding these, decreasing M. tuberculosis Ct was associated with increasing smear microscopy grade for smears of concentrated sputum pellets (r(s) = -0.77) and directly from sputum (r(s) =-0.71). A Ct cutoff of approximately 27.7 best predicted smear-positive status. The association between M. tuberculosis Ct and time-to-detection in liquid culture (r(s) = 0.68) and semiquantitative colony counts (r(s) = -0.56) was weaker than smear. Tests of paired same-patient sputum showed that high viscosity sputum samples contained ×32 more M. tuberculosis than nonviscous samples. Comparisons between the grade of the acid-fast bacilli smear and Xpert MTB/RIF quantitative data across study sites enabled us to identify a site outlier in microscopy. CONCLUSIONS Xpert MTB/RIF quantitation offers a new, standardized approach to measuring bacterial burden in the sputum of patients with tuberculosis.
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Affiliation(s)
- Robert Blakemore
- Division of Infectious Disease, Department of Medicine, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Pamela Nabeta
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Amy L. Davidow
- Department of Preventive Medicine and Community Health, University of Medicine and Dentistry of New Jersey and Global TB Institute, Newark, New Jersey
| | - Viral Vadwai
- P.D. Hinduja National Hospital and Medical Research Centre (Hinduja), Mumbai, India
| | - Rasim Tahirli
- Special Treatment Institution for Detainees with Tuberculosis, Baku, Republic of Azerbaijan
| | - Vanisha Munsamy
- Unit for Clinical and Biomedical TB Research, South African Medical Research Council, Durban, South Africa
| | - Mark Nicol
- Department of Clinical Laboratory Sciences, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa
| | | | | | | | | | - Felicity Leisegang
- Department of Clinical Laboratory Sciences, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa
| | - Carlos Zamudio
- Instituto de Medicina Tropical “Alexander von Humboldt,” Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Camilla Rodrigues
- P.D. Hinduja National Hospital and Medical Research Centre (Hinduja), Mumbai, India
| | | | - Mark D. Perkins
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - David Alland
- Division of Infectious Disease, Department of Medicine, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
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96
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Dried culture spots for Xpert MTB/RIF external quality assessment: results of a phase 1 pilot study in South Africa. J Clin Microbiol 2011; 49:4356-60. [PMID: 21976767 DOI: 10.1128/jcm.05167-11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Implementation of Xpert MTB/RIF requires quality assessment. A pilot program using dried culture spots (DCSs) of inactivated Mycobacterium tuberculosis is described. Of 274 DCS results received, 2.19% generated errors; the remainder yielded 100% correct Mycobacterium tuberculosis detection. The probe A cycle threshold (C(T)) variability of three DCS batches was ≤ 3.47. The study of longer-term DCS stability is ongoing.
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97
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Evaluation of the GeneXpert MTB/RIF assay for rapid diagnosis of tuberculosis and detection of rifampin resistance in pulmonary and extrapulmonary specimens. J Clin Microbiol 2011; 49:4138-41. [PMID: 21956978 DOI: 10.1128/jcm.05434-11] [Citation(s) in RCA: 196] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium tuberculosis remains one of the most significant causes of death from an infectious agent. The rapid diagnosis of tuberculosis and detection of rifampin (RIF) resistance are essential for early disease management. The GeneXpert MTB/RIF assay is a novel integrated diagnostic device for the diagnosis of tuberculosis and rapid detection of RIF resistance in clinical specimens. We determined the performance of the MTB/RIF assay for rapid diagnosis of tuberculosis and detection of rifampin resistance in smear-positive and smear-negative pulmonary and extrapulmonary specimens obtained from possible tuberculosis patients. Two hundred fifty-three pulmonary and 176 extrapulmonary specimens obtained from 429 patients were included in the study. One hundred ten (89 culture positive and 21 culture negative for M. tuberculosis) of the 429 patients were considered to have tuberculosis. In pulmonary specimens, sensitivities were 100% (27/27) and 68.6% (24/35) for smear-positive and smear-negative specimens, respectively. It had a lower sensitivity with extrapulmonary specimens: 100% for smear-positive specimens (4/4) and 47.7% for smear-negative specimens (21/44). The test accurately detected the absence of tuberculosis in all 319 patients without tuberculosis studied. The MTB/RIF assay also detected 1 RIF-resistant specimen and 88 RIF-susceptible specimens, and the results were confirmed by drug susceptibility testing. We concluded that the MTB/RIF test is a simple method, and routine staff with minimal training can use the system. The test appeared to be as sensitive as culture with smear-positive specimens but less sensitive with smear-negative pulmonary and extrapulmonary specimens that include low numbers of bacilli.
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98
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Lawn SD, Nicol MP. Xpert® MTB/RIF assay: development, evaluation and implementation of a new rapid molecular diagnostic for tuberculosis and rifampicin resistance. Future Microbiol 2011; 6:1067-82. [PMID: 21958145 PMCID: PMC3252681 DOI: 10.2217/fmb.11.84] [Citation(s) in RCA: 290] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Global TB control efforts have been severely hampered by the lack of diagnostic tests that are accurate, simple to use and can be applied at the point of clinical care. This has been further compounded by the widespread inability to test for drug resistance. The Xpert(®) MTB/RIF assay is a rapid molecular assay that can be used close to the point of care by operators with minimal technical expertise, enabling diagnosis of TB and simultaneous assessment of rifampicin resistance to be completed within 2 h. Moreover, this can be accomplished using unprocessed sputum samples as well as clinical specimens from extrapulmonary sites. We review in detail the development of this assay, its evaluation within the laboratory, its utility among adult and pediatric TB suspects, its use as a screening tool for HIV-associated TB and studies of its implementation at the district and sub-district levels in resource-limited settings. Following endorsement by the WHO in 2010, we consider the next steps in the implementation of the assay and its potential impact in high burden settings.
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Affiliation(s)
- Stephen D Lawn
- The Desmond Tutu HIV Centre, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa.
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Comparison of two nucleic acid amplification assays, the Xpert MTB/RIF assay and the amplified Mycobacterium Tuberculosis Direct assay, for detection of Mycobacterium tuberculosis in respiratory and nonrespiratory specimens. J Clin Microbiol 2011; 49:3659-62. [PMID: 21865419 DOI: 10.1128/jcm.00211-11] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We compared the performance of the Xpert MTB/RIF assay, a new real-time tuberculosis (TB) PCR test, with that of the Amplified Mycobacterium Tuberculosis Direct (MTD) assay using 162 respiratory and nonrespiratory specimens. Based on culture as the gold standard, the overall sensitivity and specificity for all sample types for the Xpert MTB/RIF assay were 90.9 and 89%, respectively, while for the MTD assay, the overall sensitivity and specificity were 97.3 and 87.1%, respectively. A higher proportion of total equivocal results were obtained for the MTD assay, at 10.5% (17/162), while the Xpert MTB/RIF assay generated 5.5% (9/162) of invalid reads.
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Performance of Xpert MTB/RIF RUO assay and IS6110 real-time PCR for Mycobacterium tuberculosis detection in clinical samples. J Clin Microbiol 2011; 49:3458-62. [PMID: 21849695 DOI: 10.1128/jcm.05212-11] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The Cepheid Xpert MTB/RIF research-use-only (RUO) assay and a laboratory-developed test (LDT) targeting IS6110 were evaluated and compared to mycobacterial culture as the gold standard. The performance characteristics of both molecular assays were determined by using 112 specimens from 90 patients, including 89 pulmonary specimens and 23 extrapulmonary specimens. Of the specimens tested, 37 (33%) were culture positive for the Mycobacterium tuberculosis complex; 29 were pulmonary, and 8 were extrapulmonary. Of these culture-positive specimens, 83% of the pulmonary specimens and 50% of the extrapulmonary specimens were smear positive. There was complete concordance between the smear-positive culture-positive specimens, independent of the anatomical site (100% sensitivity). The sensitivity of the MTB/RIF RUO assay for smear-negative specimens was 60% for pulmonary and 75% for extrapulmonary specimens, while the IS6110 LDT sensitivities were 40% and 0%, respectively. There was also complete concordance among the culture-negative specimens tested. Both assays showed 95% specificity, with four culture-negative specimens testing as positive. A review of patient records indicated that there was a high likelihood of the presence of M. tuberculosis complex DNA in the false-positive specimens. Biosafety analysis was performed and showed an acceptable reduction in organism viability using the processing methods described above. Both molecular assays are suitable for the detection of M. tuberculosis isolates in smear-positive pulmonary and extrapulmonary specimens, while the sensitivity of the detection of M. tuberculosis isolates in smear-negative specimens was variable.
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