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Difficulties with the implemented xpert MTB/RIF for determining diagnosis of pulmonary and extrapulmonary tuberculosis in adults and children. J Clin Tuberc Other Mycobact Dis 2020; 19:100159. [PMID: 32258438 PMCID: PMC7109450 DOI: 10.1016/j.jctube.2020.100159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background and aims Handling of PTB and EPTB patients with adequate standard detection of MTBC and anti-TB drug sensitivity using accurate and rapid methods could provide good TB management and clinical treatment outcomes. The Xpert MTB/RIF assay is an automated, cartridge-based NAAT that can simultaneously detect MTBC and RIF resistance within 2 h. The aim of this study was to evaluate the implementation of Xpert for determining diagnosis of PTB and EPTB in adults and children. Methods A descriptive study was performed using e-TB Manager data from the MDR-TB Clinic at Dr. Soetomo Academic Hospital. Suspected TB cases were from the areas of East Java Province from January 2016 to December 2018. Xpert assay was conducted using standardized criteria for clinically suspected TB, and MTBC-positive results with RR were examined by the culture method using MGIT 960 BACTEC System. Results A total of 1181 (1181/3009, 39.25%) sputum samples from suspected new MDR-PTB cases tested positive for MTBC with 3.02% RR. Among 3893 sputum samples from previously treated probable MDR-PTB cases tested using Xpert, 1936 (49.73%) were MTBC positive with 13.20% RR. Among 59 new suspected MDR-PTB cases tested using MGIT 960 BACTEC System, 55 tested positive for MTBC, although all RR strains were highly sensitive to amikacin (100%), kanamycin (95%), and ofloxacin (89%). A total of 49 children with suspected PTB were tested using Xpert, revealing low positivity (12%) for MTBC, with all RR strains being rifampicin sensitive (RS). Of the 86 suspected EPTB cases tested using Xpert, very few were MTBC-positive (26%), with 91% RS. Conclusions This study revealed that in adults and children with PTB and EPTB, the Xpert assay achieved a low positivity detection rate for MTBC in samples from new or previously treated cases, and this could be the result of many factors.
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2
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Banada PP, Deshpande S, Banik S, Shah D, Koshy R, Patel B, Kwiatkowski R, Persing D, Alland D. Multiplex Detection of Three Select Agents Directly from Blood by Use of the GeneXpert System. J Clin Microbiol 2019; 57:e00036-19. [PMID: 30842226 PMCID: PMC6498027 DOI: 10.1128/jcm.00036-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/25/2019] [Indexed: 12/20/2022] Open
Abstract
Francisella tularensis, Bacillus anthracis, and Yersinia pestis are tier 1 select agents with the potential to rapidly cause severe disease. Rapid detection of these bacteria from patient samples at the point of care could contribute to improved clinical outcomes in the event of a bioterrorism attack. A multiplex nested PCR assay for detection of F. tularensis, B. anthracis, and Y. pestis directly from patient blood samples was developed using the GeneXpert system. The multiplex GeneXpert cartridge-based assay includes all necessary sample processing and amplification reagents. Blood samples spiked with different numbers of CFU were used to measure the analytical limit of detection (LOD) and dynamic range. Sensitivity was determined by testing spiked blood samples and negative-control blood in a blind manner. Specificity was determined by testing against nontarget pathogens and blood samples from clinical patients. The assay LOD was 8.5 CFU/ml for F. tularensis, 10 CFU/ml for B. anthracis, and 4.5 CFU/ml for Y. pestis The sensitivity was 100% at the LOD for all three select agent bacteria in spiked patient blood samples. The assay specificity was 100% when it was tested against both nontarget pathogens and clinical patient blood samples. The total assay time was approximately 100 min. This automated assay, which is suitable for use at the point of care, identifies three select agents directly in blood without the need for enrichment with a high sensitivity within 100 min. This assay may enable rapid detection and treatment of patients infected with the target organisms in the event of a bioterrorism attack.
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Affiliation(s)
- Padmapriya P Banada
- Center for Emerging Pathogens, Division of Infectious Diseases, New Jersey Medical School, Rutgers Biomedical and Health Sciences University, Newark, New Jersey, USA
| | - Srinidhi Deshpande
- Center for Emerging Pathogens, Division of Infectious Diseases, New Jersey Medical School, Rutgers Biomedical and Health Sciences University, Newark, New Jersey, USA
| | - Sukalyani Banik
- Center for Emerging Pathogens, Division of Infectious Diseases, New Jersey Medical School, Rutgers Biomedical and Health Sciences University, Newark, New Jersey, USA
| | - Darshini Shah
- Department of Pathology and Laboratory Medicine, University Hospital, Newark, New Jersey, USA
| | - Ranie Koshy
- Blood Bank/Transfusion Service, University Hospital, Newark, New Jersey, USA
| | - Bhavana Patel
- Department of Pathology and Laboratory Medicine, University Hospital, Newark, New Jersey, USA
| | | | | | - David Alland
- Center for Emerging Pathogens, Division of Infectious Diseases, New Jersey Medical School, Rutgers Biomedical and Health Sciences University, Newark, New Jersey, USA
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Singh AV, Chauhan DS. Mycobacterium bovis-induced Human Tuberculosis in Central India. J Epidemiol Glob Health 2019; 8:101. [PMID: 30859795 PMCID: PMC7325821 DOI: 10.2991/j.jegh.2018.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ajay Vir Singh
- Department of Microbiology and Molecular Biology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra 282001, India
| | - Devendra Singh Chauhan
- Department of Microbiology and Molecular Biology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra 282001, India
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4
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Kim SU, Batule BS, Mun H, Byun JY, Shim WB, Kim MG. Colorimetric molecular diagnosis of the HIV gag gene using DNAzyme and a complementary DNA-extended primer. Analyst 2018; 143:695-699. [PMID: 29299545 DOI: 10.1039/c7an01520h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have developed a novel strategy for the colorimetric detection of PCR products by utilizing a target-specific primer modified at the 5'-end with an anti-DNAzyme sequence. A single-stranded DNAzyme sequence folds into a G-quadruplex structure with hemin and shows strong peroxidase activity. When the complementary strand binds to the DNAzyme sequence, it blocks the formation of the G-quadraduplex structure and loses its peroxidase activity. In the presence of the target gene, PCR amplification proceeds, and anti-DNAzyme sequence modified primers present in the reaction mixture form a double strand through primer extension. Therefore, it does not block the DNAzyme sequence. Further, a colorimetric signal is generated by the addition of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS) and H2O2 at the end of the reaction. We have successfully detected a single copy of the HIV type 1 gag gene in buffer and 10 copies in human serum. The strategy developed could be used to detect DNA and RNA in complex biological samples by simple primer designing that includes DNAzyme and a DNA extended primer.
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Affiliation(s)
- Seong U Kim
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, 261 Chemdan-gwagiro, Gwangju 500-712, Republic of Korea.
| | - Bhagwan S Batule
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 261 Chemdan-gwagiro, Gwangju 500-712, Republic of Korea
| | - Hyoyoung Mun
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 261 Chemdan-gwagiro, Gwangju 500-712, Republic of Korea
| | - Ju-Young Byun
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 261 Chemdan-gwagiro, Gwangju 500-712, Republic of Korea
| | - Won-Bo Shim
- Department of Agricultural Chemistry and Food Science and Technology, Gyeongsang National University, 900 Gajwa-dong Jinju, Gyeongnam 660-701, Republic of Korea
| | - Min-Gon Kim
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, 261 Chemdan-gwagiro, Gwangju 500-712, Republic of Korea. and Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 261 Chemdan-gwagiro, Gwangju 500-712, Republic of Korea
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5
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Kolluri N, Klapperich CM, Cabodi M. Towards lab-on-a-chip diagnostics for malaria elimination. LAB ON A CHIP 2017; 18:75-94. [PMID: 29125615 DOI: 10.1039/c7lc00758b] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Malaria continues to be one of the most devastating diseases impacting global health. Although there have been significant reductions in global malaria incidence and mortality rates over the past 17 years, the disease remains endemic throughout the world, especially in low- and middle-income countries. The World Health Organization has put forth ambitious milestones moving toward a world free of malaria as part of the United Nations Millennium Goals. Mass screening and treatment of symptomatic and asymptomatic malaria infections in endemic regions is integral to these goals and requires diagnostics that are both sensitive and affordable. Lab-on-a-chip technologies provide a path toward sensitive, portable, and affordable diagnostic platforms. Here, we review and compare currently-available and emerging lab-on-a-chip diagnostic approaches in three categories: (1) protein-based tests, (2) nucleic acid tests, and (3) cell-based detection. For each category, we highlight the opportunities and challenges in diagnostics development for malaria elimination, and comment on their applicability to different phases of elimination strategies.
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Affiliation(s)
- N Kolluri
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
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6
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Kerkhoff AD, Barr DA, Schutz C, Burton R, Nicol MP, Lawn SD, Meintjes G. Disseminated tuberculosis among hospitalised HIV patients in South Africa: a common condition that can be rapidly diagnosed using urine-based assays. Sci Rep 2017; 7:10931. [PMID: 28883510 PMCID: PMC5589905 DOI: 10.1038/s41598-017-09895-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/31/2017] [Indexed: 01/04/2023] Open
Abstract
HIV-associated disseminated TB (tuberculosis) has been under-recognised and poorly characterised. Blood culture is the gold-standard diagnostic test, but is expensive, slow, and may under-diagnose TB dissemination. In a cohort of hospitalised HIV patients, we aimed to report the prevalence of TB-blood-culture positivity, performance of rapid diagnostics as diagnostic surrogates, and better characterise the clinical phenotype of disseminated TB. HIV-inpatients were systematically investigated using sputum, urine and blood testing. Overall, 132/410 (32.2%) patients had confirmed TB; 41/132 (31.1%) had a positive TB blood culture, of these 9/41 (22.0%) died within 90-days. In contrast to sputum diagnostics, urine Xpert and urine-lipoarabinomannan (LAM) combined identified 88% of TB blood-culture-positive patients, including 9/9 who died within 90-days. For confirmed-TB patients, half the variation in major clinical variables was captured on two principle components (PCs). Urine Xpert, urine LAM and TB-blood-culture positive patients clustered similarly on these axes, distinctly from patients with localised disease. Total number of positive tests from urine Xpert, urine LAM and MTB-blood-culture correlated with PCs (p < 0.001 for both). PC1&PC2 independently predicted 90-day mortality (ORs 2.6, 95%CI = 1.3-6.4; and 2.4, 95%CI = 1.3-4.5, respectively). Rather than being a non-specific diagnosis, disseminated TB is a distinct, life-threatening condition, which can be diagnosed using rapid urine-based tests, and warrants specific interventional trials.
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Affiliation(s)
- Andrew D Kerkhoff
- Division of Infectious Disease, Department of Medicine, University of California San Francisco School of Medicine, San Francisco, CA, USA.
| | - David A Barr
- Wellcome Trust Liverpool Glasgow Centre for Global Health Research, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.,Wellcome Trust Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Charlotte Schutz
- Wellcome Trust Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Rosie Burton
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Department of Medicine, Faculty of Medicine and Health Sciences, University of Stellenbosch, Cape Town, South Africa.,Southern African Medical Unit, Médecins Sans Frontières, Cape Town, South Africa
| | - Mark P Nicol
- Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Stephen D Lawn
- The Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Graeme Meintjes
- Wellcome Trust Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Rapid Detection of Bacillus anthracis Bloodstream Infections by Use of a Novel Assay in the GeneXpert System. J Clin Microbiol 2017; 55:2964-2971. [PMID: 28747367 DOI: 10.1128/jcm.00466-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 07/13/2017] [Indexed: 11/20/2022] Open
Abstract
Bacillus anthracis is a tier 1 select agent with the potential to quickly cause severe disease. Rapid identification of this pathogen may accelerate treatment and reduce mortality in the event of a bioterrorism attack. We developed a rapid and sensitive assay to detect B. anthracis bacteremia using a system that is suitable for point-of-care testing. A filter-based cartridge that included both sample processing and PCR amplification functions was loaded with all reagents needed for sample processing and multiplex nested PCR. The assay limit of detection (LOD) and dynamic range were determined by spiking B. anthracis DNA into individual PCR mixtures and B. anthracis CFU into human blood. One-milliliter blood samples were added to the filter-based detection cartridge and tested for B. anthracis on a GeneXpert instrument. Assay specificity was determined by testing blood spiked with non-anthrax bacterial isolates or by testing blood samples drawn from patients with concurrent non-B. anthracis bacteremia or nonbacteremic controls. The assay LODs were 5 genome equivalents per reaction and 10 CFU/ml blood for both the B. anthracis Sterne and V1B strains. There was a 6-log10 dynamic range. Assay specificity was 100% for tests of non-B. anthracis bacterial isolates and patient blood samples. Assay time was less than 90 min. This automated system suitable for point-of-care detection rapidly identifies B. anthracis directly from blood with high sensitivity. This assay might lead to early detection and more rapid therapy in the event of a bioterrorism attack.
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8
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Rindi L, Alì G, Fabiani B, Fontanini G, Garzelli C. Detection of Mycobacterium tuberculosis from paraffin-embedded tissues by GeneXpert MTB/RIF. Tuberculosis (Edinb) 2017; 106:53-55. [PMID: 28802405 DOI: 10.1016/j.tube.2017.06.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 11/19/2022]
Abstract
GeneXpert MTB/RIF (Xpert) assay, a rapid and automated system based on real-time PCR and molecular beacon technology, proved to be a sensitive and specific tool capable of detecting Mycobacterium tuberculosis and rifampin resistance in clinical specimens. In this study we provide a Xpert-dedicated successful protocol for processing paraffin-embedded tissue and assess the feasibility of the Xpert assay-based tuberculosis (TB) diagnosis on these specimens, thus proving the Xpert assay as a valuable TB diagnostic tool in supporting conventional histopathological methods.
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MESH Headings
- Antibiotics, Antitubercular/pharmacology
- Automation, Laboratory
- Bacteriological Techniques
- Biopsy
- Case-Control Studies
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- Drug Resistance, Bacterial/genetics
- Humans
- Microbial Sensitivity Tests
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- Paraffin Embedding
- Predictive Value of Tests
- Real-Time Polymerase Chain Reaction/methods
- Rifampin/pharmacology
- Tuberculosis, Lymph Node/diagnosis
- Tuberculosis, Lymph Node/genetics
- Tuberculosis, Lymph Node/pathology
- Tuberculosis, Pleural/diagnosis
- Tuberculosis, Pleural/genetics
- Tuberculosis, Pleural/pathology
- Tuberculosis, Pulmonary/diagnosis
- Tuberculosis, Pulmonary/genetics
- Tuberculosis, Pulmonary/pathology
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Affiliation(s)
- Laura Rindi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, I-56127, Pisa, Italy.
| | - Greta Alì
- Unit of Pathological Anatomy, University Hospital of Pisa, I-56126, Pisa, Italy
| | - Barbara Fabiani
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, I-56127, Pisa, Italy
| | - Gabriella Fontanini
- Department of Surgical, Medical and Molecular Pathology and Critical Area, University of Pisa, I-56126, Pisa, Italy
| | - Carlo Garzelli
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, I-56127, Pisa, Italy
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Rapid culture-based detection of living mycobacteria using microchannel electrical impedance spectroscopy (m-EIS). Biol Res 2017; 50:21. [PMID: 28601089 PMCID: PMC5466763 DOI: 10.1186/s40659-017-0126-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 06/01/2017] [Indexed: 11/12/2022] Open
Abstract
Background Multiple techniques exist for detecting Mycobacteria, each having its own advantages and drawbacks. Among them, automated culture-based systems like the BACTEC-MGIT™ are popular because they are inexpensive, reliable and highly accurate. However, they have a relatively long “time-to-detection” (TTD). Hence, a method that retains the reliability and low-cost of the MGIT system, while reducing TTD would be highly desirable. Methods Living bacterial cells possess a membrane potential, on account of which they store charge when subjected to an AC-field. This charge storage (bulk capacitance) can be estimated using impedance measurements at multiple frequencies. An increase in the number of living cells during culture is reflected in an increase in bulk capacitance, and this forms the basis of our detection. M. bovis BCG and M. smegmatis suspensions with differing initial loads are cultured in MGIT media supplemented with OADC and Middlebrook 7H9 media respectively, electrical “scans” taken at regular intervals and the bulk capacitance estimated from the scans. Bulk capacitance estimates at later time-points are statistically compared to the suspension’s baseline value. A statistically significant increase is assumed to indicate the presence of proliferating mycobacteria. Results Our TTDs were 60 and 36 h for M. bovis BCG and 20 and 9 h for M. smegmatis with initial loads of 1000 CFU/ml and 100,000 CFU/ml respectively. The corresponding TTDs for the commercial BACTEC MGIT 960 system were 131 and 84.6 h for M. bovis BCG and 41.7 and 12 h for M smegmatis, respectively. Conclusion Our culture-based detection method using multi-frequency impedance measurements is capable of detecting mycobacteria faster than current commercial systems.
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Mavenyengwa RT, Shaduka E, Maposa I. Evaluation of the Xpert® MTB/RIF assay and microscopy for the diagnosis of Mycobacterium tuberculosis in Namibia. Infect Dis Poverty 2017; 6:13. [PMID: 28086955 PMCID: PMC5237317 DOI: 10.1186/s40249-016-0213-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 12/09/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) kills approximately two million people and infects around nine million worldwide annually. Its proper management, especially in resource-limited settings, has been hindered by the lack of rapid and easy-to-use diagnostic tests. Sputum smear microscopy remains the cheapest, readily available diagnostic method but it only identifies less than half of the patients with a HIV/TB co-infection because the bacilli would have disseminated from the lungs to other areas of the body. The fully automated Xpert® MTB/RIF assay is a promising innovation for diagnosing TB and detecting resistance to rifampicin. This study aimed to evaluate the use of Xpert® MTB/RIF assay and microscopy in the diagnosis of Mycobacterium tuberculosis in Namibia, by determining the disease's epidemiology and calculating the proportion of cases infected just with TB and those with a resistance to rifampicin among the total suspected cases of TB in the country. METHODS This retrospective study analysed TB cases that were diagnosed using both the Xpert® MTB/RIF assay and microscopy. Data were collected from patient records from the Meditech laboratory information system of the Namibia Institute of Pathology for the time period of July 2012-April 2013. Data from 13 regions were collected. RESULTS The total number of specimens collected from patients with symptoms of pulmonary TB was 1 842. Of these, 594 (32.20%) were found to be positive for MTB by Xpert® MTB/RIF assay, out of which 443 (24.05%) were also found to be positive by microscopy. The remainder was negative. The male patients were more resistant to rifampicin when compared to the female patients. CONCLUSIONS Tuberculosis is widely distributed throughout Namibia, with slightly more males infected than females. Most TB patients are also co-infected with HIV. Both microscopy and Xpert® MTB/RIF assay are crucial for the diagnosis of TB in the country. Screening diagnostic efforts should focus on the sexually active HIV positive male population who could be the source of more RIF-resistant TB than females to prevent its spread.
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Affiliation(s)
- Rooyen T Mavenyengwa
- Department of Health Sciences, School of Health and Applied Sciences, Namibia University of Science and Technology, Private Bag 13388, Windhoek, Namibia. .,Department of Medical Microbiology, University of Zimbabwe College of Health Sciences, P. O. Box A178, Harare, Zimbabwe.
| | - Emma Shaduka
- Department of Health Sciences, School of Health and Applied Sciences, Namibia University of Science and Technology, Private Bag 13388, Windhoek, Namibia
| | - Innocent Maposa
- Department of Mathematics and Statistics, Namibia University of Science and Technology, Private Bag 13388, Windhoek, Namibia
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11
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Sensitive Detection of Francisella tularensis Directly from Whole Blood by Use of the GeneXpert System. J Clin Microbiol 2016; 55:291-301. [PMID: 27847371 DOI: 10.1128/jcm.01126-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/02/2016] [Indexed: 11/20/2022] Open
Abstract
Francisella tularensis is a potential bioterrorism agent that is highly infectious at very low doses. Diagnosis of tularemia by blood culture and nucleic acid-based diagnostic tests is insufficiently sensitive. Here, we demonstrate a highly sensitive F. tularensis assay that incorporates sample processing and detection into a single cartridge suitable for point-of-care detection. The assay limit of detection (LOD) and dynamic range were determined in a filter-based cartridge run on the GeneXpert system. F. tularensis DNA in buffer or CFU of F. tularensis was spiked into human or macaque blood. To simulate detection in human disease, the assay was tested on blood drawn from macaques infected with F. tularensis Schu S4 at daily intervals. Assay detection was compared to that with a conventional quantitative PCR (qPCR) assay and blood culture. The assay LOD was 0.1 genome equivalents (GE) per reaction and 10 CFU/ml F. tularensis in both human and macaque blood. In infected macaques, the assay detected F. tularensis on days 1 to 4 postinfection in 21%, 17%, 60%, and 83% of macaques, respectively, compared to conventional qPCR positivity rates of 0%, 0%, 30%, and 100% and CFU detection of blood culture at 0%, 0%, 0%, and 10% positive, respectively. Assay specificity was 100%. The new cartridge-based assay can rapidly detect F. tularensis in bloodstream infections directly in whole blood at the early stages of infection with a sensitivity that is superior to that of other methods. The simplicity of the automated testing procedures may make this test suitable for rapid point-of-care detection.
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12
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Pohl C, Rutaihwa LK, Haraka F, Nsubuga M, Aloi F, Ntinginya NE, Mapamba D, Heinrich N, Hoelscher M, Marais BJ, Jugheli L, Reither K. Limited value of whole blood Xpert(®) MTB/RIF for diagnosing tuberculosis in children. J Infect 2016; 73:326-35. [PMID: 27394403 DOI: 10.1016/j.jinf.2016.04.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 04/26/2016] [Accepted: 04/28/2016] [Indexed: 10/21/2022]
Abstract
OBJECTIVES We evaluated the ability of the Xpert(®) MTB/RIF assay to detect Mycobacterium tuberculosis in whole blood of children with tuberculosis in tuberculosis endemic settings with high rates of HIV infection. METHODS From June 2011 to September 2012 we prospectively enrolled children with symptoms or signs suggestive of tuberculosis at three research centres in Tanzania and Uganda. After clinical assessment, respiratory specimens were collected for microscopy and culture, as well as whole blood for Xpert(®) MTB/RIF. Children were classified according to standardised case definitions. RESULTS A total of 232 children were evaluated; 14 (6.0%) had culture-confirmed tuberculosis. The Xpert(®) MTB/RIF assay detected M. tuberculosis in 5/232 (2.2%) blood samples with 1 (0.4%) error reading and presumably 1 (0.4%) false-positive result. The sensitivity of the assay in children with culture-confirmed (1/14) versus no tuberculosis (1/117) was 7.1% (95% CI, 1.3-31.5). Three of the five Xpert(®) MTB/RIF positive patients had negative cultures, but were classified as probable tuberculosis cases. Assay sensitivity against a composite reference standard (culture-confirmed, highly probable or probable tuberculosis) was 5.4% (95% CI, 2.1-13.1). CONCLUSION Whole blood Xpert(®) MTB/RIF demonstrated very poor sensitivity, although it may enhance the diagnostic yield in select cases, with culture-negative tuberculosis.
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Affiliation(s)
- Christian Pohl
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland; Ifakara Health Institute, Bagamoyo, Tanzania.
| | - Liliana K Rutaihwa
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland; Ifakara Health Institute, Bagamoyo, Tanzania
| | | | | | | | | | | | - Norbert Heinrich
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich, Munich, Germany; German Center for Infection Research, Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich, Munich, Germany; German Center for Infection Research, Munich, Germany
| | - Ben J Marais
- The Children's Hospital at Westmead, Sydney Medical School, University of Sydney, Sydney, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
| | - Levan Jugheli
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland; Ifakara Health Institute, Bagamoyo, Tanzania
| | - Klaus Reither
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland; Ifakara Health Institute, Bagamoyo, Tanzania
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13
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Lima JFDC, Guedes GDMR, Lima JFDA, Lira LADS, Santos FCF, Arruda MED, Montenegro LML, Schindler HC. Single-tube nested PCR assay with in-house DNA extraction for Mycobacterium tuberculosis detection in blood and urine. Rev Soc Bras Med Trop 2016; 48:731-8. [PMID: 26676498 DOI: 10.1590/0037-8682-0210-2015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/10/2015] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION Molecular analyses are auxiliary tools for detecting Koch's bacilli in clinical specimens from patients with suspected tuberculosis (TB). However, there are still no efficient diagnostic tests that combine high sensitivity and specificity and yield rapid results in the detection of TB. This study evaluated single-tube nested polymerase chain reaction (STNPCR) as a molecular diagnostic test with low risk of cross contamination for detecting Mycobacterium tuberculosis in clinical samples. METHODS Mycobacterium tuberculosis deoxyribonucleic acid (DNA) was detected in blood and urine samples by STNPCR followed by agarose gel electrophoresis. In this system, reaction tubes were not opened between the two stages of PCR (simple and nested). RESULTS STNPCR demonstrated good accuracy in clinical samples with no cross contamination between microtubes. Sensitivity in blood and urine, analyzed in parallel, was 35%-62% for pulmonary and 41%-72% for extrapulmonary TB. The specificity of STNPCR was 100% in most analyses, depending on the type of clinical sample (blood or urine) and clinical form of disease (pulmonary or extrapulmonary). CONCLUSIONS STNPCR was effective in detecting TB, especially the extrapulmonary form for which sensitivity was higher, and had the advantage of less invasive sample collection from patients for whom a spontaneous sputum sample was unavailable. With low risk of cross contamination, the STNPCR can be used as an adjunct to conventional methods for diagnosing TB.
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Affiliation(s)
| | - Gabriela de Moraes Rêgo Guedes
- Laboratório de Imunoepidemiologia, Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | - Juliana Falcão de Araújo Lima
- Laboratório de Imunoepidemiologia, Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | - Laís Ariane de Siqueira Lira
- Laboratório de Imunoepidemiologia, Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | - Fabiana Cristina Fulco Santos
- Laboratório de Imunoepidemiologia, Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | - Mercia Eliane de Arruda
- Laboratório de Imunoepidemiologia, Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | - Lílian Maria Lapa Montenegro
- Laboratório de Imunoepidemiologia, Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | - Haiana Charifker Schindler
- Laboratório de Imunoepidemiologia, Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
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14
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Banada PP, Naidoo U, Deshpande S, Karim F, Flynn JL, O’Malley M, Jones M, Nanassy O, Jeena P, Alland D. A Novel Sample Processing Method for Rapid Detection of Tuberculosis in the Stool of Pediatric Patients Using the Xpert MTB/RIF Assay. PLoS One 2016; 11:e0151980. [PMID: 27007974 PMCID: PMC4805262 DOI: 10.1371/journal.pone.0151980] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 03/07/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is difficult to diagnose in children using molecular tests, because children have difficulty providing respiratory samples. Stool could replace sputum for diagnostic TB testing if adequate sample processing techniques were available. METHODS We developed a rapid method to process large volumes of stool for downstream testing by the Xpert MTB/RIF (Xpert) TB-detection assay. The method was tested and optimized on stool samples spiked with known numbers of M. tuberculosis colony forming units (CFU), and stools from M. tuberculosis-infected cynomolgus macaques (Macaca fascicularis). Performance was scored on number of positive Xpert tests, the cycle thresholds (Cts) of the Xpert sample-processing control (SPC), and the Cts of the M. tuberculosis-specific rpoB probes. The method was then validated on 20 confirmed TB cases and 20 controls in Durban, South Africa. RESULTS The assay's analytical limit of detection was 1,000 CFU/g of stool. As much as one gram of spiked stool could be tested without showing increased PCR inhibition. In analytical spiking experiments using human stool, 1g samples provided the best sensitivity compared to smaller amounts of sample. However, in Macaques with TB, 0.6g stool samples performed better than either 0.2g or 1.2g samples. Testing the stool of pediatric TB suspects and controls suggested an assay sensitivity of 85% (95% CI 0.6-0.9) and 84% (95% CI 0.6-0.96) for 0.6g and 1.2g stool samples, respectively, and a specificity of 100% (95% CI 0.77-1) and 94% (95% CI 0.7-0.99), respectively. CONCLUSION This novel approach may permit simple and rapid detection of TB using pediatric stool samples.
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Affiliation(s)
- Padmapriya P. Banada
- Center for Infectious Diseases, New Jersey Medical School - Rutgers University, Newark, New Jersey, United States of America
| | - Uvistra Naidoo
- KwaZulu-Natal Research Institute for TB/HIV (K-RITH), Durban, South Africa
| | - Srinidhi Deshpande
- Center for Infectious Diseases, New Jersey Medical School - Rutgers University, Newark, New Jersey, United States of America
| | - Farina Karim
- KwaZulu-Natal Research Institute for TB/HIV (K-RITH), Durban, South Africa
| | - JoAnne L. Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Melanie O’Malley
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Martin Jones
- Cepheid, 904 Caribbean Drive, Sunnyvale, California, United States of America
| | | | - Prakash Jeena
- KwaZulu-Natal Research Institute for TB/HIV (K-RITH), Durban, South Africa
| | - David Alland
- Center for Infectious Diseases, New Jersey Medical School - Rutgers University, Newark, New Jersey, United States of America
- * E-mail:
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15
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García-Basteiro AL, Ismail MR, Carrilho C, Ussene E, Castillo P, Chitsungo D, Rodríguez C, Lovane L, Vergara A, López-Varela E, Mandomando I, Lorenzoni C, Ordi J, Menéndez C, Bassat Q, Martínez MJ. The role of Xpert MTB/RIF in diagnosing pulmonary tuberculosis in post-mortem tissues. Sci Rep 2016; 6:20703. [PMID: 26860394 PMCID: PMC4748254 DOI: 10.1038/srep20703] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/05/2016] [Indexed: 01/10/2023] Open
Abstract
The extent to which the Xpert MTB/RIF (Gene Xpert) contributes to tuberculosis (TB) diagnosis in samples other than sputum and cerebrospinal fluid remains uncertain. We aimed to assess the role of Xpert MTB/RIF for detecting M. tuberculosis in post-mortem tissues. We conducted a study among 30 complete diagnostic autopsies (CDA) performed at the Maputo Central Hospital (Mozambique). Lung tissues were screened for TB in all cases. In addition other tissues were tested when compatible lesions were identified in the histological exam. We used in-house real time PCR and LAMP assays to confirm the presence of M. tuberculosis DNA. The diagnosis of tuberculosis at death was established based on microbiological and histopathological results. Eight out of 30 cases (26.7%) were diagnosed of tuberculosis. Xpert had a sensitivity to detect TB in lung tissue of 87.5% (95% CI 47.3–99.7) and a specificity of 95.7% (95% CI: 78.1–99.9). In-house DNA amplification methods and Xpert showed 93.6% concordance for lung tissue and 100% concordance for brain and liver tissues. The final cause of death was attributable to tuberculosis in four cases. Xpert MTB/RIF may represent a valuable, easy-to perform technique for post-mortem TB diagnosis.
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Affiliation(s)
- Alberto L García-Basteiro
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique.,ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Mamudo R Ismail
- Department of Pathology, Faculty of Medicine/Eduardo Mondlane University and Maputo Central Hospital, Maputo, Mozambique
| | - Carla Carrilho
- Department of Pathology, Faculty of Medicine/Eduardo Mondlane University and Maputo Central Hospital, Maputo, Mozambique
| | - Esperança Ussene
- Department of Pathology, Faculty of Medicine/Eduardo Mondlane University and Maputo Central Hospital, Maputo, Mozambique
| | - Paola Castillo
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Department of Pathology, Hospital Clinic, Universitat de Barcelona, Spain
| | - Dércio Chitsungo
- Department of Pathology, Faculty of Medicine/Eduardo Mondlane University and Maputo Central Hospital, Maputo, Mozambique
| | - Cristina Rodríguez
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Department of Clinical Microbiology, Hospital Clinic, Universitat de Barcelona, Spain
| | - Lucília Lovane
- Department of Pathology, Faculty of Medicine/Eduardo Mondlane University and Maputo Central Hospital, Maputo, Mozambique
| | - Andrea Vergara
- Department of Clinical Microbiology, Hospital Clinic, Universitat de Barcelona, Spain
| | - Elisa López-Varela
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique.,ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Inacio Mandomando
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique.,Instituto Nacional de Saúde (INS), Ministério da Saúde, Maputo, Moçambique
| | - Cesaltina Lorenzoni
- Department of Pathology, Faculty of Medicine/Eduardo Mondlane University and Maputo Central Hospital, Maputo, Mozambique
| | - Jaume Ordi
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Department of Pathology, Hospital Clinic, Universitat de Barcelona, Spain
| | - Clara Menéndez
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique.,ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Quique Bassat
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique.,ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Miguel J Martínez
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Department of Clinical Microbiology, Hospital Clinic, Universitat de Barcelona, Spain
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16
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Hanrahan CF, Shah M. Economic challenges associated with tuberculosis diagnostic development. Expert Rev Pharmacoecon Outcomes Res 2014; 14:499-510. [PMID: 24766367 PMCID: PMC4605384 DOI: 10.1586/14737167.2014.914438] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Tuberculosis remains a global health crisis in part due to underdiagnosis. Technological innovations are needed to improve diagnostic test accuracy and reduce the reliance on expensive laboratory infrastructure. However, there are significant economic challenges impeding the development and implementation of new diagnostics. The aim of this piece is to examine the current state of TB diagnostics, outline the unmet needs for new tests, and detail the economic challenges associated with development of new tests from the perspective of developers, policy makers and implementers.
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Affiliation(s)
- Colleen F. Hanrahan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St., E6039, Baltimore, MD 21205, USA
| | - Maunank Shah
- Department of Medicine, Johns Hopkins School of Medicine, 725 N. Wolfe St., Room 224, Baltimore, MD 21205, USA
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17
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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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18
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Pandie S, Peter JG, Kerbelker ZS, Meldau R, Theron G, Govender U, Ntsekhe M, Dheda K, Mayosi BM. Diagnostic accuracy of quantitative PCR (Xpert MTB/RIF) for tuberculous pericarditis compared to adenosine deaminase and unstimulated interferon-γ in a high burden setting: a prospective study. BMC Med 2014; 12:101. [PMID: 24942470 PMCID: PMC4073812 DOI: 10.1186/1741-7015-12-101] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 05/28/2014] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Tuberculous pericarditis (TBP) is associated with high morbidity and mortality, and is an important treatable cause of heart failure in developing countries. Tuberculous aetiology of pericarditis is difficult to diagnose promptly. The utility of the new quantitative PCR test (Xpert MTB/RIF) for the diagnosis of TBP is unknown. This study sought to evaluate the diagnostic accuracy of the Xpert MTB/RIF test compared to pericardial adenosine deaminase (ADA) and unstimulated interferon-gamma (uIFNγ) in suspected TBP. METHODS From October 2009 through September 2012, 151 consecutive patients with suspected TBP were enrolled at a single centre in Cape Town, South Africa. Mycobacterium tuberculosis culture and/or pericardial histology served as the reference standard for definite TBP. Receiver-operating-characteristic curve analysis was used for selection of ADA and uIFNγ cut-points. RESULTS Of the participants, 49% (74/151) were classified as definite TBP, 33% (50/151) as probable TBP and 18% (27/151) as non TBP. A total of 105 (74%) participants were human immunodeficiency virus (HIV) positive. Xpert-MTB/RIF had a sensitivity and specificity (95% confidence interval (CI)) of 63.8% (52.4% to 75.1%) and 100% (85.6% to 100%), respectively. Concentration of pericardial fluid by centrifugation and using standard sample processing did not improve Xpert MTB/RIF accuracy. ADA (≥35 IU/L) and uIFNγ (≥44 pg/ml) both had a sensitivity of 95.7% (88.1% to 98.5%) and a negative likelihood ratio of 0.05 (0.02 to 0.10). However, the specificity and positive likelihood ratio of uIFNγ was higher than ADA (96.3% (81.7% to 99.3%) and 25.8 (3.6 to 183.4) versus 84% (65.4% to 93.6%) and 6.0 (3.7 to 9.8); P = 0.03) at an estimated background prevalence of TB of 30%. The sensitivity and negative predictive value of both uIFNγ and ADA were higher than Xpert-MT/RIF (P < 0.001). CONCLUSIONS uIFNγ offers superior accuracy for the diagnosis of microbiologically confirmed TBP compared to the ADA assay and the Xpert MTB/RIF test.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Bongani M Mayosi
- The Cardiac Clinic, Department of Medicine, Groote Schuur Hospital and University of Cape Town, Groote Schuur Drive, Observatory, Cape Town 7925, South Africa.
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19
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Diagnostic accuracy of Xpert MTB/RIF for extrapulmonary tuberculosis specimens: establishing a laboratory testing algorithm for South Africa. J Clin Microbiol 2014; 52:1818-23. [PMID: 24622091 DOI: 10.1128/jcm.03553-13] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
South Africa implemented Xpert MTB/RIF as the initial diagnostic test for pulmonary tuberculosis (TB). Xpert MTB/RIF's accuracy for diagnosing extrapulmonary tuberculosis (EPTB) was investigated. EPTB specimens (n = 7,916) from hospitalized patients received over a 6-month period at a high-throughput TB referral laboratory in Johannesburg were investigated. Large-volume specimens were centrifuged, tissue biopsy specimens homogenized, and all specimens checked for growth of contaminating bacteria on blood agar. Contaminated samples received NALC-NaOH (N-acetyl-l-cysteine-sodium hydroxide) decontamination prior to liquid culture. Residual specimens (volumes > 1 ml) after inoculation of culture (n = 1,175) were tested using the Xpert MTB/RIF sputum protocol. Using culture as the reference, Xpert MTB/RIF's overall sensitivity was 59% (95% confidence interval [95% CI], 53% to 65%) and specificity was 92% (CI, 90% to 94%), with the highest sensitivities of 91% (95% CI, 78% to 97%) for pus, 80% (95% CI, 56% to 94%) for lymph node aspirates, and 51% (95% CI, 44% to 58%) for fluids (ascitic, 59%; pleural, 47%). A difference in sensitivities was noticed between specimens classified as having a thick (87% [95% CI, 76% to 94%]) versus clear (watery) (48% [95% CI, 36% to 61%]) appearance. This was unchanged with traces of blood (52% [95% CI, 44% to 60%]) or precentrifugation (57% [95% CI, 28% to 82%]) among clear specimens. Xpert MTB/RIF generated an additional 124 specimen results that were contaminated by Mycobacterial Growth Indicator Tubes (MGIT; 10.5%) and diagnosed rifampin (RIF) resistance earlier (9.6% [25/260]). Xpert MTB/RIF's performance on EPTB specimens provides very promising results and should be considered for incorporation into national TB guidelines. Xpert MTB/RIF is less affected by contaminating bacteria and reduces laboratory labor and diagnostic delay compared to traditional methods.
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20
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Exploring alternative biomaterials for diagnosis of pulmonary tuberculosis in HIV-negative patients by use of the GeneXpert MTB/RIF assay. J Clin Microbiol 2013; 51:4161-6. [PMID: 24108610 DOI: 10.1128/jcm.01743-13] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The utility of the GeneXpert MTB/RIF (Xpert) assay for detection of Mycobacterium tuberculosis in sputum samples has been extensively studied. However, the performance of the Xpert assay as applied to other readily accessible body fluids such as exhaled breath condensate (EBC), saliva, urine, and blood has not been established. We used the Xpert assay to test EBC, saliva, urine, and blood samples from HIV-negative, smear- and culture-positive pulmonary tuberculosis (TB) patients for the presence of M. tuberculosis. To compare the ability of the assay to perform bacterial load measurements on sputum samples with versus without sample processing, the assay was also performed on paired direct and processed sputum samples from each patient. The Xpert assay detected M. tuberculosis in none of the 26 EBC samples (sensitivity, 0.0%; 95% confidence interval [95% CI], 0.0%, 12.9%), 10 of the 26 saliva samples (sensitivity, 38.5%; 95% CI, 22.4%, 57.5%), 1 of 26 urine samples (sensitivity, 3.8%; 95% CI, 0.7%, 18.9%), and 2 of 24 blood samples (sensitivity, 8.3%; 95% CI, 2.3%, 25.8%). For bacterial load measurements in the different types of sputum samples, the cycle thresholds of the two M. tuberculosis-positive sputum types were well correlated (Spearman correlation of 0.834). This study demonstrates that the Xpert assay should not be routinely used to detect M. tuberculosis in EBC, saliva, urine, or blood samples from HIV-negative patients suspected of having pulmonary tuberculosis. As a test of bacterial load, the assay produced similar results when used to test direct versus processed sputum samples. Sputum remains the optimal sample type for diagnosing pulmonary tuberculosis in HIV-negative patients with the Xpert assay.
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Evaluation of Xpert MTB/RIF for detection of tuberculosis from blood samples of HIV-infected adults confirms Mycobacterium tuberculosis bacteremia as an indicator of poor prognosis. J Clin Microbiol 2013; 51:2311-6. [PMID: 23678061 PMCID: PMC3697654 DOI: 10.1128/jcm.00330-13] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Tuberculosis (TB) remains a leading cause of death among HIV-infected adults, in part because of delayed diagnosis and therefore delayed initiation of treatment. Recently, the Gene-Xpert platform, a rapid, PCR-based diagnostic platform, has been validated for the diagnosis of TB with sputum. We have evaluated the Xpert MTB/RIF assay for the diagnosis of Mycobacterium tuberculosis bacteremia and investigated its impact on clinical outcomes. Consecutive HIV-infected adults with fever and cough presenting to Queen Elizabeth Central Hospital, Blantyre, Malawi, were recruited and followed up for 2 months. At presentation, three sputum samples were examined by smear, culture, and Xpert MTB/RIF assay for the presence of M. tuberculosis and blood was drawn for PCR with Xpert, for mycobacterial culture (Myco/F Lytic), and for aerobic culture. One hundred four patients were recruited, and 44 (43%) were sputum culture positive for M. tuberculosis. Ten were Xpert blood positive, for a sensitivity of 21% and a specificity of 100%. The 2-week mortality rate was significantly higher among patients who were Xpert blood positive than among those who were negative (40% versus 3%; multivariate odds ratio [OR] for death if positive, 44; 95% confidence interval [CI], 3 to 662). This effect persisted on assessment of the mortality rate at 2 months (40% versus 11%; OR, 5.6; 95% CI, 1.3 to 24.6). When screening uncomplicated patients presenting with a productive cough for pulmonary TB, Xpert blood offers no diagnostic advantage over sputum testing. Despite this, Xpert blood positivity is highly predictive of early death and this test rapidly identifies a group of patients in urgent need of initiation of treatment.
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