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Iúdice TNDS, da Conceição ML, de Brito AC, de Souza NM, Mesquita CR, Guimarães RJDPSE, Furlaneto IP, Saboia ADS, Lourenço MCDS, Lima KVB, Conceição EC. The Role of GeneXpert ® for Tuberculosis Diagnostics in Brazil: An Examination from a Historical and Epidemiological Perspective. Trop Med Infect Dis 2023; 8:483. [PMID: 37999602 PMCID: PMC10674801 DOI: 10.3390/tropicalmed8110483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 11/25/2023] Open
Abstract
The rapid molecular test (RMT) performed on the GeneXpert® system is widely used as a control strategy and surveillance technique for tuberculosis (TB). In the region of the Americas, TB incidence is slowly increasing owing to an upward trend in Brazil, which is among the high TB-burden countries (HBCs), ranking in the 19th position. In this context, we aimed to (i) describe the implementation and history of RMT-TB (Xpert® MTB/RIF and Xpert® MTB/RIF Ultra) in Brazil; (ii) to evaluate the national RMT laboratory distribution, TB, and resistance to RIF detection by RMT; and (iii) to correlate these data with Brazilian TB incidence. The quantitative data of Xpert® MTB/RIF and Xpert® MTB/RIF Ultra assays performed in the pulmonary TB investigation from 2014 to 2020 were provided by the Brazilian Ministry of Health. A spatial visualization using ArcGIS software was performed. The Southeast region constituted about half of the RMT laboratories-from 39.4% to 45.9% of the total value over the five regions. Regarding the federal units, the São Paulo state alone represented from 20.2% to 34.1% (5.0 to 8.5 times the value) of RMT laboratories over the years observed. There were significant differences (p < 0.0001) in the frequency of RMT laboratories between all years of the historical series. There was an unequal distribution of RMT laboratories between Brazilian regions and federal units. This alerts us for the surveillance of rapid molecular detection of TB in different parts of the country, with the possibility of improving the distribution of tests in areas of higher incidence in order to achieve the level of disease control recommended by national and worldwide authorities.
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Affiliation(s)
- Tirça Naiara da Silva Iúdice
- Programa de Pós-Graduação Biologia Parasitária na Amazônia, Universidade do Estado do Pará, Belém-Pará 66087-670, PA, Brazil; (T.N.d.S.I.); (C.R.M.)
| | | | - Artemir Coelho de Brito
- Coordenação-Geral de Vigilância da Tuberculose, Micoses Endêmicas e Micobactérias Não Tuberculosas—CGTM, Ministério da Saúde, Brasília 70000-000, DF, Brazil; (A.C.d.B.)
| | - Nicole Menezes de Souza
- Coordenação-Geral de Vigilância da Tuberculose, Micoses Endêmicas e Micobactérias Não Tuberculosas—CGTM, Ministério da Saúde, Brasília 70000-000, DF, Brazil; (A.C.d.B.)
| | - Cristal Ribeiro Mesquita
- Programa de Pós-Graduação Biologia Parasitária na Amazônia, Universidade do Estado do Pará, Belém-Pará 66087-670, PA, Brazil; (T.N.d.S.I.); (C.R.M.)
| | | | | | - Alessandra de Souza Saboia
- Laboratório de Bacteriologia e Bioensaios em Micobactérias, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 21040-360, RJ, Brazil; (A.d.S.S.); (M.C.d.S.L.)
| | - Maria Cristina da Silva Lourenço
- Laboratório de Bacteriologia e Bioensaios em Micobactérias, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 21040-360, RJ, Brazil; (A.d.S.S.); (M.C.d.S.L.)
| | - Karla Valéria Batista Lima
- Programa de Pós-Graduação Biologia Parasitária na Amazônia, Universidade do Estado do Pará, Belém-Pará 66087-670, PA, Brazil; (T.N.d.S.I.); (C.R.M.)
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil;
| | - Emilyn Costa Conceição
- Pós-Graduação em Pesquisa Clínica e Doenças Infecciosas, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro 67030-000, RJ, Brazil
- Department of Science and Innovation–National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
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Hassanin ESA, Mohamed Hussein AA, Abdelrheem SS, Dongol E, Mhsb AHA, Zahran AM, Zein M, G Sayed I. Frequency of rifampicin-resistant mycobacterium tuberculosis by GeneXpert MTB/RIF assay and its correlates among 2605 probable tuberculosis patients in upper Egypt. Indian J Tuberc 2023; 70:345-355. [PMID: 37562911 DOI: 10.1016/j.ijtb.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/24/2022] [Accepted: 09/14/2022] [Indexed: 08/12/2023]
Abstract
RATIONALE GeneXpert MTB/RIF (Mycobacterium tuberculosis/rifampicin) assay is a method for detecting rifampicin resistance (RR-MTB) in suspected samples in less than 2 hours with high sensitivity and specificity yield. This study aimed to use the GeneXpert MTB/RIF assay to determine the frequency of RR-MTB and to study the possible influencing correlates associated with positive results. SUBJECTS AND METHODS This is a retrospective cross-sectional study of patients who visited TB clinic in 5 years (2016-2021). According to the data sheet of the patients, all the collected specimens were divided into 2 parts one for diagnosis by Ziehl-Neelsen stain and the other part for GeneXpert analysis. GeneXpert was also used to look for evidence of RR. RESULTS Out of the 2605 total samples screened, 718 (27.6%) tested positive for MTB on GeneXpert assay; of them 633 (88.4%) were sensitive to Rifampicin, 83 (11.6%) were resistant to Rifampicin and 2 cases were undetermined. Factors contributing to RR-MTB were: smoker/ex-smoker, with 2.5 times more risk (p = 0.013.0, p = 0.001); recurrence cases had a 4-fold increased risk (p < 0.001); patients with very low M. tuberculosis detected on the GeneXpert MTB/RIF test were 8 times more likely to have RR-TB (P = 0.004). CONCLUSION This study disclosed a high-rate MTB in Egyptian probable TB cases. Smoking, recurrence and cases with a very low M. tuberculosis burden noticed on the GeneXpert MTB/RIF test had augmented risk of RR-TB.
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Affiliation(s)
| | | | - Shaimaa S Abdelrheem
- Department of Public Health and Community Medicine, Faculty of Medicine, Aswan University, Egypt and Armed Forces College of Medicine (AFCM), Cairo, Egypt
| | | | | | - Asmaa M Zahran
- Clinical Pathology Department, South Egypt Cancer Institute Assiut University, Egypt
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Shaik J, Pillay M, Moodley J, Jeena P. Predominance of the Mycobacterium tuberculosis Beijing strain amongst children from a high tuberculosis burden township in South Africa. Tuberculosis (Edinb) 2022; 136:102250. [PMID: 36055152 DOI: 10.1016/j.tube.2022.102250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 10/15/2022]
Abstract
The objective was to determine the molecular epidemiology and drug susceptibility patterns of Mycobacterium tuberculosis (MTB) of children and their household contacts (HHC) in Umlazi, a high TB-burden township in South Africa. Sixty eight MTBRifPLUS positive TB-infected children (TIC) (≤14 years) and 111 HHC were enrolled. Drug susceptibility testing (DST) was performed on sputum samples using the proportion method and GenoType® MTBDR. Genotyping of MTB was conducted using IS6110-restriction fragment length polymorphism (RFLP) and spoligotyping. Rifampicin (RIF) susceptibility was observed in 67/68 TIC. GenoType® MTBDRplus and phenotypic DST identified drug resistant strains in five of 16 culture-confirmed TIC. The Beijing strain was identified in six and the F15/LAM4/KZN strain in one of the 13 TIC respectively. Four patients with unknown RFLP strains belonged to spoligoclades S, T1, T3 variant and X2. The S-lineage and an unknown strain were identified in two HHC. MDR-TB and pre-XDR-TB were identified in one HHC each. Household transmission could not be determined as none of the culture-confirmed TIC resided with the six culture-confirmed contacts. The predominance of the hypervirulent Beijing strain and presence of drug-resistant strains must be considered in the implementation of effective TB control strategies and development of efficacious vaccines.
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Affiliation(s)
- Junaid Shaik
- Department of Paediatrics and Child Health, School of Clinical Medicine, College of Health Sciences, University of Kwa-Zulu Natal, South Africa; Faculty of Health Sciences, Durban University of Technology, South Africa; Doctoral Research Office, MANCOSA, Samora Machel Street, Durban, South Africa.
| | - Manormoney Pillay
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, South Africa
| | - Julie Moodley
- Medical Microbiology, National Health Laboratory Service, Inkosi Albert Luthuli Central Hospital, South Africa
| | - Prakash Jeena
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, South Africa
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Nguyen HV, de Haas P, Nguyen HB, Nguyen NV, Cobelens FGJ, Mirtskhulava V, Finlay A, Van Nguyen H, Huyen PTT, Tiemersma EW. Discordant results of Xpert MTB/Rif assay and BACTEC MGIT 960 liquid culture to detect Mycobacterium tuberculosis in community screening in Vietnam. BMC Infect Dis 2022; 22:506. [PMID: 35641936 PMCID: PMC9153144 DOI: 10.1186/s12879-022-07481-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/17/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Xpert MTB/Rif, a molecular test to detect tuberculosis (TB), has been proven to have high sensitivity and specificity when compared with liquid culture in clinical settings. However, little is known about its performance in community TB screening. METHODS In Vietnam, a national TB prevalence survey was conducted in 2017. Survey participants who screened positive by chest X-ray, cough symptoms and/or recent history of tuberculosis were requested to provide at least two sputum samples that were tested for Mycobacterium tuberculosis by Xpert MTB/Rif G4 (Xpert) and BACTEC MGIT960 culture (MGIT). RESULTS There were 4,649 eligible participants provided both samples for testing. Among them, 236 (5.1%) participants tested positive for TB by Xpert, 244 (5.3%) tested positive by MGIT and 317 tested positive by at least one test; 163 (51.4%) had discordant test results. Of the positive Xpert, 162 (68.6%) showed a low or very low bacterial load. In multivariate logistic regression comparing discordant with Xpert-MGIT concordant positive results, discordant Xpert-positive results occurred more often among participants who had low sputum bacterial load, male sex, a history of TB treatment, or night sweats. The associated factors were male sex, abnormal chest X-ray and having night sweats when the logistic model was against those with both Xpert and MGIT negative. CONCLUSIONS We found high rates of discordance in the performance of Xpert and MGIT for community-based TB case finding. In situations where the majority of TB cases are expected to have a low bacterial load, multiple diagnostic tests and/or multiple samples are required to reach sufficient sensitivity.
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Affiliation(s)
- Hai Viet Nguyen
- National Tuberculosis Programme, 463 Hoang Hoa Tham, Ba Dinh District, Hanoi, Vietnam
- Department of Global Health and Amsterdam Institute of Global Health and Development, Amsterdam University Medical Centres location University of Amsterdam, Amsterdam, the Netherlands
| | - Petra de Haas
- KNCV Tuberculosis Foundation, The Hague, the Netherlands
| | - Hoa Binh Nguyen
- National Tuberculosis Programme, 463 Hoang Hoa Tham, Ba Dinh District, Hanoi, Vietnam
| | - Nhung Viet Nguyen
- National Tuberculosis Programme, 463 Hoang Hoa Tham, Ba Dinh District, Hanoi, Vietnam
| | - Frank G. J. Cobelens
- Department of Global Health and Amsterdam Institute of Global Health and Development, Amsterdam University Medical Centres location University of Amsterdam, Amsterdam, the Netherlands
| | - Veriko Mirtskhulava
- KNCV Tuberculosis Foundation, The Hague, the Netherlands
- David Tvildiani Medical University, Tbilisi, Georgia
| | - Alyssa Finlay
- Centers for Disease Control - Vietnam Office, Hanoi, Vietnam
| | - Hung Van Nguyen
- National Tuberculosis Programme, 463 Hoang Hoa Tham, Ba Dinh District, Hanoi, Vietnam
| | - Pham T. T. Huyen
- National Tuberculosis Programme, 463 Hoang Hoa Tham, Ba Dinh District, Hanoi, Vietnam
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Hong JM, Lee H, Menon NV, Lim CT, Lee LP, Ong CWM. Point-of-care diagnostic tests for tuberculosis disease. Sci Transl Med 2022; 14:eabj4124. [PMID: 35385338 DOI: 10.1126/scitranslmed.abj4124] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rapid diagnosis is one key pillar to end tuberculosis (TB). Point-of-care tests (POCTs) facilitate early detection, immediate treatment, and reduced transmission of TB disease. This Review evaluates current diagnostic assays endorsed by the World Health Organization and identifies the gaps between existing conventional tests and the ideal POCT. We discuss the commercial development of new rapid tests and research studies on nonsputum-based diagnostic biomarkers from both pathogen and host. Last, we highlight advances in integrated microfluidics technology that may aid the development of new POCTs.
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Affiliation(s)
- Jia Mei Hong
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Hyeyoung Lee
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Nishanth V Menon
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore
| | - Chwee Teck Lim
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.,Institute for Health Innovation & Technology (iHealthtech), National University of Singapore, Singapore 117599, Singapore.,Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Luke P Lee
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA.,Berkeley Sensor and Actuator Center, University of California, Berkeley, Berkeley, CA 94720-1764, USA.,Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Biophysics Graduate Program, University of California, Berkeley, Berkeley, CA 94720, USA.,Harvard Medical School, Brigham and Women's Hospital, Harvard Institute of Medicine, Harvard University, Boston, MA 02115, USA.,Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon, Korea
| | - Catherine W M Ong
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore.,Institute for Health Innovation & Technology (iHealthtech), National University of Singapore, Singapore 117599, Singapore
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Value of Xpert MTB/RIF Using Bronchoalveolar Lavage Fluid for the Diagnosis of Pulmonary Tuberculosis: a Systematic Review and Meta-analysis. J Clin Microbiol 2021; 59:JCM.02170-20. [PMID: 33177121 DOI: 10.1128/jcm.02170-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The performance of Xpert MTB/RIF using bronchoalveolar lavage fluid (BAL) for the diagnosis of pulmonary tuberculosis (PTB) remains unclear. Therefore, a systematic review/meta-analysis was conducted. Studies published before 31 December 2019 were retrieved from the PubMed, Embase, and Web of Science databases using the keywords "pulmonary tuberculosis," "Xpert MTB/RIF," and "BAL." Two independent evaluators extracted the data and assessed the bias risk of the included studies. A random-effects model was used to calculate the overall sensitivity, specificity, positive and negative likelihood ratios (PLR and NLR, respectively), diagnostic odds ratio (DOR), and the area under the curve (AUC), as well as the respective 95% confidence intervals (CIs). Nineteen trials involving 3,019 participants met the inclusion criteria. Compared to the culture method, the pooled sensitivity, specificity, PLR, NLR, DOR, and the AUC with 95% CIs of Xpert MTB/RIF were 0.87 (0.84 to 0.90), 0.92 (0.91 to 0.93), 10.21 (5.78 to 18.02), 0.16 (0.12 to 0.22), 78.95 (38.59 to 161.53), and 0.9467 (0.9462 to 0.9472), respectively. Relative to the composite reference standard, the observed values were 0.69 (0.65 to 0.72), 0.98 (0.98 to 0.99), 37.50 (18.59 to 75.62), 0.30 (0.21 to 0.43), 171.98 (80.82 to 365.96), and 0.9691 (0.9683 to 0.9699), respectively. All subgroups, except children, showed high sensitivity and specificity. In conclusion, the use of Xpert MTB/RIF in the context of BAL samples has a high diagnostic performance for PTB (except for children) and may serve as an alternative rapid diagnostic tool.
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Lv C, Wu J, Pierre-Audigier C, Lu L, Alame-Emane AK, Takiff H, Xu Y, Wang J, Gicquel B, Liu S. Combination of Xpert MTB/RIF and MTBDRplus for Diagnosing Tuberculosis in a Chinese District. Med Sci Monit 2020; 26:e923508. [PMID: 32504464 PMCID: PMC7297034 DOI: 10.12659/msm.923508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background The incidence of tuberculosis (TB) remains high in many countries, including some middle- and high-income countries without financial constraints for diagnosis and treatment. The implementation of an improved algorithm for diagnosis using 2 rapid molecular tests should help reduce the TB burden. Material/Methods Between April 2018 and March 2019, sputum samples from 711 patients suspected of TB in Nanshan, Shenzhen, China, were included in this prospective study. All sputum samples were examined by smear microscopy, Mycobacterium Growth Indicator Tube (MGIT) 960 culture, and Xpert MTB/RIF. The sputum remnants of Xpert MTB/RIF were used for MTBDRplus to confirm the Xpert results both for the presence of TB bacilli and for resistance to rifampicin (RIF), and also to diagnose multidrug-resistant tuberculosis (MDR-TB). Results In total, 200 (28.1%) of the 711 sputa were positive for TB by Xpert MTB/RIF, and the sputum remnants were used for MTBDRplus. The simultaneous use of Xpert MTB/RIF and MTBDRplus directly on sputum samples permitted accurate bacteriologic confirmation of TB in 64% (119/187) of cases and detection of 70% (7/10) of strains that were MDR. Conclusions The implementation of 2 rapid nucleic acid-based tests on sputum samples could facilitate the prompt and appropriate treatment of most TB cases.
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Affiliation(s)
- Chunfang Lv
- Department of Clinical Laboratory, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, Guangdong, China (mainland)
| | - Jianhong Wu
- Department of Clinical Laboratory, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, Guangdong, China (mainland)
| | | | - Liuzhu Lu
- Department of Clinical Laboratory, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, Guangdong, China (mainland)
| | - Amel Kévin Alame-Emane
- Department of Tuberculosis Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, Guangdong, China (mainland)
| | - Howard Takiff
- Department of Tuberculosis Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, Guangdong, China (mainland)
| | - Yangfeng Xu
- Department of Clinical Laboratory, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, Guangdong, China (mainland)
| | - Jian Wang
- Department of Tuberculosis Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, Guangdong, China (mainland)
| | - Brigitte Gicquel
- Department of Tuberculosis Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, Guangdong, China (mainland)
| | - Shengyuan Liu
- Department of Tuberculosis Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, Guangdong, China (mainland)
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