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Pereira, Giovana Rodrigues. "Impacto do teste Xpert MTB/RIF no diagnóstico da tuberculose." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2018. http://hdl.handle.net/10183/179848.
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Introdução: O teste Xpert MTB / RIF está sendo cada vez mais utilizado em muitos países como diagnóstico inicial para a tuberculose (TB). Poucos estudos avaliaram o impacto do Xpert no diagnóstico em rotinas de programas de controle de TB no Brasil. O objetivo do presente estudo foi avaliar o impacto da introdução do Xpert MTB / RIF no diagnóstico de TB em uma cidade com alta incidência de TB no Brasil. Métodos: Incluímos pacientes avaliados com testes diagnósticos convencionais durante um ano antes da introdução do Xpert (grupo pré-Xpert) e pacientes avaliados usando Xpert durante um ano após a introdução do teste (grupo pós-Xpert). Resultados: 620 pacientes preencheram os critérios de inclusão (208 no grupo pré-Xpert e 412 no grupo pós-Xpert) e foram incluídos na análise. O tempo até o diagnóstico de TB foi menor no grupo pós-Xpert (0,7 dias, IQR: 0,5-1,0 dias) do que no grupo pré-Xpert (2,0 dias, IQR: 2,0-2,0 dias) (p <0,0001). Características atípicas da doença, como menor perda de peso, febre, dispneia, sudorese noturna e hemoptise; baciloscopia de escarro negativa; cultura negativa e radiografia de tórax atípica de TB foram mais comuns no grupo pós-Xpert do que no grupo pré-Xpert (p <0,0001 para todos). Conclusões: Observamos que a implementação do ensaio Xpert MTB / RIF, em rotinas de programas de controle de TB, melhora e facilita o diagnóstico de tuberculose, especialmente nos casos com manifestações da doença atípica. Esses resultados podem provavelmente ser generalizados para locais com incidência de TB similar.Introduction: The receptor for advanced glycation end products (RAGE) is expressed in normal lungs and is upregulated during inflammation and infection. The interaction between AGEs and RAGE on the plasma membrane causes oxidative stress and apoptosis in lung cells. The objective of this study is to evaluate plasma levels of AGEs and its soluble receptor (sRAGE) in patients with active TB and healthy controls, and to investigate their relationship with food intake and nutritional status. Methods: Case-control study. AGE (carboxymethil lysine, CML) and RAGE were measured by Elisa. Nutritional assessment was performed by body mass index, triceps skin-fold thickness, mid-arm circumference, mid-arm muscle circumference, bioelectrical impedance analysis, and food frequency questionnaire. Results: 35 TB patients and 35 controls were included in the study. The mean S-RAGE levels were higher in TB patients than in controls (68.5 ± 28.1 vs 57.5 ± 24.0, p=0.046). Among cases that were current smokers, lower S-RAGE levels were associated with mortality (S-RAGE levels= 58.0 ± 36.5 [non-survivors] vs 71.3 ± 25.6 [survivors], p=0.006), and with weight loss (S-RAGE levels= 65.6 ± 27.4 [weight loss] vs 98.6 ± 16.7 [no weight loss], p=0.034). There was no statistically significant difference in CML levels and diet CML content between cases and controls. Malnutrition was more frequent in cases than in controls, but there was no correlation between nutritional parameters and CML or S-RAGE levels. Conclusions: TB patients had higher S-RAGE levels than controls. S-RAGE may play a role in disease manifestations and outcomes, being associated with weight loss and mortality.
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Held, Michael. "Evaluation of diagnostic advances in musculoskeletal tuberculosis; the automated xpert MTB/RIF assay." Doctoral thesis, University of Cape Town, 2016. http://hdl.handle.net/11427/20495.
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The aim of this thesis was to investigate the diagnostic accuracy of Xpert for musculoskeletal TB and for rifampicin resistance against a gold standard of culture or histology. Site of disease, HIV status, and age of patients, and accuracy in spinal compared to extraspinal TB were investigated as secondary objectives. The overarching hypothesis was that Xpert is more accurate and would provide results faster than the gold standard for musculoskeletal TB, and that it would have a higher yield in HIV infected patients, adult patients, and patients with spinal disease.
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Held, Michael. "Evaluation of diagnostic advances in Musculoskeletal Tuberculosis; the automated xpert MTB/RIF assay." Doctoral thesis, Faculty of Health Sciences, 2019. http://hdl.handle.net/11427/30373.
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Background Xpert MTB/RIF (Xpert) is a rapid, automated, onsite nucleic acid amplification test for tuberculosis (TB). It is effective for the diagnosis of pulmonary TB but there is limited evidence for its usefulness in extrapulmonary TB, particularly musculoskeletal TB. Aims and hypothesis The aim of this thesis was to investigate the diagnostic accuracy of Xpert for musculoskeletal TB and for rifampicin resistance against a gold standard of culture or histology. Site of disease, HIV status, and age of patients, and accuracy in spinal compared to extraspinal TB were investigated as secondary objectives. The overarching hypothesis was that Xpert is more accurate and would provide results faster than the gold standard for musculoskeletal TB, and that it would have a higher yield in HIV infected patients, adult patients, and patients with spinal disease. Methods Prospective studies of patients with suspected musculoskeletal TB, at the tertiary care hospitals Groote Schuur and Red Cross Children’s Hospital in Cape Town, South Africa, were undertaken from June 2013 to March 2015. The diagnostic accuracy of Xpert was compared to culture or histopathology. Findings 206 biopsies of 201 patients older than 13 years of age (23% HIV positive) were analysed. The sensitivity and specificity of Xpert was 92.3% and 99.1% respectively. Xpert detected 8 cases more than culture (p = 0.069) and positive results were available 17 days earlier (<0.001). The sensitivity of Xpert in HIV positive patients was 96.9% (31/32) versus 89.6% (43/48) in HIV negative patients (p=0.225). The sensitivity of Xpert for spinal biopsies was 93.8% (95% CI 86.0-97.9) with specificity of 97.6% (95% CI 87.4 – 99.9), compared to extraspinal biopsies with a sensitivity of 81.8% (95% CI 48.2 – 99.7, p=0.164) and specificity of 100% (95% CI 95.1 – 100%, p=0.186). 109 osteoarticular samples of children 12 years of age or younger, with a median age of 5.6 years (IQR 2.2 – 8.7) were analysed. Xpert provided a sensitivity of 73.9% (95% CI 51.6-89.8) with a specificity of 100% (95% CI 95.7 - 100) and was available at a mean of 0.8 days (0.46- 1.4) compared to 21 days (19 – 30) for culture (p< 0.001). All rifampicin resistant cases were correctly diagnosed. A trend towards higher sensitivity in spinal tissue as well as HIV infected patients was observed. This study also provides evidence that Xpert has a lower sensitivity in children than in adults, yet, still detects more cases of paediatric musculoskeletal TB and is faster than culture. Histology was a useful test for the diagnosis of musculoskeletal TB, especially in children, and should be used alongside Xpert to provide the highest yield possible to detect TB. Conclusion: These first large studies on the accuracy of Xpert for musculoskeletal TB provide evidence for the usefulness of Xpert in the diagnosis of spinal TB, extraspinal TB, in HIV positive patients, and in childhood musculoskeletal TB. Based on these results, Xpert should be recommended as the initial test for diagnosis as it is more sensitive and faster than the gold standard of liquid culture.
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Neto, Wilson Oliveira Ezequiel. "Associação dos achados radiológicos com o teste Xpert MTB/RIF em pacientes com suspeita de tuberculose pulmonar." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2017. http://hdl.handle.net/10183/179752.
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Introdução: O tratamento da tuberculose (TB) geralmente é realizado de forma empírica, baseado nos achados clínicos e radiológicos. O raio-x (RX) do tórax tem boa sensibilidade, mas uma baixa especificidade para o diagnóstico de tuberculose. O Xpert MTB/RIF está sendo usado cada vez mais em diversos países como teste inicial para diagnóstico de TB.O objetivo deste estudo foi de avaliar a associação dos achados radiológicos com o teste Xpert MTB/RIF em pacientes com suspeita de TB pulmonar. Métodos: Estudo transversal com pacientes de um ambulatório de TB. Foram realizados testes de baciloscopia no escarro, Xpert MTB/RIF e RX de tórax em pacientes com suspeita de TB pulmonar. Resultados: Durante o período do estudo, 312 pacientes preencheram os critérios de inclusão e incluídos na análise. Dentre os pacientes com Xpert MTB/RIF positivo, os padrões radiológicos foram classificados como típico de TB, compatível com TB e normal em 78 (70,3%), 31 (27,9%) e 2 (1,8%) dos pacientes, respectivamente. Os RX de tórax foram considerados típico de TB, compatível com TB e normal em 20 (10,0%), 25 (12,4%) e 152 (75,6%) dos pacientes, respectivamente, em casos Xpert MTB/RIF negativos. Conclusões: Foi encontrada uma associação entre os padrões radiológicos e os resultados do Xpert MTB/RIF em pacientes com suspeita de tuberculose pulmonar. O RX de tórax ainda é uma ferramenta diagnóstica útil e sensível, mas o seu papel nos algoritmos diagnósticos em lugares onde o Xpert MTB/RIF está disponível requer uma discussão mais aprofundada.Background: Tuberculosis (TB) treatment is often carried out empirically, based on clinical and radiological findings. Chest X-ray (CXR) has good sensitivity but poor specificity in TB diagnosis. Xpert MTB/RIF is increasingly used in many countries as the initial diagnostic test for TB. The aim of the present study was to evaluate the association of radiological findings with the Xpert MTB/RIF test in patients with suspected pulmonary TB. Methods: Cross-sectional study in an outpatient TB clinic. Sputum AFB smear, culture, Xpert MTB/RIF and CXR were collected in patients with suspected pulmonary TB. Results: During the study period, 312 patients met the inclusion criteria and were included in the analysis. Among Xpert MTB/RIF positive cases, the radiographic patterns were classified as typical of TB, compatible of TB, and normal in 78 (70.3%), 31 (27.9%), and 2 (1.8%) patients, respectively. CXRs were classified as typical of TB, compatible of TB, and normal in 20 (10.0%), 25 (12.4%), and 152 (75.6%) patients, respectively, in Xpert MTB/RIF negative cases. Conclusions: We found an association between radiographic patterns and Xpert MTB/RIF results in patients with suspected pulmonary TB. CXR is still a useful and sensitive diagnostic tool, but its place at the diagnostic algorithms in the context of Xpert MTB/RIF availability warrants further discussion.
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Lessells, R. J. "Impact of the Xpert MTB/RIF tuberculosis diagnostic system in individuals at high risk of mortality in rural South Africa." Thesis, London School of Hygiene and Tropical Medicine (University of London), 2015. http://researchonline.lshtm.ac.uk/2222113/.
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This thesis investigates the clinical impact of a point-of-care diagnostic strategy for pulmonary tuberculosis (TB) in a setting at the heart of the TB and human immunodeficiency virus (HIV) epidemics in rural KwaZulu-Natal, South Africa. Although the identification and prompt treatment of active pulmonary TB disease remains the cornerstone of global TB control strategies, weak diagnostic systems contribute to substantial delays and default during the diagnostic process. As new diagnostic technologies are developed, evidence is needed around how best to deliver them within health systems in order to maximize their impact. The impact of positioning of a molecular diagnostic system (Xpert MTB/RIF) was investigated in a cluster randomised trial. Clusters (two-week time periods) were randomised to one of two strategies: centralised laboratory Xpert MTB/RIF testing or point-of-care Xpert MTB/RIF at the clinic. The trial enrolled 1297 adults with symptoms of pulmonary TB who were HIV infected and/or at high risk of drugresistant TB. There was some evidence that point-of-care placement shortened the time to initiation of treatment but there was no difference in the overall proportion of culture-positive pulmonary TB cases initiated on appropriate anti-TB treatment within 30 days. Overall mortality was lower than anticipated and, although it was higher with the point-of-care strategy, this effect was not maintained after adjusting for the presence of TB disease and CD4+ T-cell count. Further analysis suggested that the point-of-care strategy increased the proportion of valid Xpert results from the initial sputum specimen, increased the proportion of individuals receiving test results and allowed same-day treatment initiation for half of all culture-positive cases that tested positive with Xpert. The diagnostic performance of the Xpert MTB/RIF system was comparable under both strategies. However, delays in initiation of treatment for drug-resistant TB cases and for Xpertnegative/ culture-positive cases occurred similarly with both strategies, reducing the potential to detect a real impact on outcomes. Although not a primary focus of the study, the results highlighted deficiencies in the performance of sputum culture, which raise questions about its place as the gold standard diagnostic test. The development of simple, rapid diagnostics suitable for point-of-care use remains important for TB control in high burden settings. The findings will improve understanding of the key requirements for successful diagnostic strategies and the lessons learnt will help to inform future diagnostic clinical trials. Further research is needed to evaluate how different diagnostic strategies might impact on TB transmission in health care facilities and more broadly in the community.
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Norin, Johanna. "A retrospective evaluation study of diagnostic accuracy of Xpert® MTB/RIF assay, used for detection of Mycobacterium tuberculosis in Greece." Thesis, Örebro universitet, Institutionen för hälsovetenskap och medicin, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-44978.
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Birungi, Francine Mwayuma. "An evaluation of Isoniazid prophylaxis treatment and the role of Xpert MTB/RIF test in improving the diagnosis and prevention of tuberculosis in children exposed to index cases with pulmonary tuberculosis in Kigali, Rwanda." University of the Western Cape, 2018. http://hdl.handle.net/11394/6880.
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Philosophiae Doctor - PhDBackground: Tuberculosis (TB) is a major cause of morbidity and mortality among children (<15 years) in resource-limited countries. The World Health Organization (WHO) identified active contact screening and isoniazid preventive therapy (IPT) as essential actions for detecting and preventing childhood TB. Despite their benefits and inclusion in the policy of most National TB Programme (NTP) guidelines of the resource-limited countries, there is still a wide gap between policy and implementation. The implementation of contact screening for active case finding might be improved by the decentralised use of the Xpert MTB/RIF test in gastric lavage (GL) specimens, but this has not been previously assessed. Furthermore, although the provision of IPT to eligible child contacts has been a focus for implementation by the NTP of Rwanda since 2005, implementation has not previously been evaluated. The assessment of IPT uptake and adherence as well as associated factors could be informative for the programme. Therefore, we aimed to assess the diagnostic yield of Xpert MTB/RIF in GL among child contacts with suspected pulmonary tuberculosis (PTB) and the uptake of and adherence to IPT by eligible child contacts to make recommendations towards strengthening TB diagnostic and prevention in children in Kigali, Rwanda. Methods: The proposed study setting Kigali, the capital city of Rwanda, was the location for 30% of the national PTB case notifications in 2013-14.A conceptual framework based on ecological theory was used in this study. Quantitative, qualitative and mixed (using both quantitative and qualitative research methods in one study) research methods were applied, and various research designs were used depending on the research questions. The study involved a cross-sectional analysis of the diagnostic yield of Xpert MTB/RIF in GL among all child contacts with suspected TB. Across-sectional and prospective cohort study design was used to assess the uptake and adherence of IPT among eligible child contacts.
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Mendonça, Tiago João Carvalho. "Xpert MTB/RIF®, um método diagnóstico rápido para a tuberculose?" Master's thesis, 2014. http://hdl.handle.net/10451/24488.
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Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014Despite the availability of effective treatment, tuberculosis still accounts for millions of cases of active disease and deaths worldwide. Sub-Saharan Africa has the highest incidence of tuberculosis, where the deficient laboratory capacity remains a serious obstacle towards a rapid diagnosis and correct treatment of tuberculosis. One of the solutions proposed, to improve the diagnosis of tuberculosis, is the use of molecular techniques, like the Xpert MTB/RIF, that detect Mycobacterium tuberculosis and mutations associated with drug resistance. Xpert MTB/RIF is an automated self-contained platform that can be used with minimal technical skills and was endorsed by the World Health Organization in 2010. It is one of the most advanced new generation automated molecular diagnostics platforms available at the moment. My experience in Cape Verde, during the implementation of Xpert MTB/RIF motivated a review of available clinical data. Sputum analysis by the Xpert MTB/RIF is a rapid and highly sensitive (87% globally and 80% in patients co-infected by HIV) direct test. However, conventional drug susceptibility testing continues to be necessary in selected clinical cases. More data would be desirable to evaluate the real clinical impact of Xpert MTB/RIF.
Apesar da disponibilidade de tratamento eficaz, a tuberculose é responsável por milhões de casos de doença activa e mortes em todo o mundo. A incidência mais alta de tuberculose encontra-se na África subsariana onde a fraca capacidade laboratorial mantém-se como um sério impedimento ao diagnóstico e tratamento da tuberculose. Uma das soluções para melhorar o diagnóstico de tuberculose é o uso de técnicas moleculares rápidas, como o Xpert MTB/RIF, que detectam Mycobacterium tuberculosis e mutações associadas a resistências. O Xpert MTB/RIF é uma plataforma automática e auto contida que pode ser usada com habilidade técnica mínima, aprovada pela OMS em 2010, e neste momento é uma das ferramentas de diagnóstico da tuberculose da nova geração cujo desenvolvimento está mais avançado. A experiência vivida em Cabo Verde durante a implementação do Xpert MTB/RIF levou à revisão dos dados disponíveis. Confirmou-se: a análise da expectoração pelo Xpert MTB/RIF é um método directo rápido com alta sensibilidade para o diagnóstico de tuberculose pulmonar (87% global e 80% em doentes co-infectados por VIH); contudo não elimina a necessidade de realizar testes de susceptibilidade convencionais em casos seleccionados; são necessários mais estudos para avaliar o impacto clínico real do Xpert MTB/RIF.
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YU, FANG-LAN, and 余芳蘭. "The Feasibility of Screening Test for Mycobacterium Tuberculosis Using Xpert MTB/RIF." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/c46535.
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碩士元培醫事科技大學
醫務管理系碩士在職專班
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Tuberculosis is a chronic infectious disease and it is still common in the world today, especially in untapped and developing countries. Tuberculosis has almost no obvious symptoms in the early stages and it is easily overlooked. Therefore, it is relatively important that TB can be correctly and quickly diagnosed. Mycobacterium tuberculosis is transmitted through the air. Therefore, in laboratory inspection operations, it is necessary to consider how to avoid the negative pressure setting by air spreading and the operator's safety protection. The flood prevention work of the public security in Taiwan is facing many challenges. The correct and rapid inspection of tuberculosis is really an important part. However, the lack of TB inspection hardware facilities and insufficient protective equipment, high risk of TB inspection, and low investment return rate have caused the general hospitals and inspectors' willingness to engage in tuberculosis-related tests to be low, so they are seeking high sensitivity and convenient operation procedures. The inspection method, after screening most of the negative samples, relatively reduces the manpower required for inspection, thereby addressing the high risk of tuberculosis testing and the low willingness of inspectors to engage in tuberculosis-related tests, and on the other hand, evaluating their cost-effectiveness. A total of 36,674 Mycobacterium tuberculosis tests were collected from a medical center from January 2016 to December 2016. The sensitivity, specificity, and PPV were calculated and calculated. The correlations were calculated, together with the timeliness of reports and labor costs. The results showed that although the smear could be reported within 24 hours but the sensitivity was < 50%, the sensitivity of Xpert MTB/RIF was up to 90%, which was reported in about 2 hours, while the RIF drug was tested for its PPV and NPV also reached more than 92%. Xpert MTB/RIF test reagents are simple, fast and have good sensitivity, correctness, and can overcome the space and technical requirements. It is feasible to apply screening, but it is expected that the price is high and sensitive. Improvements and diversification of drugs can be further breakthroughs.
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Ngabonziza, J. C. S., T. Decroo, P. Migambi, Y. M. Habimana, Duen A. Van, Conor J. Meehan, G. Torrea, et al. "Prevalence and drivers of false-positive rifampicin-resistant Xpert MTB/RIF results: a prospective observational study in Rwanda." 2020. http://hdl.handle.net/10454/18533.
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YesBackground: The Xpert MTB/RIF (Xpert) assay is used globally to rapidly diagnose tuberculosis and resistance to rifampicin. We investigated the frequency and predictors of false-positive findings of rifampicin resistance with Xpert. Methods: We did a prospective, observational study of individuals who were enrolled in a Rwandan nationwide diagnostic cohort study (DIAMA trial; NCT03303963). We included patients identified to have rifampicin resistance on initial Xpert testing. We did a repeat Xpert assay and used rpoB Sanger and deep sequencing alongside phenotypic drug susceptibility testing (pDST) to ascertain final rifampicin susceptibility status, with any (hetero)resistant result overriding. We used multivariable logistic regression to assess predictors of false rifampicin resistance on initial Xpert testing, adjusted for HIV status, tuberculosis treatment history, initial Xpert semi-quantitative bacillary load, and initial Xpert probe. Findings: Between May 4, 2017, and April 30, 2019, 175 people were identified with rifampicin resistance at initial Xpert testing, of whom 154 (88%) underwent repeat Xpert assay. 54 (35%) patients were confirmed as rifampicin resistant on repeat testing and 100 (65%) were not confirmed with resistance. After further testing and sequencing, 121 (79%) of 154 patients had a final confirmed status for rifampicin susceptibility. 57 (47%) of 121 patients were confirmed to have a false rifampicin resistance result and 64 (53%) had true rifampicin resistance. A high pretest probability of rifampicin resistance did not decrease the odds of false rifampicin resistance (adjusted odds ratio [aOR] 6·0, 95% CI 1·0–35·0, for new tuberculosis patients vs patients who needed retreatment). Ten (16%) of the 64 patients with true rifampicin resistance did not have confirmed rifampicin resistance on repeat Xpert testing, of whom four had heteroresistance. Of 63 patients with a very low bacillary load on Xpert testing, 54 (86%) were falsely diagnosed with rifampicin-resistant tuberculosis. Having a very low bacillary load on Xpert testing was strongly associated with false rifampicin resistance at the initial Xpert assay (aOR 63·6, 95% CI 9·9–410·4). Interpretation: The Xpert testing algorithm should include an assessment of bacillary load and retesting in case rifampicin resistance is detected on a paucibacillary sputum sample. Only when rifampicin resistance has been confirmed on repeat testing should multidrug-resistant tuberculosis treatment be started. When rifampicin resistance has not been confirmed on repeat testing, we propose that patients should be given first-line anti-tuberculosis drugs and monitored closely during treatment, including by baseline culture, pDST, and further Xpert testing.
The European & Developing Countries Clinical Trials Partnership 2 programme, and Belgian Directorate General for Development Cooperation.
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Alves, Pedro Miguel dos Anjos Rocha. "Diagnóstico da tuberculose pulmonar no adulto nos países de baixo rendimento : será o XPERT® MTB/RIF a escolha correcta?" Master's thesis, 2014. http://hdl.handle.net/10451/24427.
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Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014Tuberculosis is the infectious disease responsible the highest mortality rates in the world, mainly in low income countries. During the last years, new diagnostic tests for tuberculosis have been investigated and developed, but not all of them are suitable for these countries. In 2010, the World Health Organization endorsed Xpert® MTB/RIF, a fast molecular test that allows the diagnosis of tuberculosis, but also tests the resistance to rifampicin and is simple enough to be implemented in primary healthcare setting. In spite of its numerous advantages, the cost and the infrastructure requirements are still an obstacle to its disseminated use. However, the question remains if Xpert® will ever replace sputum smear microscopy in the diagnosis of tuberculosis in low income countries or if the latter should remain the standard and be improved until a better test is found.
A tuberculose é a doença infecciosa que mais mata em todo o mundo, principalmente nos países economicamente mais desfavorecidos. Durante os últimos anos, novos métodos de diagnóstico têm sido investigados e desenvolvidos, mas nem todos são aplicáveis nestes países. Em 2010, a Organização Mundial de Saúde afirma o seu apoio ao Xpert® MTB/RIF, um método de diagnóstico molecular rápido, simples e passível de ser implementado ao nível dos cuidados de saúde primários, que permite o diagnóstico de tuberculose e, simultaneamente, de resistência à rifampicina. Apesar das inúmeras vantagens deste teste, os custos e as infraestruturas necessárias ainda são um grande obstáculo ao seu uso disseminado. Contudo, mantém-se a dúvida se o Xpert® poderá substituir a baciloscopia no diagnóstico da tuberculose nos países de baixo rendimento ou se esta última deve ser mantida e melhorada até que seja descoberta uma alternativa melhor.
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Subramony, Nishanti Nadhiya. "The evaluation of the diagnostic utility and sensitivity of the Xpert® MTB/RIF in the detection of Mycobacterium tuberculosis and rifampicin resistance on bone marrow aspirate samples." Thesis, 2017. https://hdl.handle.net/10539/24771.
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A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in partial fulfilment of the requirements for the degree of Master of Medicine in the Branch of Pathology (Haematology). Johannesburg, 20 November 2017.In South Africa, the World Health Organisation estimated 454 000 new cases of Mycobacterium Tuberculosis (M.tb) infection (MTB) in 2015. Disseminated tuberculosis arises from haematogenous spread of the bacilli and seeding of the bacilli in extrapulmonary sites. The current gold standard for the detection of MTB of the bone marrow is TB culture which has an average turnaround time of 6 weeks. Although shorter, histological examinations of trephine biopsy cores to diagnose MTB also have a time delay owing mainly to the 5-7 day processing period prior to microscopic examination. Adding to the diagnostic delay is the non-specific nature of granulomatous inflammation which is the hallmark of MTB involvement of the bone marrow. A Ziehl-Neelson stain (which highlights acid-fast bacilli) is therefore mandatory to confirm the diagnosis but can take up to 3 days for processing and evaluation. Owing to this delay in diagnosis, many patients are lost to follow up or remain untreated for up to six weeks while the results are awaited, thus encouraging the spread of undiagnosed TB. The Xpert MTB/RIF (Cepheid, Sunnyvale, CA) is the molecular test used in the South African national TB program as the initial diagnostic test for pulmonary TB in adults and children. In 2013 the Xpert MTB/RIF was applied to diagnose extrapulmonary TB and despite being available in 207 testing sites nationwide, it was never investigated for its potential application in diagnosing TB in bone marrow. Therefore, this study investigates the optimisation and performance of Xpert MTB/RIF on bone marrow aspirate specimens. BMA specimens received for routine immunophenotypic analysis as part of the investigation into disseminated MTB or in the evaluation of cytopenias in immunocompromised patients were used in this study. Processing BMA on the Xpert® MTB/RIF was optimised to ensure bone marrow in EDTA and heparin did not inhibit the PCR reaction. Inactivated M.tb from an Xpert MTB/RIF external quality assessment program was spiked into the clinical bone marrow specimen and distilled water (as a control). A volume of 500μl and an incubation time of 15 minutes with sample reagent were investigated as the processing protocol. A total of 135 BMA specimens had sufficient residual volume for Xpert® MTB/RIF testing however 22 specimens (16.3%) were not included in the final statistical analysis as an adequate trephine biopsy and/or TB culture was not available. Xpert MTB/RIF testing was possible in v the presence of heparin or EDTA, but the overall detection of MTB in BMA was low compared to histology and culture. The sensitivity of the Xpert® MTB/RIF when compared to both histological and culture findings was 8.7% with a 95% confidence interval (CI) of 1.07-28.04%. The sensitivity of the Xpert® MTB/RIF compared to histological findings only was 11.1% with a 95% CI of 1.38-34.7%. The specificity of the Xpert® MTB/RIF was 98.9% (95% CI: 93.9-99.7%). Although the Xpert® MTB/RIF has a shorter turnaround time than histology and TB culture and is less expensive than culture and drug susceptibility testing, the low sensitivity of the Xpert® MTB/RIF in this study limits its current use for the diagnosis of MTB in bone marrow aspirate specimens until the diagnostic algorithm or the assay is further defined.
LG2018
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Kilfoil, Kim Michelle. "The evaluation of the Xpert MTB/RIF in the diagnosis of mycobacterium tuberculosis complex and detection of rifampicin resistance in extrapulmonary (pleural and ascitic) fluid samples received for routine immunophenotypic analysis in a high-burden tuberculosis setting." Thesis, 2015. http://hdl.handle.net/10539/19955.
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A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in partial fulfilment of the requirements for the degree of Master of Medicine in the branch of Haematology.
Johannesburg, 2015.Introduction: The Gene Xpert MTB/Rif assay (Xpert) is a nucleic acid amplification technique that has been studied in the diagnosis of both pulmonary and, to a lesser extent, extrapulmonary tuberculosis (TB). This study was performed in the National Health Laboratory Services (NHLS) laboratory at Charlotte Maxeke Hospital which services a population with a high prevalence of Mycobacterium Tuberculosis Complex (MTBC) infection. The study aimed to develop a protocol for the processing of pleural and ascitic fluid samples to be run on Xpert for MTBC diagnosis, to evaluate the sensitivity and specificity of the Xpert assay as compared to the gold standard MTBC culture assays and to assess the utility of the Xpert assay as part of the diagnostic algorithm for fluid samples received in high prevalence MTBC laboratories. Materials and methods: A total of 392 pleural and ascitic fluid specimens were received for routine immunophenotypic analysis between August 2012 and February 2013 at the NHLS flow cytometry laboratory in Charlotte Maxeke hospital. Of these specimens, 229 had sufficient residual volume (>0.5ml) after routine immunophenotypic analysis to be tested on Xpert. Specimens were processed as per the manufacturer’s guidelines for pulmonary specimens and results were compared to the gold standard culture for Mycobacterium tuberculosis. Results: Xpert positivity was detected in 8.7% (20/229) of the total specimens. Only 43% (99/229) of these specimens were submitted for concurrent MTBC liquid culture (Mycobacterium Growth Indicator tube, MGIT) testing based on the laboratory information system history. Positivity on Xpert was shown in 9% (9/99) of specimens compared to 17% (17/99) on MGIT. One false positive was detected on Xpert. More than half of the specimens, 57% (130/229) were not referred for concurrent MTBC culture. The Xpert detected MTBC in 8.5% (11/130) of these specimens, with 1 Rifampicin resistant case identified. Xpert sensitivity and specificity in this study were 50% (CI:26-75%) and 99% (CI:91-100%) respectively Conclusion: The sensitivity and specificity of Xpert in this study was comparable to that found in other studies performed on fluid samples. Importantly, this study demonstrates that in a high burden HIV/TB setting like South Africa, more than 50% of fluid specimens referred for immunophenotypic analysis to exclude lymphoma are not referred for concurrent MTBC culture testing. Incorporation of Xpert into the laboratory diagnostic algorithm (LDA) in the immunophenotypic laboratory would, therefore, have a number of benefits, improving overall patient work-up and care. Implementation and policy uptake, however, would require a full costing analysis as Xpert testing would be performed in addition to, and not instead of, routine testing.
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Ng, K. C. S., J. C. S. Ngabonziza, P. Lempens, Jong B. C. de, Leth F. van, and Conor J. Meehan. "Bridging the TB data gap: in silico extraction of rifampicin-resistant tuberculosis diagnostic test results from whole genome sequence data." 2019. http://hdl.handle.net/10454/17491.
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YesBackground: Mycobacterium tuberculosis rapid diagnostic tests (RDTs) are widely employed in routine laboratories and national surveys for detection of rifampicinresistant (RR)-TB. However, as next-generation sequencing technologies have become more commonplace in research and surveillance programs, RDTs are being increasingly complemented by whole genome sequencing (WGS). While comparison between RDTs is difficult, all RDT results can be derived from WGS data. This can facilitate continuous analysis of RR-TB burden regardless of the data generation technology employed. By converting WGS to RDT results, we enable comparison of data with different formats and sources particularly for low- and middle-income high TB-burden countries that employ different diagnostic algorithms for drug resistance surveys. This allows national TB control programs (NTPs) and epidemiologists to utilize all available data in the setting for improved RR-TB surveillance. Methods: We developed the Python-based MycTB Genome to Test (MTBGT) tool that transforms WGS-derived data into laboratory-validated results of the primary RDTs—Xpert MTB/RIF, XpertMTB/RIF Ultra, GenoType MDRTBplus v2.0, and GenoscholarNTM+MDRTB II. The tool was validated through RDT results of RR-TB strains with diverse resistance patterns and geographic origins and applied on routine-derived WGS data. Results: The MTBGT tool correctly transformed the single nucleotide polymorphism (SNP) data into the RDT results and generated tabulated frequencies of the RDT probes as well as rifampicin-susceptible cases. The tool supplemented the RDT probe reactions output with the RR-conferring mutation based on identified SNPs. The MTBGT tool facilitated continuous analysis of RR-TB and Xpert probe reactions from different platforms and collection periods in Rwanda. Conclusion: Overall, the MTBGT tool allows low- and middle-income countries to make sense of the increasingly generated WGS in light of the readily available RDT.
Erasmus Mundus Joint Doctorate Fellowship grant 2016- 1346.
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Ng, K. C., Conor J. Meehan, G. Torrea, L. Goeminne, M. Diels, L. Rigouts, Jong B. C. de, and E. André. "Potential application of digitally linked tuberculosis diagnostics for real-time surveillance of drug-resistant tuberculosis transmission: Validation and analysis of test results." 2018. http://hdl.handle.net/10454/17512.
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YesBackground: Tuberculosis (TB) is the highest-mortality infectious disease in the world and the main cause of death related to antimicrobial resistance, yet its surveillance is still paper-based. Rifampicin-resistant TB (RR-TB) is an urgent public health crisis. The World Health Organization has, since 2010, endorsed a series of rapid diagnostic tests (RDTs) that enable rapid detection of drug-resistant strains and produce large volumes of data. In parallel, most high-burden countries have adopted connectivity solutions that allow linking of diagnostics, real-time capture, and shared repository of these test results. However, these connected diagnostics and readily available test results are not used to their full capacity, as we have yet to capitalize on fully understanding the relationship between test results and specific rpoB mutations to elucidate its potential application to real-time surveillance. Objective: We aimed to validate and analyze RDT data in detail, and propose the potential use of connected diagnostics and associated test results for real-time evaluation of RR-TB transmission. Methods: We selected 107 RR-TB strains harboring 34 unique rpoB mutations, including 30 within the rifampicin resistance–determining region (RRDR), from the Belgian Coordinated Collections of Microorganisms, Antwerp, Belgium. We subjected these strains to Xpert MTB/RIF, GenoType MTBDRplus v2.0, and Genoscholar NTM + MDRTB II, the results of which were validated against the strains’ available rpoB gene sequences. We determined the reproducibility of the results, analyzed and visualized the probe reactions, and proposed these for potential use in evaluating transmission. Results: The RDT probe reactions detected most RRDR mutations tested, although we found a few critical discrepancies between observed results and manufacturers’ claims. Based on published frequencies of probe reactions and RRDR mutations, we found specific probe reactions with high potential use in transmission studies: Xpert MTB/RIF probes A, Bdelayed, C, and Edelayed; Genotype MTBDRplus v2.0 WT2, WT5, and WT6; and Genoscholar NTM + MDRTB II S1 and S3. Inspection of probe reactions of disputed mutations may potentially resolve discordance between genotypic and phenotypic test results. Conclusions: We propose a novel approach for potential real-time detection of RR-TB transmission through fully using digitally linked TB diagnostics and shared repository of test results. To our knowledge, this is the first pragmatic and scalable work in response to the consensus of world-renowned TB experts in 2016 on the potential of diagnostic connectivity to accelerate efforts to eliminate TB. This is evidenced by the ability of our proposed approach to facilitate comparison of probe reactions between different RDTs used in the same setting. Integrating this proposed approach as a plug-in module to a connectivity platform will increase usefulness of connected TB diagnostics for RR-TB outbreak detection through real-time investigation of suspected RR-TB transmission cases based on epidemiologic linking.
KCN was supported by Erasmus Mundus Joint Doctorate Fellowship grant 2016-1346, and BCdJ, LR, and CJM were supported by European Research Council-INTERRUPTB starting grant 311725.