Rapid diagnosis of tuberculosis using Xpert MTB/RIF assay - Report from a developing country

Evaluation of the GeneXpert MTB/RIF to diagnose tuberculosis in a public health laboratory

OBJECTIVES

To evaluate the performance of geneXpert MTB/Rif versus conventional methods (bacilloscopy and culture) in the diagnosis of tuberculosis in a Central Public Health Laboratory (LACEN, Tocantins), Northern Brazil.

METHODS

Retrospective study, with information from 1,973 suspected cases of tuberculosis from patients treated from January 2015 to December 2020.

RESULTS

From the culture (reference standard), the sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of the geneXpert MTB/Rif were 100%, 97%, 74%, 100%, and 97%, respectively, against 85%, 98%, 80%, 98%, and 97% of bacilloscopy.

CONCLUSIONS

The geneXpert MTB/Rif performed similarly to culture and better than bacilloscopy. Although positive cases with negative culture should be evaluated with caution, its routine use is important for the early detection of tuberculosis.

Concordance and discordance of GeneXpert MTB/RIF and conventional culture method for diagnosis of Extra-Pulmonary Tuberculosis at a tertiary care hospital in Pakistan

Objective

To identify concordance and discordance between GeneXpert MTB/RIF assay and gold standard bacteriologic culture for the diagnosis of Mycobacterium tuberculosis (MTB) in Extra-Pulmonary tuberculosis (EPTB) specimens in our region.

Methods

This is a retrospective cross-sectional study conducted at the Indus Hospital and Health Network. Data from 1st January, 2020 to 31st December, 2021 was analyzed. A total of 1499 EPTB specimens were included for which GeneXpert was requested along with acid-fast bacteria (AFB) culture from the same specimen. Specimens were processed according to specimen type following standard operating procedures of the laboratory. Fluorescent staining was performed on all specimens along with bacteriologic culture. The GeneXpert MTB/RIF assay was carried out in exact accordance with the manufacturer's instructions.

Results

Out of 1499 EPTB specimens, 1370 (91.39%) specimens exhibited concordance between GeneXpert and conventional culture method, while 129 (8.60%) specimens showed discordance. GeneXpert exhibited sensitivity and specificity of 69.4% and 94.3% respectively in comparison to culture.

Conclusion

GeneXpert sensitivity for the diagnosis of EPTB varied with the site involved. Lower sensitivity was observed in ascitic and pleural fluids as compared to higher sensitivity observed among urine samples and pus aspirates. However, given the quick turnaround time and ease of use, it is a helpful tool in the diagnosis of EPTB when utilized in the appropriate clinical context. Caution is advised while interpreting negative GeneXpert results in endemic settings and should be interpreted along with other supporting clinical and diagnostic features.

Diagnostic Utility of Cartridge-Based Nucleic Acid Amplification Test (CBNAAT) on Induced Sputum Versus Gastric Aspirate Samples for the Diagnosis of Paediatric Pulmonary Tuberculosis

BACKGROUND

Tuberculosis (TB) in children is neglected, mainly due to a lack of sensitive diagnostic tools. Paediatric TB is now a global priority. More paediatric TB cases are being recorded as a result of the introduction of Xpert® Mycobacterium tuberculosis (MTB)/rifampicin (RIF) (Cepheid Inc., Sunnyvale, USA). This study was undertaken to evaluate the performance of Xpert MTB/RIF in the diagnosis of pulmonary TB in children.

METHODS

We recruited 70 paediatric patients with probable pulmonary TB and their gastric aspirate (GA), and induced sputum (IS) samples were collected between January 2021 and June 2022 in Saifai, Etawah, Uttar Pradesh, at the Microbiology Department of the Uttar Pradesh University of Medical Sciences (U.P.U.M.S.). All samples were subjected to smear examination, Bacterial Activation of Continuous Temperature and Environmental Control - Mycobacterial Growth Indicator Tube (BACTEC-MGIT) culture, and Xpert MTB/RIF.

RESULTS

 The specimens included 70 GAs and 70 IS samples. The total number of specimens were 140 and we collected GA as well as IS from each of the patient enrolled in the study. When compared to microscopy, GeneXpert provides a quicker and earlier detection of paediatric TB. The sensitivity of the cartridge-based nucleic acid amplification test (CBNAAT) against mycobacterial growth indicator tube (MGIT) was 75.0% for GA samples and 63.64% for IS samples.

CONCLUSION

Paediatric TB, owing to its paucibacillary nature and difficulty in the collection of samples, makes the diagnosis difficult by conventional methods. Our study shows that smear and culture yield in GA samples are superior to those of IS samples and the sensitivity of Xpert MTB/RIF assay is also significantly different in GA and IS samples, but a combination of GA and IS yielded the best results.

Detection of Mycobacterium tuberculosis using Gene Xpert-MTB/RIF assay among tuberculosis suspected patients at Mizan-Tepi university teaching hospital, southwest Ethiopia: An institution based cross-sectional study

BACKGROUND

Consistently deciding its current extent and chance elements of tuberculosis (TB) in all levels of clinical settings contributes to the anticipation and control exertion of the disease. In Ethiopia, updated information is still needed at every healthcare level and in different risk groups to monitor the national program's performance, which aims to attain the 2035 goal. Hence, this study aimed to generate additional evidence data on the magnitude of Mycobacterium tuberculosis using the Gene Xpert assay among TB-suspected patients at Mizan-Tepi university teaching hospital, southwest Ethiopia.

METHODS

A cross-sectional descriptive study was conducted from June to September 30, 2021. The required socio-demographic and other risk factor data were collected from a total of 422 suspected TB patients using a structured questionnaire. Approximately 392 pulmonary and 30 extra-pulmonary samples were collected and examined using the Gene Xpert-MTB/RIF assay. The statistical package for social sciences (SPSS) version 25 software was used to analyze the data.

RESULTS

In this study, Mycobacterium tuberculosis was detected in 12.5% (49/392) of pulmonary samples and 13.3% (4/30) of extra-pulmonary samples, giving an overall TB positivity of 12.6% (53/422). Rifampicin-resistant M. tuberculosis was detected in 3/53 (5.7%). Male sex (AOR: 2.54; 95% CI: 1.210, 5.354), previous contact (AOR: 4.25; 95% CI: 1.790, 10.092), smoking cigarette (AOR: 4.708; 95% CI: 1.004, 22.081), being HIV-positive (AOR: 4.27; 95% CI: 1.606, 11.344), and malnutrition (AOR: 3.55; 95% CI: 1.175, 10.747) were all significantly associated with M. tuberculosis detection using the GeneXpert MTB/RIF assay.

CONCLUSION

The overall frequency of M. tuberculosis in this study was still significant in different risk groups, despite the proposed strategies, which aimed to reduce TB prevalence to as low as 10 per 100,000 populations by 2035. Early case detection with better diagnostic tools and public health measures are important prevention and control strategies to meet the proposed target and reduce the burden of TB in the country.

Coloración de Ziehl-Neelsen en el laboratorio de patología: rendimiento y contribución al diagnóstico de micobacterias en el lavado broncoalveolar

Introducción.

La coloración de Ziehl-Neelsen, con más de 100 años de uso, continúa vigente mundialmente.

Objetivo.

Comparar el rendimiento de las pruebas diagnósticas utilizadas para la determinación de micobacterias en el laboratorio clínico de patología en muestras de lavado broncoalveolar.

Materiales y métodos.

Se revisaron retrospectivamente 737 muestras de lavado broncoalveolar procesadas en el 2019 y el 2020 en el Hospital San Vicente Fundación (Medellín, Colombia) y se compararon las características de tres pruebas diagnósticas realizadas en paralelo: la reacción en cadena de la polimerasa (PCR) para micobacterias con detección de resistencia, el cultivo, y la coloración de Ziehl-Neelsen.

Resultados.

Se catalogaron como enfermos a 93 de los 737 pacientes a partir de los resultados positivos en alguna de las tres pruebas. El cultivo tuvo una sensibilidad de 0,80, la PCR una de 0,76 y la coloración de Ziehl-Neelsen una de 0,51. Sin embargo, solo 5 de 75 (6,5 %) cultivos fueron positivos a las cuatro semanas y el resto lo fue a las ocho semanas. La PCR combinada con la coloración de Ziehl-Neelsen mejoró la sensibilidad de la PCR por sí sola, de 0,76 a 0,88, diferencia que fue estadísticamente signifcativa (p=0,022)

Conclusión.

En las muestras de lavado broncoalveolar, el cultivo sigue siendo la prueba con mejor sensibilidad. El uso conjunto de la prueba de PCR y la coloración de ZiehlNeelsen mejora signifcativamente la sensibilidad de la primera, lo que compensa la demora relativa en la entrega de los resultados debida al tiempo requerido para la tinción de Ziehl-Neelsen.

Innovations in Molecular Identification of Mycobacterium tuberculosis

Tuberculosis (TB) continues to be a significant public health concern on a global scale. Quick and precise identification of Mycobacterium tuberculosis (MTB) in symptomatic patients is pivotal for worldwide TB eradication initiatives. As an infectious disorder induced by MTB, it remains a critical threat to public health, particularly in poor countries, due to an inadequate diagnostic research laboratory. There is a need for a persistent incentive to reduce response time for effective diagnosis and control of TB infection, which is a benefit that molecular techniques provide over traditional methods. Although there is a tremendous overall prevalence of TB and a relatively poor probability of case identification worldwide. Common screening techniques have focused on tests that have many fundamental shortcomings. Due to the development of antibiotic-resistant Mycobacterium strains, TB is one of the leading contributors to fatalities. It is now possible to examine TB using molecular detection techniques, which are faster and more cost-effective than previous methods, such as standard culture procedures to test and verify antibiotic resistance in patients with TB. Whole genome sequencing (WGS), faster nucleic acid amplification tests, has made it easier to diagnose and treat TB more quickly. This article addresses the genetic approaches for detecting Mycobacterium tuberculosis complex (MTBC) in clinical specimens as well as antibiotic resistance in mycobacterium and discusses the practical limitations of using these methods.

Effectiveness of GeneXpert® in the diagnosis of tuberculosis in people living with HIV/AIDS

OBJECTIVE

To identify and synthesize the scientific knowledge produced regarding the effectiveness of the GeneXpert test in the diagnosis of pulmonary tuberculosis (TB) in people living with HIV/AIDS.

METHODS

Integrative literature review, which was searched on Embase, Scopus, PubMed, Cinahl, Academic Search Premier, Socindex, and LILACS platforms, in December 2019. The studies surveyed went through two stages of selection: reading of titles and abstracts by two reviewers independently; using the Rayyan platform and reading. Nineteen primary studies in English, Portuguese, and Spanish that answered the study's guiding question were included: How effective is the GeneXpert test in the diagnosis of pulmonary TB in people living with HIV/AIDS?

RESULTS

The use of GeneXpert substantially increased the detection of TB cases among the population co-infected with HIV/AIDS, with sensitivity ranging from 68% to 100%, superior to sputum smear microscopy. Specificity ranged from 91.7% to 100%; the positive predictive value from 79.2% to 96.1%; and the negative predictive value from 84.6% to 99.3%. These values were considered similar to sputum smear microscopy by most studies. We also compared these results with different ways of performing culture and other molecular tests, being considered inferior only to the Xpert Ultra.

CONCLUSION

It is possible to affirm that places with a high incidence of HIV/AIDS would benefit from the implementation of the GeneXpert test, entailing effectiveness in diagnosing pulmonary TB in this population when compared to sputum smear microscopy, a widely used test for detection of cases.

Prevalence of active tuberculosis disease among healthcare workers and support staff in healthcare settings of the Amhara region, Ethiopia

Background

Health care workers (HCWs) are at an increased risk of acquiring tuberculosis (TB) compared to the general population, because of the frequent face to face contact or potential exposure to TB through shared air or space with infectious patient(s), regardless of economic setting and local TB incidence. Information on the burden of active TB disease among HCWs will help guide control measures, can be utilized to evaluate the effectiveness of TB infection prevention programs in the health care setting, and guide necessary actions. However, data on TB among HCW in Ethiopia is limited. Therefore, this study aimed to determine the prevalence of active TB disease among healthcare workers and support staff in healthcare settings in the Amhara region of Ethiopia.

Methods

A cross-sectional study design was used to recruit a total of 580 randomly selected study participants in the Amhara region. Data were collected over four months in selected hospitals and health centers. Implementation of TB prevention and control measures was evaluated using a standardized checklist. The main outcome indicator was active TB as measured by a laboratory diagnosis using GeneXpert technology.

Results

A total of 580 study participants were enrolled. The mean age was 31.3 (±7.8 standard deviation) years, with about two-thirds (65.3%) aged between 18–24 years. A total of 9 (1.6%) MTB cases were detected, 4 (1.4%) in HCWs and 5 (1.7%) in support staff, which did not significantly differ (P = 0.50). About 90% of the participants had not received TB infection prevention and control training ever. More than half (54%) of the study participants worked in poorly ventilated rooms. Triage of coughing patients was not practiced in 32% of the studied facilities (health centers and hospitals).

Conclusions

The magnitude of TB among healthcare workers and support staff in healthcare settings was higher than in the general population (140 per 100000 population). The status of implementation of tuberculosis prevention and control measures indicated missed opportunities. Hence, strict implementation of developed infection control plans of TB in healthcare settings needs to be improved.

Diagnostic challenges and Gene-Xpert utility in detecting Mycobacterium tuberculosis among suspected cases of Pulmonary tuberculosis

The incidence of pulmonary tuberculosis (PTB) can be reduced by preventing transmission with rapid and precise case detection and early treatment. The Gene-Xpert MTB/RIF assay is a useful tool for detecting Mycobacterium tuberculosis (MTB) with rifampicin resistance within approximately two hours by using a nucleic acid amplification technique. This study was designed to reduce the underdiagnosis of smear-negative pulmonary TB and to assess the clinical and radiological characteristics of PTB patients. This cross-sectional study included 235 participants who went to the Luyang primary health care clinic from September 2016 to June 2017. The demographic data were analyzed to investigate the association of patient gender, age group, and ethnicity by chi-square test. To assess the efficacy of the diagnostic test, the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy were calculated. The area under the curve for sputum for both AFB and gene-Xpert was analyzed to compare their accuracy in diagnosing TB. In this study, TB was more common in males than in females. The majority (50.71%) of the cases belonged to the 25-44-year-old age group and the Bajau ethnicity (57.74%). Out of 50 pulmonary TB cases (smear-positive with AFB staining), 49 samples were positive according to the Gene-Xpert MTB/RIF assay and was confirmed by MTB culture. However, out of 185 smear-negative presumptive cases, 21 cases were positive by Gene-Xpert MTB/RIF assay in that a sample showed drug resistance, and these results were confirmed by MTB culture, showing resistance to isoniazid. In comparison to sputum for AFB, Gene-Xpert showed more sensitivity and specificity with almost complete accuracy. The additional 21 PTB cases detection from the presumptive cases by GeneXpert had significant impact compared to initial observation by the routine tests which overcame the diagnostic challenges and ambiguities.

Prevalence of rifampicin resistance tuberculosis among HIV/TB coinfected patients in Benue State, Nigeria

Introduction

the emergence of HIV/TB co-infection has changed the global health landscape globally, particularly in sub-Saharan Africa and Asia with a high prevalence rate. It has further worsened and compound patient diagnosis, treatment/management approach and infection control. Rifampicin resistance TB (RR-TB) is a good indicator of treatment failure and infection control in the community. This study determines the prevalence of RR-TB among HIV/TB coinfected patients in Benue State, Nigeria.

Methods

the case-control study was carried out at Federal Medical Centre, Makurdi and General Hospital, Otupko, between January 2017 and February 2018. One thousand and ten suspected tuberculosis and HIV patients were enrolled in the study, diagnosed according to WHO guidelines. Sputum samples were collected and then analyzed by acid-fast bacilli smear test and GeneXpert MTB/RIF assay.

Results

overall prevalence of tuberculosis by acid-fast test was 74 (7.3%), 171 (16.93%) by GeneXpert assay and 2.18% by RR-TB test respectively. Significant difference was observed between the detection technique and demographic variables, high prevalence among urban patient compared to rural (8.85%vs 5.40%; X²= 4.38; P = 0.036) and ethnic background of the patients (X²= 23.21; P = 0.000) by acid fast test. With GeneXpert, high prevalence recorded among patient within age-group15-45years (X²= 8.01; P = 0.046) and ethnic group (X²= 6.30; P = 0.044). The occurrence of HIV/TB co-infection was less associated with Idoma ethnic group (COR; 0.440; 95% C.I; 0.246 - 0.786).

Conclusion

the relatively high prevalence of HIV/TB co-infection and RR-TB is a tremendous public health threat, considering society's attendant implication. Further surveillance studies are needed to evaluate the situation in Benue State better.

A Two-Gene Signature for Tuberculosis Diagnosis in Persons With Advanced HIV

Background: Transcriptomic signatures for tuberculosis (TB) have been proposed and represent a promising diagnostic tool. Data remain limited in persons with advanced HIV.

Methods: We enrolled 30 patients with advanced HIV (CD4 <100 cells/mm³) in India; 16 with active TB and 14 without. Whole-blood RNA sequencing was performed; these data were merged with a publicly available dataset from Uganda (n = 33; 18 with TB and 15 without). Transcriptomic profiling and machine learning algorithms identified an optimal gene signature for TB classification. Receiver operating characteristic analysis was used to assess performance.

Results: Among 565 differentially expressed genes identified for TB, 40 were shared across India and Uganda cohorts. Common upregulated pathways reflect Toll-like receptor cascades and neutrophil degranulation. The machine-learning decision-tree algorithm selected gene expression values from RAB20 and INSL3 as most informative for TB classification. The signature accurately classified TB in discovery cohorts (India AUC 0.95 and Uganda AUC 1.0; p < 0.001); accuracy was fair in external validation cohorts.

Conclusions: Expression values of RAB20 and INSL3 genes in peripheral blood compose a biosignature that accurately classified TB status among patients with advanced HIV in two geographically distinct cohorts. The functional analysis suggests pathways previously reported in TB pathogenesis.

Xpert MTB/RIF Ultra and Xpert MTB/RIF assays for extrapulmonary tuberculosis and rifampicin resistance in adults

BACKGROUND

Xpert MTB/RIF Ultra (Xpert Ultra) and Xpert MTB/RIF are World Health Organization (WHO)-recommended rapid nucleic acid amplification tests (NAATs) widely used for simultaneous detection of Mycobacterium tuberculosis complex and rifampicin resistance in sputum. To extend our previous review on extrapulmonary tuberculosis (Kohli 2018), we performed this update to inform updated WHO policy (WHO Consolidated Guidelines (Module 3) 2020).

OBJECTIVES

To estimate diagnostic accuracy of Xpert Ultra and Xpert MTB/RIF for extrapulmonary tuberculosis and rifampicin resistance in adults with presumptive extrapulmonary tuberculosis.

SEARCH METHODS

Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, Web of Science, Latin American Caribbean Health Sciences Literature, Scopus, ClinicalTrials.gov, the WHO International Clinical Trials Registry Platform, the International Standard Randomized Controlled Trial Number Registry, and ProQuest, 2 August 2019 and 28 January 2020 (Xpert Ultra studies), without language restriction.

SELECTION CRITERIA

Cross-sectional and cohort studies using non-respiratory specimens. Forms of extrapulmonary tuberculosis: tuberculous meningitis and pleural, lymph node, bone or joint, genitourinary, peritoneal, pericardial, disseminated tuberculosis. Reference standards were culture and a study-defined composite reference standard (tuberculosis detection); phenotypic drug susceptibility testing and line probe assays (rifampicin resistance detection).

DATA COLLECTION AND ANALYSIS

Two review authors independently extracted data and assessed risk of bias and applicability using QUADAS-2. For tuberculosis detection, we performed separate analyses by specimen type and reference standard using the bivariate model to estimate pooled sensitivity and specificity with 95% credible intervals (CrIs). We applied a latent class meta-analysis model to three forms of extrapulmonary tuberculosis. We assessed certainty of evidence using GRADE.

MAIN RESULTS

69 studies: 67 evaluated Xpert MTB/RIF and 11 evaluated Xpert Ultra, of which nine evaluated both tests. Most studies were conducted in China, India, South Africa, and Uganda. Overall, risk of bias was low for patient selection, index test, and flow and timing domains, and low (49%) or unclear (43%) for the reference standard domain. Applicability for the patient selection domain was unclear for most studies because we were unsure of the clinical settings. Cerebrospinal fluid Xpert Ultra (6 studies) Xpert Ultra pooled sensitivity and specificity (95% CrI) against culture were 89.4% (79.1 to 95.6) (89 participants; low-certainty evidence) and 91.2% (83.2 to 95.7) (386 participants; moderate-certainty evidence). Of 1000 people where 100 have tuberculous meningitis, 168 would be Xpert Ultra-positive: of these, 79 (47%) would not have tuberculosis (false-positives) and 832 would be Xpert Ultra-negative: of these, 11 (1%) would have tuberculosis (false-negatives). Xpert MTB/RIF (30 studies) Xpert MTB/RIF pooled sensitivity and specificity against culture were 71.1% (62.8 to 79.1) (571 participants; moderate-certainty evidence) and 96.9% (95.4 to 98.0) (2824 participants; high-certainty evidence). Of 1000 people where 100 have tuberculous meningitis, 99 would be Xpert MTB/RIF-positive: of these, 28 (28%) would not have tuberculosis; and 901 would be Xpert MTB/RIF-negative: of these, 29 (3%) would have tuberculosis. Pleural fluid Xpert Ultra (4 studies) Xpert Ultra pooled sensitivity and specificity against culture were 75.0% (58.0 to 86.4) (158 participants; very low-certainty evidence) and 87.0% (63.1 to 97.9) (240 participants; very low-certainty evidence). Of 1000 people where 100 have pleural tuberculosis, 192 would be Xpert Ultra-positive: of these, 117 (61%) would not have tuberculosis; and 808 would be Xpert Ultra-negative: of these, 25 (3%) would have tuberculosis. Xpert MTB/RIF (25 studies) Xpert MTB/RIF pooled sensitivity and specificity against culture were 49.5% (39.8 to 59.9) (644 participants; low-certainty evidence) and 98.9% (97.6 to 99.7) (2421 participants; high-certainty evidence). Of 1000 people where 100 have pleural tuberculosis, 60 would be Xpert MTB/RIF-positive: of these, 10 (17%) would not have tuberculosis; and 940 would be Xpert MTB/RIF-negative: of these, 50 (5%) would have tuberculosis. Lymph node aspirate Xpert Ultra (1 study) Xpert Ultra sensitivity and specificity (95% confidence interval) against composite reference standard were 70% (51 to 85) (30 participants; very low-certainty evidence) and 100% (92 to 100) (43 participants; low-certainty evidence). Of 1000 people where 100 have lymph node tuberculosis, 70 would be Xpert Ultra-positive and 0 (0%) would not have tuberculosis; 930 would be Xpert Ultra-negative and 30 (3%) would have tuberculosis. Xpert MTB/RIF (4 studies) Xpert MTB/RIF pooled sensitivity and specificity against composite reference standard were 81.6% (61.9 to 93.3) (377 participants; low-certainty evidence) and 96.4% (91.3 to 98.6) (302 participants; low-certainty evidence). Of 1000 people where 100 have lymph node tuberculosis, 118 would be Xpert MTB/RIF-positive and 37 (31%) would not have tuberculosis; 882 would be Xpert MTB/RIF-negative and 19 (2%) would have tuberculosis. In lymph node aspirate, Xpert MTB/RIF pooled specificity against culture was 86.2% (78.0 to 92.3), lower than that against a composite reference standard. Using the latent class model, Xpert MTB/RIF pooled specificity was 99.5% (99.1 to 99.7), similar to that observed with a composite reference standard. Rifampicin resistance Xpert Ultra (4 studies) Xpert Ultra pooled sensitivity and specificity were 100.0% (95.1 to 100.0), (24 participants; low-certainty evidence) and 100.0% (99.0 to 100.0) (105 participants; moderate-certainty evidence). Of 1000 people where 100 have rifampicin resistance, 100 would be Xpert Ultra-positive (resistant): of these, zero (0%) would not have rifampicin resistance; and 900 would be Xpert Ultra-negative (susceptible): of these, zero (0%) would have rifampicin resistance. Xpert MTB/RIF (19 studies) Xpert MTB/RIF pooled sensitivity and specificity were 96.5% (91.9 to 98.8) (148 participants; high-certainty evidence) and 99.1% (98.0 to 99.7) (822 participants; high-certainty evidence). Of 1000 people where 100 have rifampicin resistance, 105 would be Xpert MTB/RIF-positive (resistant): of these, 8 (8%) would not have rifampicin resistance; and 895 would be Xpert MTB/RIF-negative (susceptible): of these, 3 (0.3%) would have rifampicin resistance.

AUTHORS' CONCLUSIONS

Xpert Ultra and Xpert MTB/RIF may be helpful in diagnosing extrapulmonary tuberculosis. Sensitivity varies across different extrapulmonary specimens: while for most specimens specificity is high, the tests rarely yield a positive result for people without tuberculosis. For tuberculous meningitis, Xpert Ultra had higher sensitivity and lower specificity than Xpert MTB/RIF against culture. Xpert Ultra and Xpert MTB/RIF had similar sensitivity and specificity for rifampicin resistance. Future research should acknowledge the concern associated with culture as a reference standard in paucibacillary specimens and consider ways to address this limitation.

Magnitude and Associated Factors of Pulmonary Tuberculosis Among HIV/AIDS Patients Attending Antiretroviral Therapy Clinic at Debre Tabor Specialized Hospital, Northwest Ethiopia, 2019

BACKGROUND

Tuberculosis (TB) has remained as a top global public health concern of the 21st century. It is the leading cause of morbidity and mortality among people living with human immunodeficiency virus (HIV) worldwide.

OBJECTIVE

The study aimed to investigate the magnitude of pulmonary tuberculosis and its associated factors among HIV-positive patients attending antiretroviral treatment (ART) clinic in Debre Tabor specialized hospital, Northwest, Ethiopia.

METHODS

A hospital-based cross-sectional study was conducted among 362 HIV-positive adult participants attending the ART clinic from October 1st to December 30th 2019. Socio-demographic data were collected using a pre-tested questionnaire. Sputum was collected aseptically into a sterile and leak-proof container. Following aseptic techniques, each sample was processed using the GeneXpert assay based on the manufacturer's instructions. Similarly, about 3-5 mL of whole blood was drawn for CD4+ T-cell count and plasma viral load tests following standard blood collection procedures. CD4+ T-cell count was performed using the BD FACS caliber flow cytometry while the plasma viral load was performed by using a quantitative real-time polymerase chain reaction. Then, collected data were double-checked, cleaned and entered into Epi-Info version 7.2.0.1 and exported to SPSS version 20.0 for further statistical analysis. The bivariate and multivariate logistic regression were conducted to address risk factor analysis. The 95%confidence interval with its corresponding cure and adjusted odds ratio was computed. Finally, p-value ≤0.05 was considered as a statistically significant association.

RESULTS

In this study, the overall prevalence of tuberculosis among HIV-positive patients was 18 [(5%), 95% CI: 2.8-7.5]. A high viral load (≥1000 copies/mL) was positively associated [AOR (95% CI: 6.4 (1.6-25.7)), p < 0.001] with developing tuberculosis among HIV-positive patients.

CONCLUSION

The prevalence of TB is low among ART-receiving patients in our study site.

Diagnostic Accuracy of Sputum Microscopy in Comparison With GeneXpert in Pulmonary Tuberculosis

Background

Tuberculosis (TB) is a major health problem. In Pakistan, the diagnosis of pulmonary tuberculosis mainly relies on acid-fast bacilli (AFB) smear microscopy and Xpert® MTB/RIF assay (Cepheid Inc., Sunnyvale, CA) - a nucleic acid amplification test - where available. There is a wide variation in the reported sensitivity of Ziehl-Neelsen (ZN) smear microscopy across previous studies. This study aimed to determine the accuracy of sputum ZN smear microscopy in diagnosing pulmonary tuberculosis as compared with the sputum GeneXpert (Xpert MTB/RIF assay) as the reference test.

Materials and methods

This is a retrospective cross-sectional study conducted in the outpatient department of the Pakistan Institute of Medical Sciences. This study included 326 patients, aged 12 years and above, who had their sputum samples tested for ZN smear microscopy and GeneXpert during the period January to June 2019. Patients' demographic details, sputum ZN smear microscopy, and GeneXpert test results were collected for data analysis. A case of pulmonary tuberculosis was defined as a patient with positive sputum GeneXpert test result.

Results

Out of the 326 patients, GeneXpert detected MTB deoxyribonucleic acid (DNA) in 50 patients and ZN smear microscopy detected AFB in 30 patients. There was a marginal male predominance among GeneXpert positive cases. Adolescents were the least affected age group. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of ZN smear microscopy were 60%, 100%, 100%, 93.24%, and 93.87%, respectively. The positive likelihood ratio was infinite whereas the negative likelihood ratio was 0.4. The area under curve (AUC) for ZN smear microscopy was 0.800 and receiver operating characteristic (ROC) curve analysis revealed a diagonal straight line closer to the left upper corner.

Conclusion

Sputum ZN smear microscopy is a highly specific but moderately sensitive test for the diagnosis of pulmonary tuberculosis. This study recommends the sputum GeneXpert MTB/RIF test to avoid a missed diagnosis of smear-negative pulmonary TB.

Rifampicin-Resistant Multidrug-Resistant Tuberculosis Cases in Selected Hospitals in Western Oromia, Ethiopia: Cross-Sectional Retrospective Study

Purpose

With the recommendation of World Health Organization (WHO) and as per the Ethiopian National Implementation Guideline, GeneXpert is used for rapid diagnosis of rifampicin (RIF)-resistant multidrug-resistant tuberculosis (MDR-TB) from the suspected TB patients; however, there were limited findings in Ethiopia particularly in the study area showing the magnitude of RIF-resistant MDR-TB and related factors among suspected TB cases. Hence, we aimed to assess resistance to RIF as a biomarker for the detection of MDR-TB cases from the suspected TB patients in selected hospitals, Western Oromia, Ethiopia.

Patients and Methods

We have conducted a cross-sectional review on 2300 registered GeneXpert data as clinically suspected TB cases in three governmental hospitals, Western Oromia, Ethiopia, between October 2015 and April 2016 to assess resistance to RIF as a biomarker for the detection of MDR-TB cases. Trained data collectors enumerated the data using pre-tested semi-structured questionnaires from the Gene Xpert records found in the registration logbook available at each hospital laboratories. Following checking the data for completeness, we have cleaned and entered our data into SPSS version 20 to compute different analyses. P-value of ≤0.05 was taken as statistically significant.

Results

A total of 2300 TB suspected cases were included in the study. The overall prevalence of TB diagnosed by the GeneXpert assay was 21.3% (491/2300). In all TB confirmed cases, RIF-resistant TB accounted for 25.9% (127/491) which expressed rpoB gene mutations. Sex (being male), age (within 16-30 age group), patient category (relapse, loss to follow-up, treatment failure and had MDR-TB contact) were significantly associated with rifampicin-resistant TB. Relapse patient was 20 times more likely to develop MDR-TB when compared to the new patient (P-value= 0.01, COR = 20.0, 95%C.I = 17.5-42.5).

Conclusion

The rifampicin-resistant TB is prevalent in all age groups. The strong association and high prevalence of RIF-resistant TB to failure after treatment in this study require more attention towards improving the treatment to minimize evolving of the MDR-TB cases.

Evaluation of GeneXpert MTB/RIF system performances in the diagnosis of extrapulmonary tuberculosis

Background

Tuberculosis represents a serious public health problem and a significant diagnostic and therapeutic challenge worldwide. Molecular diagnostic techniques are crucial in the World Health Organization’s new tuberculosis control strategy.

This study aims to evaluate the performance of GeneXpert MTB/RIF (Cepheid Sunnyvale, CA, United States) in diagnosis of extra-pulmonary tuberculosis then compare it’s performance in detecting Rifampicin resistance to GenoType MTBDRplus (HAIN Life Sciences, Nehren, Germany).

Methods

Samples from pulmonary and/or extra-pulmonary origins were analysed in a 21 months retrospective study. Samples were sent to the bacteriology laboratory for Mycobacterium tuberculosis detection using conventional bacteriological and molecular methods (GeneXpert MTB/RIF and MTBDRplus). Sensitivity and specificity were calculated for the stained smear and GeneXpert according to culture (Gold Standard) as well as for GeneXpert MTB/RIF in both negative and positive microscopy tuberculosis cases. Data’s statistical analysis was performed with SPSS13.0 software.

Results

Seven hundred fourteen patients’ samples were analysed; the average age was 47.21 ± 19.98 years with a male predominance (66.4%). Out of 714 samples: 285 were from pulmonary and 429 were from extra-pulmonary origins. The positivity rates for microscopy, GeneXpert MTB/RIF and culture were 12.88, 20.59 and 15.82%, respectively. These rates were 18.9, 23.85 and 20.35% for pulmonary samples and 9.71, 18.41 and 12.82% for extra-pulmonary samples, respectively. The sensitivity and specificity of GeneXpert MTB/RIF were almost the same in both pulmonary and extra-pulmonary samples (78.2 and 90.4%) and (79,3 and 90.3%) respectively.

Rifampicin resistance rate found by GeneXpert MTB/RIF was 0.84%. Comparison of Rifampicin resistance obtained by GeneXpert MTB/RIF and Genotype MTBDRplus, showed 100% agreement between the two techniques for studied samples.

Conclusions

This confirms GeneXpert MTB/RIF advantage for tuberculosis diagnosis, particularly extra-pulmonary tuberculosis with negatively stained smear. The performance of GeneXpert and Genotype MTBDRplus are similar in detection of Rifampicin resistance. However, variability of detection performance according to tuberculosis endemicity deserves more attention in the choice of screening techniques of Rifampicin resistance, hence the interest of conducting comparative studies of detection performance under low and medium endemicity on large samples of tuberculosis populations.

EBUS-TBNA in the rapid microbiological diagnosis of drug-resistant mediastinal tuberculous lymphadenopathy

This study aimed to examine the use of endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) in the rapid diagnosis of mediastinal tuberculous lymphadenitis and drug-resistant mediastinal tuberculous lymphadenitis. A diagnosis of TB was confirmed by a positive Xpert MTB/RIF test or Mycobacterium tuberculosis culture. Rifampicin-resistant TB (RR-TB) or multidrug-resistant TB (MDR-TB) was diagnosed upon the detection of rifampicin resistance by Xpert MTB/RIF or resistance to rifampicin and isoniazid by phenotypic drug susceptibility testing (DST). Xpert MTB/RIF was positive in 43 of 56 patients (77%) and TB culture was positive in 31 of 56 patients (55%). Of these 56 patients, 25 (45%) were Xpert MTB/RIF positive and TB culture negative, 13 (23%) were Xpert MTB/RIF negative and TB culture positive, and 18 (32%) were Xpert MTB/RIF positive and TB culture positive. 11 patients (20%) had drug-resistant TB: seven with RR/MDR-TB, one with pre-extensively drug-resistant (XDR) TB, two with XDR-TB and one with isoniazid mono-resistance. An Xpert MTB/RIF assay carried out on EBUS-TBNA specimens provides rapid diagnosis of TB. Xpert MTB/RIF testing appears to have additional and more rapid sensitivity compared with culture alone. Culture-based DST provides an additional exclusive yield and the full resistance profile in addition to or instead of rifampicin resistance.

Use of Xpert MTB/RIF for the Identification of TB and Drug Resistance Among Smear-Negative and Re-Treatment Cases in Rural Areas of Ethiopia

Introduction:

Tuberculosis (TB) remains a leading infectious cause of morbidity and mortality worldwide. A key contributor to this burden is poor diagnosis as only 60% of new pulmonary tuberculosis (TB) cases in Africa are ever detected. Therefore, this study aimed to assess the feasibility of Xpert MTB/RIF test implementation in the region, and the performance of the assay to increase case detection on the selected rural health care setting.

Objective:

To assess the feasibility of Xpert MTB/RIF test implementation in the rural health care setting in Southern Ethiopia.

Methods:

Two Xpert MTB/RIF machines were brought in 2012 through TB REACH project. It was placed at Yirgalem hospital and at Aletawondo health centre. The instruments were installed after formal training was provided to laboratory technologists for three days. We collected sputum sample from participants who repeatedly had negative smear microscopy and those who had not responded to first-line anti-TB drugs.

Result:

Of the total participants tested, 1828 have valid result (MTB-, MTB+/RIF-, MTB+/RIF+, MTB+/RIF Indeterminate). From the participants with valid results, 217 (11.9%) were Xpert-positive of which were 165 (9.0%) RIF-negative, 6 (0.3%) RIF-indeterminate and 46 (2.5%) RIF-positive. Among TB suspects with previous treatment history and positive by Xpert, RIF resistance was detected in 10 (2.2%). From the new TB suspects with positive Xpert, RIF resistance was detected in 29 (2.7%). All cases identified were linked with TB/MDR-TB treatment centers.

Conclusion:

Xpert provides an additional tool for the diagnosis of TB and drug resistance, with almost 12% of new and retreatment cases obtaining information that is useful for clinical management. To enhance its efficient utilisation, operational challenges should be minimized particularly in relation to availing robust alternative power source.

Xpert MTB/RIF and Xpert MTB/RIF Ultra for pulmonary tuberculosis and rifampicin resistance in adults

BACKGROUND

Xpert MTB/RIF (Xpert MTB/RIF) and Xpert MTB/RIF Ultra (Xpert Ultra), the newest version, are the only World Health Organization (WHO)-recommended rapid tests that simultaneously detect tuberculosis and rifampicin resistance in persons with signs and symptoms of tuberculosis, at lower health system levels. A previous Cochrane Review found Xpert MTB/RIF sensitive and specific for tuberculosis (Steingart 2014). Since the previous review, new studies have been published. We performed a review update for an upcoming WHO policy review.

OBJECTIVES

To determine diagnostic accuracy of Xpert MTB/RIF and Xpert Ultra for tuberculosis in adults with presumptive pulmonary tuberculosis (PTB) and for rifampicin resistance in adults with presumptive rifampicin-resistant tuberculosis.

SEARCH METHODS

We searched the Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, Web of Science, Latin American Caribbean Health Sciences Literature, Scopus, the WHO International Clinical Trials Registry Platform, the International Standard Randomized Controlled Trial Number Registry, and ProQuest, to 11 October 2018, without language restriction.

SELECTION CRITERIA

Randomized trials, cross-sectional, and cohort studies using respiratory specimens that evaluated Xpert MTB/RIF, Xpert Ultra, or both against the reference standard, culture for tuberculosis and culture-based drug susceptibility testing or MTBDRplus for rifampicin resistance.

DATA COLLECTION AND ANALYSIS

Four review authors independently extracted data using a standardized form. When possible, we also extracted data by smear and HIV status. We assessed study quality using QUADAS-2 and performed meta-analyses to estimate pooled sensitivity and specificity separately for tuberculosis and rifampicin resistance. We investigated potential sources of heterogeneity. Most analyses used a bivariate random-effects model. For tuberculosis detection, we first estimated accuracy using all included studies and then only the subset of studies where participants were unselected, i.e. not selected based on prior microscopy testing.

MAIN RESULTS

We identified in total 95 studies (77 new studies since the previous review): 86 studies (42,091 participants) evaluated Xpert MTB/RIF for tuberculosis and 57 studies (8287 participants) for rifampicin resistance. One study compared Xpert MTB/RIF and Xpert Ultra on the same participant specimen.Tuberculosis detectionOf the total 86 studies, 45 took place in high tuberculosis burden and 50 in high TB/HIV burden countries. Most studies had low risk of bias.Xpert MTB/RIF pooled sensitivity and specificity (95% credible Interval (CrI)) were 85% (82% to 88%) and 98% (97% to 98%), (70 studies, 37,237 unselected participants; high-certainty evidence). We found similar accuracy when we included all studies.For a population of 1000 people where 100 have tuberculosis on culture, 103 would be Xpert MTB/RIF-positive and 18 (17%) would not have tuberculosis (false-positives); 897 would be Xpert MTB/RIF-negative and 15 (2%) would have tuberculosis (false-negatives).Xpert Ultra sensitivity (95% confidence interval (CI)) was 88% (85% to 91%) versus Xpert MTB/RIF 83% (79% to 86%); Xpert Ultra specificity was 96% (94% to 97%) versus Xpert MTB/RIF 98% (97% to 99%), (1 study, 1439 participants; moderate-certainty evidence).Xpert MTB/RIF pooled sensitivity was 98% (97% to 98%) in smear-positive and 67% (62% to 72%) in smear-negative, culture-positive participants, (45 studies). Xpert MTB/RIF pooled sensitivity was 88% (83% to 92%) in HIV-negative and 81% (75% to 86%) in HIV-positive participants; specificities were similar 98% (97% to 99%), (14 studies).Rifampicin resistance detectionXpert MTB/RIF pooled sensitivity and specificity (95% Crl) were 96% (94% to 97%) and 98% (98% to 99%), (48 studies, 8020 participants; high-certainty evidence).For a population of 1000 people where 100 have rifampicin-resistant tuberculosis, 114 would be positive for rifampicin-resistant tuberculosis and 18 (16%) would not have rifampicin resistance (false-positives); 886 would be would be negative for rifampicin-resistant tuberculosis and four (0.4%) would have rifampicin resistance (false-negatives).Xpert Ultra sensitivity (95% CI) was 95% (90% to 98%) versus Xpert MTB/RIF 95% (91% to 98%); Xpert Ultra specificity was 98% (97% to 99%) versus Xpert MTB/RIF 98% (96% to 99%), (1 study, 551 participants; moderate-certainty evidence).

AUTHORS' CONCLUSIONS

We found Xpert MTB/RIF to be sensitive and specific for diagnosing PTB and rifampicin resistance, consistent with findings reported previously. Xpert MTB/RIF was more sensitive for tuberculosis in smear-positive than smear-negative participants and HIV-negative than HIV-positive participants. Compared with Xpert MTB/RIF, Xpert Ultra had higher sensitivity and lower specificity for tuberculosis and similar sensitivity and specificity for rifampicin resistance (1 study). Xpert MTB/RIF and Xpert Ultra provide accurate results and can allow rapid initiation of treatment for multidrug-resistant tuberculosis.

Diagnostic Performance of Xpert MTB/RIF Assay Versus Ziehl-Neelsen Method for the Diagnosis of Pulmonary Tuberculosis in Addis Ababa, Ethiopia

Background:

Worldwide Tuberculosis (TB) is the ninth leading cause of death from a single infectious agent, positioning on top of Human Immuno Deficiency Virus (HIV) and it is still an eminently serious public health problem. In developing countries, Ziehl-Neelsen (ZN)-stained sputum smear microscopy is the most widely used diagnostic method in diagnosing Pulmonary Tuberculosis (PTB). This study was aimed to compare the diagnostic performances of ZN-method with Xpert MTB/RIF assay for the diagnosis of PTB in Addis Ababa, Ethiopia.

Methods:

Facility-based cross-sectional study design was conducted from September 2016 to June 2017 on a total of 244 sputum samples collected from presumptive TB patients. The L-J sputum culture was used as a gold standard to compare the diagnostic performances of Xpert MTB/RIF assay and ZN-methods. Kappa values were analyzed by using statistical package for Social Science (SPSS) version 20 software at 95% Confidence Interval (CI). The Sensitivity, Specificity, Positive Predictive Value (PPV) and Negative Predictive Value (NPV) of ZN-stained sputum smear microscopy and Xpert MTB/RIF assay were calculated against the gold standard.

Results:

The Sensitivity, Specificity, PPV and NPV of ZN-stained sputum smear microscopy were 68.38%, 95.28%, 93.02% and 76.58% respectively, while for Xpert MTB/ RIF assay were 88.89%, 81.89%, 81.89% and 88.89% respectively. The results of the two diagnostic approaches were concordant with the gold standard with a kappa value of ZN 0.650 and 0.743 for Xpert MTB/RIF assay.

Conclusion:

This study concludes that the sensitivity of Xpert MTB/RIF assay was better than ZN-stained direct sputum smear microscopy for the diagnosis of pulmonary tuberculosis.

Xpert® MTB/RIF assay for extrapulmonary tuberculosis and rifampicin resistance

BACKGROUND

Tuberculosis (TB) is the world's leading infectious cause of death. Extrapulmonary TB accounts for 15% of TB cases, but the proportion is increasing, and over half a million people were newly diagnosed with rifampicin-resistant TB in 2016. Xpert^® MTB/RIF (Xpert) is a World Health Organization (WHO)-recommended, rapid, automated, nucleic acid amplification assay that is used widely for simultaneous detection of Mycobacterium tuberculosis complex and rifampicin resistance in sputum specimens. This Cochrane Review assessed the accuracy of Xpert in extrapulmonary specimens.

OBJECTIVES

To determine the diagnostic accuracy of Xpert a) for extrapulmonary TB by site of disease in people presumed to have extrapulmonary TB; and b) for rifampicin resistance in people presumed to have extrapulmonary TB.

SEARCH METHODS

We searched the Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, Web of Science, Latin American Caribbean Health Sciences Literature (LILACS), Scopus, ClinicalTrials.gov, the WHO International Clinical Trials Registry Platform, the International Standard Randomized Controlled Trial Number (ISRCTN) Registry, and ProQuest up to 7 August 2017 without language restriction.

SELECTION CRITERIA

We included diagnostic accuracy studies of Xpert in people presumed to have extrapulmonary TB. We included TB meningitis and pleural, lymph node, bone or joint, genitourinary, peritoneal, pericardial, and disseminated TB. We used culture as the reference standard. For pleural TB, we also included a composite reference standard, which defined a positive result as the presence of granulomatous inflammation or a positive culture result. For rifampicin resistance, we used culture-based drug susceptibility testing or MTBDRplus as the reference standard.

DATA COLLECTION AND ANALYSIS

Two review authors independently extracted data, assessed risk of bias and applicability using the QUADAS-2 tool. We determined pooled predicted sensitivity and specificity for TB, grouped by type of extrapulmonary specimen, and for rifampicin resistance. For TB detection, we used a bivariate random-effects model. Recognizing that use of culture may lead to misclassification of cases of extrapulmonary TB as 'not TB' owing to the paucibacillary nature of the disease, we adjusted accuracy estimates by applying a latent class meta-analysis model. For rifampicin resistance detection, we performed univariate meta-analyses for sensitivity and specificity separately to include studies in which no rifampicin resistance was detected. We used theoretical populations with an assumed prevalence to provide illustrative numbers of patients with false positive and false negative results.

MAIN RESULTS

We included 66 unique studies that evaluated 16,213 specimens for detection of extrapulmonary TB and rifampicin resistance. We identified only one study that evaluated the newest test version, Xpert MTB/RIF Ultra (Ultra), for TB meningitis. Fifty studies (76%) took place in low- or middle-income countries. Risk of bias was low for patient selection, index test, and flow and timing domains and was high or unclear for the reference standard domain (most of these studies decontaminated sterile specimens before culture inoculation). Regarding applicability, in the patient selection domain, we scored high or unclear concern for most studies because either patients were evaluated exclusively as inpatients at tertiary care centres, or we were not sure about the clinical settings.Pooled Xpert sensitivity (defined by culture) varied across different types of specimens (31% in pleural tissue to 97% in bone or joint fluid); Xpert sensitivity was > 80% in urine and bone or joint fluid and tissue. Pooled Xpert specificity (defined by culture) varied less than sensitivity (82% in bone or joint tissue to 99% in pleural fluid and urine). Xpert specificity was ≥ 98% in cerebrospinal fluid, pleural fluid, urine, and peritoneal fluid.Xpert testing in cerebrospinal fluidXpert pooled sensitivity and specificity (95% credible interval (CrI)) against culture were 71.1% (60.9% to 80.4%) and 98.0% (97.0% to 98.8%), respectively (29 studies, 3774 specimens; moderate-certainty evidence).For a population of 1000 people where 100 have TB meningitis on culture, 89 would be Xpert-positive: of these, 18 (20%) would not have TB (false-positives); and 911 would be Xpert-negative: of these, 29 (3%) would have TB (false-negatives).For TB meningitis, ultra sensitivity and specificity against culture (95% confidence interval (CI)) were 90% (55% to 100%) and 90% (83% to 95%), respectively (one study, 129 participants).Xpert testing in pleural fluidXpert pooled sensitivity and specificity (95% CrI) against culture were 50.9% (39.7% to 62.8%) and 99.2% (98.2% to 99.7%), respectively (27 studies, 4006 specimens; low-certainty evidence).For a population of 1000 people where 150 have pleural TB on culture, 83 would be Xpert-positive: of these, seven (8%) would not have TB (false-positives); and 917 would be Xpert-negative: of these, 74 (8%) would have TB (false-negatives).Xpert testing in urineXpert pooled sensitivity and specificity (95% CrI) against culture were 82.7% (69.6% to 91.1%) and 98.7% (94.8% to 99.7%), respectively (13 studies, 1199 specimens; moderate-certainty evidence).For a population of 1000 people where 70 have genitourinary TB on culture, 70 would be Xpert-positive: of these, 12 (17%) would not have TB (false-positives); and 930 would be Xpert-negative: of these, 12 (1%) would have TB (false-negatives).Xpert testing for rifampicin resistanceXpert pooled sensitivity (20 studies, 148 specimens) and specificity (39 studies, 1088 specimens) were 95.0% (89.7% to 97.9%) and 98.7% (97.8% to 99.4%), respectively (high-certainty evidence).For a population of 1000 people where 120 have rifampicin-resistant TB, 125 would be positive for rifampicin-resistant TB: of these, 11 (9%) would not have rifampicin resistance (false-positives); and 875 would be negative for rifampicin-resistant TB: of these, 6 (1%) would have rifampicin resistance (false-negatives).For lymph node TB, the accuracy of culture, the reference standard used, presented a greater concern for bias than in other forms of extrapulmonary TB.

AUTHORS' CONCLUSIONS

In people presumed to have extrapulmonary TB, Xpert may be helpful in confirming the diagnosis. Xpert sensitivity varies across different extrapulmonary specimens, while for most specimens, specificity is high, the test rarely yielding a positive result for people without TB (defined by culture). Xpert is accurate for detection of rifampicin resistance. For people with presumed TB meningitis, treatment should be based on clinical judgement, and not withheld solely on an Xpert result, as is common practice when culture results are negative.

Rapid molecular assays for detection of tuberculosis

Tuberculosis (TB) is an infectious disease that remains an important public health problem at the global level. It is one of the main causes of morbidity and mortality, due to the emergence of antibiotic resistant Mycobacterium strains and HIV co-infection. Over the past decade, important progress has been made for better control of the disease. While microscopy and culture continue to be indispensible for laboratory diagnosis of tuberculosis, the range of several molecular diagnostic tests, including the nucleic acid amplification test (NAAT) and whole-genome sequencing (WGS), have expanded tremendously. They are becoming more accessible not only for detection and identification of Mycobacterium tuberculosis complex in clinical specimens, but now extend to diagnosing multi-drug resistant strains. Molecular diagnostic tests provide timely results useful for high-quality patient care, low contamination risk, and ease of performance and speed. This review focuses on the current diagnostic tests in use, including emerging technologies used for detection of tuberculosis in clinical specimens. The sensitivity and specificity of these tests have also been taken into consideration.

GeneXpert technology. A breakthrough for the diagnosis of tuberculous pericarditis and pleuritis in less than 2 hours

Objectives:

To evaluate the diagnostic validity of GeneXpert for the detection of Mycobacterium tuberculosis (MTB) in pericardial and pleural effusions samples.

Methods:

A cross sectional study was conducted at the Mycobacteriology Laboratory, Allama Iqbal Medical College, Lahore, Pakistan. A total of 286 (158 pleural and 128 pericardial fluids) samples were received from tuberculosis (TB) suspects between January 2014 and August 2016. Every sample was processed for Ziehl-Neelsen (Zn) smear, Lowenstein Jensen (LJ) culture, GeneXpert MTB/RIF assay according to standard protocols. Validity of GeneXpert assay for the detection of MTB was evaluated using LJ culture as gold standard.

Results:

Out of 286 effusions samples, MTB was isolated by LJ culture in 51 (17.8%) samples followed by GeneXpert in 43 (15%), and acid- fast bacilli (AFB) was detected by Zn smear microscopy in 11 (3.8%) samples. GeneXpert showed high sensitivity (84.3%), specificity (100%), with positive predictive value (100%), and negative predictive value (96.7%), while Zn smear showed sensitivity 18.3%, specificity 99.1%, positive predictive value 81.8%, and negative predictive value 85.4%. A strikingly high sensitivity of 72.2% was observed for pericardial fluid by GeneXpert.

Conclusion:

GeneXpert assay is an innovative tool, for prompt detection of MTB and drug resistance. It is definitely an attractive point of care test, with high sensitivity and specificity along with turn around time of 2 hours, which facilitates timely diagnosis and appropriate management of TB pleuritis and pericarditis.

Programmatic Impact of Implementing GeneXpert MTB/ RIF Assay for the Detection of Mycobacterium Tuberculosis in Respiratory Specimens from Pulmonary Tuberculosis Suspected Patients in Resource Limited Laboratory Settings of Eastern Nepal

Background

In Nepal, introduction of GeneXpert MTB/RIF assay (Xpert assay) as an initial confirmation test for tuberculosis (TB) has been considered to have impact as a significant decrease in number of clinically diagnosed pulmonary tuberculosis (PTB) cases than previous years. This study aims to find out the distribution profile of suspected tuberculosis cases according to patients age, gender, treatment history and HIV status as well as to evaluate the utility of the Xpert assay over conventional acid-fast bacilli (AFB) staining method for the proper diagnosis of M. Tuberculosis in respiratory specimens from the tuberculosis (TB) suspected patient samples.

Methods

The prospective cross-sectional analytical study was conducted in National Anti-Tuberculosis Center (NATA) center- Biratnagar and Primary Healthcare Center (PHC) - Manglabare, Morang District, of eastern Nepal from January 2014 to August 2014. Laboratory investigation was done by conventional AFB staining followed by Xpert assay.

Results

A total of 1549 sputum samples were initially analyzed. AFB staining resulted in 1441 AFB smear negative samples and 88 AFB smear positive samples, whereas 20 samples were directly processed for Xpert assay. The male: female smear positive ratio was 2.8:1 and was higher among age groups (21-40) years. Tuberculosis among HIV patients was found 22.22%. Xpert assay demonstrates that out of 1441 smear negative AFB cases, 258 were found to have TB positive, whereas out of 88 smears positive AFB cases 12 were found to have TB negative. The sensitivity of the Xpert assay in patients classified as AFB smear positive was found 85.4% and the specificity in smear negative patients was 81%.

Conclusion

The study concluded that implementation of Gene Xpert MTB/RIF assay is a helpful tool for early and rapid detection of tuberculosis with greater sensitivity and specificity over traditional AFB staining techniques.

Comparative Study of GeneXpert MTB/RIF Assay and Multiplex PCR Assay for Direct Detection of Mycobacterium tuberculosis in Suspected Pulmonary Tuberculosis Patients

Pulmonary tuberculosis (PTB) is one of the major infectious diseases in developing countries. The objective of this study was to compare rapid diagnostics technique, GeneXpert MTB/RIF (GeneXpert) and Multiplex PCR assay (MPCR) targeting IS6110 segment and mpb64 gene for direct detection of Mycobacterium tuberculosis (MTB) in suspected PTB patients. A cross sectional study was carried among 105 sputum samples from suspected PTB patients to evaluate GeneXpert and Multiplex PCR who visited National Tuberculosis Center, Nepal. The patient's sputum samples were used directly for the GeneXpert whereas DNA extraction by CTAB method was followed to process the sample for MPCR. The sensitivity and specificity of GeneXpert and MPCR in smear positive cases was 78.6, 33.3, and 100.0%, 66.7%, respectively (P = 0.125). However, in smear negative cases sensitivity and specificity of both methods exhibited 90.9, 95.2, and 100.0%, 100.0% respectively (P = 0.625). Finally, the sensitivity and specificity of GeneXpert and MPCR were 82.9, 95.3 and 100.0%, 98.5% respectively, (P = 0.549) in pulmonary cases. Comparatively, we observed higher sensitivity and specificity for MPCR than GeneXpert for both smear positive and negative samples. Thus, we recommend MPCR alongside GeneXpert for the better diagnostic accuracy of PTB in a resource-limited country where tuberculosis is endemic.

Evaluation of the Xpert® MTB/RIF assay and microscopy for the diagnosis of Mycobacterium tuberculosis in Namibia

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.

[Performance of GeneXpert MTB / RIF® in the diagnosis of extrapulmonary tuberculosis in Dakar: 2010-2015]

Introduction

Le défi des pays en voie de développement est la disponibilité de méthodes de diagnostic rapide et précis pour le management de la tuberculose. Des techniques moléculaires offrent cet avantage et nous avons utilisé le test GeneXpert MTB/RIF dans le diagnostic de la tuberculose extra-pulmonaire pour évaluer sa performance par rapport aux méthodes conventionnelles.

Méthodes

Entre 2010 et 2015, 544 échantillons cliniques extra-pulmonaires ont été recueillis et traitées par la microscopie, la culture et le GeneXpert. L'étude de la sensibilité aux antituberculeux a été effectué avec le MGIT 960. Le Génotype MTBDRplus a été utilisé pour confirmer les cas de résistance à la rifampicine détectés par le système GX.

Résultats

La population d'étude de 544 patients incluait 55,15% d'hommes et 44,85% de femmes. L'âge des patients variait entre 1 à 92 avec la majorité dans le groupe d'âge 18-45 ans. La sensibilité et la spécificité globale de la microscopie étaient de 43,86% et 98,36%, et pour le GeneXpert^® 94,74% et 97,95% respectivement avec 95% IC. Deux résultats de résistance à la rifampicine discordants ont été trouvées entre le test GeneXpert et la méthode phénotypique. Les résultats du test MTBDRplus ont montré une concordance de 100% avec ceux du MGIT 960 pour les cas discordants de résistance à la rifampicine.

Conclusion

Cette étude a montré que le test GeneXpert a une plus grande sensibilité pour le diagnostic de routine de la tuberculose extra-pulmonaire et devrait être utilisé à la place de la microscopie. Les cas de résistance à la rifampicine détectés par le GeneXpert doivent être confirmés par d'autres tests moléculaires avant d'initier un traitement.

The reliability analysis of Xpert-positive result for smear-negative and culture-negative specimen collected from bone and joint tuberculosis suspects

BACKGROUND

The Xpert MTB/RIF assay (Xpert; Cepheid, Sunnyvale, CA, USA) has been widely used for pulmonary and extra-pulmonary tuberculosis (TB) diagnosis. In clinical practice, specimen yielding smear-negative, culture-negative but Xpert-positive results is frequently confronted. Due to the notorious possibility of contamination that molecular tests always been thought of, Xpert-positive results without bacteriological supporting evidence arouse great confusions to clinicians.

METHODS

A retrospective study was performed. From April 2014 to February 2015, 852 clinical specimens were Xpert-positive. The results of Xpert assay, bacteriological and pathological examinations from either the same specimens or from the specimens collected during same clinical operations were investigated.

RESULTS

A total of 90 specimens with Xpert-positive but smear-negative and culture-negative results were recruited, and 81 of them were pus specimens collected from Bone and Joint Tuberculosis (BJTB) patients. According to the pathological examination results, 77 of the 81 pus specimens, 8 of 9 other types of specimens were confirmed as either TB or strongly suggestive of TB; three pus specimens and one biopsy tissue were also suggested TB but with less stronger evidence; only one pus specimen was not TB suggestive.

CONCLUSIONS

Our study demonstrated that Xpert could be trusted for BJTB diagnosis even when no supporting bacteriological evidence is available in high TB prevalence settings. Our results will alleviate the confusion among clinicians in such scenarios.

Qualitative Assessment of Challenges in Tuberculosis Control in West Gojjam Zone, Northwest Ethiopia: Health Workers' and Tuberculosis Control Program Coordinators' Perspectives

Background. Weak health systems pose many barriers to effective tuberculosis (TB) control. This study aimed at exploring health worker's and TB control program coordinator's perspectives on health systems challenges facing TB control in West Gojjam Zone, Amhara Region, Ethiopia. Methods. This was a qualitative descriptive study. Eight in-depth interviews with TB control program coordinators and two focus group discussions among 16 health workers were conducted. Purposive sampling was used to recruit study participants. Thematic analysis was used to identify and analyse main themes. Results. We found that intermittent interruptions of laboratory reagents and anti-TB drugs supplies, absence of trained and motivated health workers, poor TB data documentation, lack of adherence to TB treatment guideline, and lack of access to TB diagnostic tools at peripheral health institutions were challenges facing the TB control program performance in the study zone. Conclusions. Ensuring uninterrupted supply of anti-TB drugs and laboratory reagents to all health institutions is essential. Continuous refresher training of health workers on standard TB care and data handling and developing and implementing a sound retention strategy to attract and motivate health professionals to work in rural areas are necessary interventions to improve the TB control program performance in the study zone.

Diagnostic Accuracy of Xpert Test in Tuberculosis Detection: A Systematic Review and Meta-analysis

BACKGROUND

World Health Organization (WHO) recommends the use of Xpert MTB/RIF assay for rapid diagnosis of tuberculosis (TB) and detection of rifampicin resistance. This systematic review was done to know about the diagnostic accuracy and cost-effectiveness of the Xpert MTB/RIF assay.

METHODS

A systematic literature search was conducted in following databases: Cochrane Central Register of Controlled Trials and Cochrane Database of Systematic Reviews, MEDLINE, PUBMED, Scopus, Science Direct and Google Scholar for relevant studies for studies published between 2010 and December 2014. Studies given in the systematic reviews were accessed separately and used for analysis. Selection of studies, data extraction and assessment of quality of included studies was performed independently by two reviewers. Studies evaluating the diagnostic accuracy of Xpert MTB/RIF assay among adult or predominantly adult patients (≥14 years), presumed to have pulmonary TB with or without HIV infection were included in the review. Also, studies that had assessed the diagnostic accuracy of Xpert MTB/RIF assay using sputum and other respiratory specimens were included.

RESULTS

The included studies had a low risk of any form of bias, showing that findings are of high scientific validity and credibility. Quantitative analysis of 37 included studies shows that Xpert MTB/RIF is an accurate diagnostic test for TB and detection of rifampicin resistance.

CONCLUSION

Xpert MTB/RIF assay is a robust, sensitive and specific test for accurate diagnosis of tuberculosis as compared to conventional tests like culture and microscopic examination.