Rapid molecular test for tuberculosis: impact of its routine use at a referral hospital

The Imperative Role of Xpert® Mycobacterium Tuberculosis Complex/Resistance to Rifampin (MTB/RIF) in Rapid Diagnosis of Pulmonary and Extrapulmonary Tuberculosis

Background The Xpert® mycobacterium tuberculosis complex/resistance to rifampin (MTB/RIF) test is widely recognized for its ability to provide rapid and accurate results for diagnosing tuberculosis (TB) in both pulmonary and extrapulmonary samples. Its utility is especially critical in smear-negative and paucibacillary cases where traditional diagnostic methods often fail. This study aimed to evaluate the role of Xpert® MTB/RIF in diagnosing TB in various pulmonary and extrapulmonary samples and TB in smear-negative pulmonary samples. Methods This retrospective study analyzed records from 2017 to 2021, focusing on presumptive TB patients who underwent Xpert® MTB/RIF testing at a tertiary care hospital. Data from 1174 samples (671 pulmonary and 503 extrapulmonary) were included. The Xpert® MTB/RIF reports were assessed for Mycobacterium tuberculosis (MTB) detection rates across different sample types. Results Of the pulmonary samples, MTB detection was highest in sputum samples, 122 (48.41%), followed by bronchial washing samples, 49 (16.33%). In smear-negative pulmonary cases, Xpert® MTB/RIF detected MTB in 72 (16.55%) samples, demonstrating its utility in paucibacillary cases. The test also proved valuable in diagnosing extrapulmonary TB, where symptoms are often atypical. Conclusion Xpert® MTB/RIF is a reliable tool for the rapid and accurate diagnosis of pulmonary and extrapulmonary TB, including smear-negative and paucibacillary cases. Its application can significantly enhance the timely diagnosis and treatment of TB, especially in resource-limited settings.

Operational indicators for pulmonary tuberculosis diagnosis in people living with HIV before and after Xpert MTB/RIF implementation in the state of São Paulo, Brazil

Tuberculosis (TB) in people living with HIV (PLHIV) is usually paucibacillary and the smear microscopy has limitations and may lead to high proportions of non-confirmed pulmonary tuberculosis (NC-PTB). Despite culture being the reference method, it usually takes 6 to 8 weeks to produce the results. This study aimed to analyze the effect of a rapid molecular test (Xpert) in the confirmatory rate of PTB among PLHIV, from 2010 to 2020, in São Paulo state, Brazil. This is an ecological study with time series analysis of the trend and the NC-PTB rates before and after Xpert implementation in 21 municipalities. The use of Xpert started and gradually increased after 2014, while the rate of NC-PTB in PLHIV decreased over this time, being more significant between late 2015 and mid-2017. The city of Ribeirão Preto stands out for having the highest percentage (75.0%) of Xpert testing among PLHIV and for showing two reductions in the NC-PTB rate. The cities with low Xpert coverage had a slower and smaller decrease in the NC-PTB rate. Despite being available since 2014, a significant proportion of PLHIV suspected of PTB in the state of São Paulo did not have an Xpert ordered by the doctors. The implementation of Xpert reduced the NC-PTB rates with growing effect as the coverage increased in the municipality.

Time series of cases and treatment outcomes from tuberculosis in Sergipe, 2012-2021

OBJECTIVE

The objectives of this study were: (1) to analyze the temporal trend of tuberculosis treatment outcomes in the state of Sergipe; (2) to identify the existence of seasonality of tuberculosis; (3) to verify the influence of the rapid molecular test (MTB-RIF) in the time series of tuberculosis and its treatment outcomes in the state of Sergipe; and (4) to verify treatment outcomes.

METHODS

Ecological study on tuberculosis and three treatment outcomes (cure, interruption of treatment, and death) extracted from Datasus. Incidence and mortality rates were calculated for the crude occurrences of cases and deaths and the proportions of cure and interruption of treatment (%). The time series was analyzed using Prais-Winsten regression from Jan to Dec/2021.

RESULTS

The total incidence rate was 36.35 cases per 100,000 inhabitants, with an increase of 0.44% per month (95%CI 0.35; 0.54). The cure rate was 64.0% with a steady trend (p>0.05). The percentage of treatment interruption was 13.3%, with a reduction of -0.73%/month (95%CI -1.11; -0.34). The total mortality rate was 1.92 deaths/100,000 inhabitants with a stationary trend. After the implementation of the MTB-RIF, there was an increase in the incidence rate of 0.65% per month. Seasonality was not identified in any of the analyses performed (p>0.05).

CONCLUSION

There was an increase in incidence rates, reduction in treatment interruption and mortality in the state of Sergipe. Seasonality was not identified. The rapid molecular test showed a growth effect on the incidence rate.

Middlebrook 7h11 reduces invalid results and turnaround time of phenotypic drug-susceptibility testing of M. tuberculosis

Background

Phenotypic drug-susceptibility testing (pDST), which relies on growth inhibition in the drug-containing media, remains a challenge for fastidious Mycobacterium tuberculosis complex (MTBc) isolates due to insufficient growth on the growth controls (GC). Middlebrook 7H11 (M7H11) medium contains casein hydrolysate, which may favor the growth of such strains.

Method

In this study, we tested whether M7H11 reduces invalid results due to insufficient growth on the GCs and the turnaround time (TAT) of pDST for MTBc compared to Middlebrook 7H10 (M7H10) without affecting the accuracy of the pDST results and how it differs between rifampicin- and isoniazid-susceptible non multi-drug resistant (non-MDR), MDR and MDR with additional resistance to fluoroquinolones (Pre-XDR) MTBc isolates. We compared the proportions of invalid pDST results due to lack of growth on the GCs, TATs of valid parallel drug-susceptibility testings as an indicator of speed of MTBc growth, and colony-forming unit (CFU) count on the most diluted GC of the parallel pDSTs after equal incubation periods as an indicator of growth abundance on M7H11 and M7H10. We also analyzed the agreement between the pDST results of the same drug or drugs in the same drug class, tested in parallel on both media.

Results

For MDR and pre-XDR isolates, relative to M7H10, M7H11 significantly reduced the occurrence of invalid pDST results due to insufficient growth on the GCs (odds ratio [OR] = ∞ [95% confidence interval (CI) 1.9-∞], P = 0.004 for MDR, OR = ∞ [95% CI 3.3-∞], P = 0.0001 for pre-XDR) and the TAT of pDSTs (OR = 17 [95% CI 2.6-710.4], P = 0.0001 for MDR, OR = 9.3 [95% CI 4.0-26.5], P < 0.0001 for pre-XDR). The growth abundance of MTBc on M7H11 was significantly higher compared to M7H10 (17 CFU on M7H10 vs. 28 on M7H11), irrespective of drug-resistance profiles. The agreement between the pDST results between the two media was high (Cohen's k > 0.98).

Conclusion

Our study findings suggest that M7H11 is preferred over M7H10 for pDSTs of MTBc isolates.

Evaluation of xpert Mycobacterium tuberculosis rifampicin for tuberculosis diagnosis in a reference laboratory

Background

The Xpert Mycobacterium tuberculosis Rifampicin (MTB-RIF) is a technological innovation that presents precision and speed in the diagnosis of tuberculosis (TB). The study aimed to evaluate the performance of Xpert MTB/RIF in the TB diagnosis and compare its results with those of culture, species identification, Antimicrobial Susceptibility Testing (AST), and rpoB gene sequencing of discordant results in AST, used for the diagnosis of TB in a reference laboratory.

Methods

Cross-sectional descriptive study of pulmonary and extrapulmonary samples requesting Xpert MTB/RIF and culture for TB diagnosis from 2015 to 2019 at Adolfo Lutz Institute-São Paulo/Brazil. The analysis was performed with Epi-Info 7.2.1, presenting the distribution of frequencies and, for comparative analyses, Pearson's Chi-square test and Fisher's exact test were used, considering P ≤ 0.05 as statistically significant. For variables agreement, the Kappa method was used.

Results

A total of 1575 pulmonary and extrapulmonary samples were analyzed using Xpert MTB/RIF and culture, of which 293 were positive for the MTB Complex in both methodologies with a sensitivity of 94.55%; specificity of 95.97%; accuracy 95.69%; positive predictive value 85.53%; negative predictive value 98.59%, substantial agreement by Kappa 0.87, and detection sensitivity even at lower levels of bacillary load (P < 0.05). The Xpert MTB/RIF and AST showed concordant results (P < 0.05).

Conclusion

The study brings forward that the Xpert MTB/RIF shows substantial agreement with the results of culture and AST, contributing to the diagnosis of TB and the rapid detection of resistance. The sequencing of resistant cultures in Xpert MTB/RIF and sensitivity in AST identified the H526N mutation, characterized by a low level of resistance to RIF.

Differential yield of universal versus selective drug susceptibility testing of patients with tuberculosis in high-burden countries: a systematic review and meta-analysis

Introduction

Although universal drug susceptibility testing (DST) is a component of the End-TB Strategy, over 70% of drug-resistant tuberculosis (DR-TB) cases globally remain undetected. This detection gap reflects difficulties in DST scale-up and substantial heterogeneity in policies and implemented practices. We conducted a systematic review and meta-analysis to assess whether implementation of universal DST yields increased DR-TB detection compared with only selectively testing high-risk groups.

Methods

PubMed, Embase, Global Health, Cochrane Library and Web of Science Core Collection were searched for publications reporting on the differential yield of universal versus selective DST implementation on the proportion of DR-TB, from January 2007 to June 2019. Random-effects meta-analyses were used to calculate respective pooled proportions of DR-TB cases detected; Higgins test and prediction intervals were used to assess between-study heterogeneity. We adapted an existing risk-of-bias assessment tool for prevalence studies.

Results

Of 18 736 unique citations, 101 studies were included in the qualitative synthesis. All studies used WHO-endorsed DST methods, and most (87.1%) involved both high-risk groups and the general population. We found only cross-sectional, observational, non-randomised studies that compared universal with selective DST strategies. Only four studies directly compared the testing approaches in the same study population, with the proportion of DR-TB cases detected ranging from 2.2% (95% CI: 1.4% to 3.2%) to 12.8% (95% CI: 11.4% to 14.3%) with selective testing, versus 4.4% (95% CI: 3.3% to 5.8%) to 9.8% (95% CI: 8.9% to 10.7%) with universal testing. Broad population studies were very heterogeneous. The vast majority (88/101; 87.1%) reported on the results of universal testing. However, while 37 (36.6%)/101 included all presumptive TB cases, an equal number of studies applied sputum-smear as a preselection criterion. A meaningful meta-analysis was not possible.

Conclusion

Given the absence of randomised studies and the paucity of studies comparing strategies head to head, and selection bias in many studies that applied universal testing, our findings have limited generalisability. The lack of evidence reinforces the need for better data to inform policies.

The Xpert® MTB/RIF diagnostic test for pulmonary and extrapulmonary tuberculosis in immunocompetent and immunocompromised patients: Benefits and experiences over 2 years in different clinical contexts

Xpert^® MTB/RIF has been widely used for tuberculosis (TB) diagnosis in Brazil, since 2014. This prospective observational study aimed to evaluate the performance of Xpert in different contexts during a two-year period: (i) laboratory and clinical/epidemiological diagnosis; (ii) HIV-positive and -negative populations; (iii) type of specimens: pulmonary and extrapulmonary. Overall, 924 specimens from 743 patients were evaluated. The performance of the assays was evaluated considering culture (Lowenstein Jensen or LJ medium) results and composite reference standard (CRS) classification as gold standard. According to CRS evaluation, 219 cases (29.5%) were classified as positive cases, 157 (21.1%) as ‘possible TB’, and 367 (49.3%) as ‘not TB’. Based on culture, Xpert and AFB smear achieved a sensitivity of 96% and 62%, respectively, while based on CRS, the sensitivities of Xpert, AFB smear, and culture were 40.7%, 20%, and 25%, respectively. The pooled sensitivity and specificity of Xpert were 96% and 94%, respectively. Metric evaluations were similar between pulmonary and extrapulmonary samples against culture, whereas compared to CRS, the sensitivities were 44.6% and 29.3% for the pulmonary and extrapulmonary cases, respectively. The Xpert detected 42/69 (60.9%) patients with confirmed TB and negative culture on LJ medium, and 52/69 (75.4%) patients with negative AFB smear results. There was no significant difference in the diagnostic accuracy based on the types of specimens and population (positive- and negative-HIV). Molecular testing detected 13 cases of TB in culture-negative patients with severe immunosuppression. Resistance to rifampicin was detected in seven samples. Herein, Xpert showed improved detection of pulmonary and extrapulmonary TB cases, both among HIV-positive and -negative patients, even in cases with advanced immunosuppression, thereby performing better than multiple other diagnostic parameters.

Comprehensive Computer-Aided Decision Support Framework to Diagnose Tuberculosis From Chest X-Ray Images: Data Mining Study

Background

Tuberculosis (TB) is one of the most infectious diseases that can be fatal. Its early diagnosis and treatment can significantly reduce the mortality rate. In the literature, several computer-aided diagnosis (CAD) tools have been proposed for the efficient diagnosis of TB from chest radiograph (CXR) images. However, the majority of previous studies adopted conventional handcrafted feature-based algorithms. In addition, some recent CAD tools utilized the strength of deep learning methods to further enhance diagnostic performance. Nevertheless, all these existing methods can only classify a given CXR image into binary class (either TB positive or TB negative) without providing further descriptive information.

Objective

The main objective of this study is to propose a comprehensive CAD framework for the effective diagnosis of TB by providing visual as well as descriptive information from the previous patients’ database.

Methods

To accomplish our objective, first we propose a fusion-based deep classification network for the CAD decision that exhibits promising performance over the various state-of-the-art methods. Furthermore, a multilevel similarity measure algorithm is devised based on multiscale information fusion to retrieve the best-matched cases from the previous database.

Results

The performance of the framework was evaluated based on 2 well-known CXR data sets made available by the US National Library of Medicine and the National Institutes of Health. Our classification model exhibited the best diagnostic performance (0.929, 0.937, 0.921, 0.928, and 0.965 for F1 score, average precision, average recall, accuracy, and area under the curve, respectively) and outperforms the performance of various state-of-the-art methods.

Conclusions

This paper presents a comprehensive CAD framework to diagnose TB from CXR images by retrieving the relevant cases and their clinical observations from the previous patients’ database. These retrieval results assist the radiologist in making an effective diagnostic decision related to the current medical condition of a patient. Moreover, the retrieval results can facilitate the radiologists in subjectively validating the CAD decision.

Xpert MTB/RIF performance to diagnose tuberculosis and rifampicin resistance in a reference centre in southern Brazil

Effective treatment of tuberculosis (TB) remains a serious public health problem in many countries, including Brazil, especially when considering drug-resistant disease. Xpert MTB/RIF has been implemented in many countries to reduce the time to TB diagnosis and to rapidly detect rifampicin resistance. The study aimed to describe and evaluate Xpert MTB/RIF performance in diagnosing pulmonary TB and rifampicin resistance in a tertiary healthcare facility in Brazil. A cross-sectional study was performed, which included all isolates of confirmed pulmonary TB patients from 2015 to 2018. Both Xpert MTB/RIF and GenoType MTBDRplus assays were performed to detect rifampicin and isoniazid resistance. In addition, isolates with detected resistance to rifampicin and/or isoniazid were analysed by phenotypic testing using MGIT-960 SIRE kit and whole-genome sequencing (WGS) using Illumina MiSeq Sequencing System. 2148 respiratory specimens tested with Xpert MTB/RIF were included: n=1556 sputum, n=348 bronchoalveolar lavage and n=244 gastric washing. The overall Xpert MTB/RIF sensitivity in sputum was 94% and the overall specificity was 98%. The negative predictive value in sputum of all the patients was 99% with a positive predictive value of 89%. The concordance between Xpert MTB/RIF and phenotypic susceptibility test was 94.1%, while its concordance with WGS was 78.9%. Xpert MTB/RIF is a rapid and accurate diagnostic strategy for pulmonary TB, which can contribute to improvement in TB control. However, detection of rifampicin resistance might be associated with false-positive results.

Performance of diagnostic tests for pulmonary tuberculosis in indigenous populations in Brazil: the contribution of Rapid Molecular Testing

OBJECTIVE

To evaluate the accuracy of rapid molecular testing as a diagnostic tool and estimate the incidence of smear-positive pulmonary tuberculosis among the indigenous population.

METHODS

This is an epidemiological study based on secondary data. We calculated the incidence of smear-positive pulmonary tuberculosis between January 1st, 2011 and December 31, 2016, and the performance of bacilloscopy and rapid molecular testing in diagnosing pulmonary tuberculosis compared to sputum culture (standard test).

RESULTS

We included 4,048 cases of indigenous people with respiratory symptoms who provided sputum samples for analysis. Among them, 3.7%, 6.7%, and 3.7% had positive results for bacilloscopy, sputum culture, and rapid molecular testing, respectively. The mean incidence of pulmonary tuberculosis was 269.3/100 thousand inhabitants. Rapid molecular testing had 93.1% sensitivity and 98.2% specificity, compared to sputum culture. Bacilloscopy showed 55.1% sensitivity and 99.6% specificity.

CONCLUSIONS

Rapid molecular testing can be useful in remote areas with limited resources and a high incidence of tuberculosis, such as indigenous villages in rural regions of Brazil. In addition, the main advantages of rapid molecular testing are its easy handling, fast results, and the possibility of detecting rifampicin resistance. Together, these attributes enable the early start of treatment, contributing to reduce the transmission in communities recognized as vulnerable to infection and disease.