Low diagnostic accuracy of Xpert MTB/RIF assay for extrapulmonary tuberculosis: A multicenter surveillance

Using cerebrospinal fluid nanopore sequencing assay to diagnose tuberculous meningitis: a retrospective cohort study in China

OBJECTIVE

This study aimed to evaluate the efficiency of nanopore sequencing for the early diagnosis of tuberculous meningitis (TBM) using cerebrospinal fluid and compared it with acid-fast bacilli (AFB) smear, mycobacterial growth indicator tube culture and Xpert Mycobacterium tuberculosis (MTB)/rifampicin (RIF).

DESIGN

Single-centre retrospective study.

SETTING

The Tuberculosis Diagnosis and Treatment Center of Zhejiang Chinese and Western Medicine Integrated Hospital.

PARTICIPANTS

We enrolled 64 adult patients with presumptive TBM admitted to our hospital from August 2021 to August 2023.

METHODS

We calculated the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of AFB smear, culture, Xpert MTB/RIF and nanopore sequencing to evaluate their diagnostic efficacy compared with a composite reference standard for TBM.

RESULTS

Among these 64 patients, all tested negative for TBM by AFB smear. The sensitivity, specificity, PPV and NPV were 11.11%, 100%, 100% and 32.2% for culture, 13.33%, 100%, 100% and 2.76% for Xpert MTB/RIF, and 77.78%, 100%, 100% and 65.52% for nanopore sequencing, respectively.

CONCLUSION

The diagnostic accuracy of the nanopore sequencing test was significantly higher than that of conventional testing methods used to detect TBM.

Mycobacterium tuberculosis and human immunodeficiency virus co-infection and associated variables among presumptive pulmonary tuberculosis patients in Ethiopia; a health institution based cross-sectional study

Background

Co-infection of Mycobacterium tuberculosis (MTB) and the Human Immunodeficiency Virus (HIV) is a major global public health issue, particularly in border areas of resource-limited nations, including Ethiopia.

Objective

To explore the prevalence and associated variables of MTB/HIV co-infection among PTB presumptive patients in Northwest Ethiopia.

Methods

From February to August 2021, a cross-sectional institutional investigation was conducted at the Metema and Abrehajira hospitals. Semi-structured questionnaires were used to collect socio-demographic and clinical data. The MTB/RIF Xpert assay was used to process sputum, and 3 ml of veins blood was collected for HIV rapid test (STAT-PAK, ABON, and SD BIOLINE HIV test algorithm) following the Ethiopian National HIV test algorithm. The Gene Xpert assay's sample processing control was checked to ensure data quality. Data entered into Epi-Data were exported to SPSS version 20 for analysis. Statistically significant variables (p-value ≤0.2) from bivariable analysis were included in multivariable analysis. A p-value ≤ 0.05 was judged statistically significant.

Results

This study included 314 PTB presumptive patients with a median age of 35.0 years, of which 178 (56.69 %) were males. Among all patients, 40(12.7 %) and 51(16.2 %) were PTB, and HIV seropositivity, respectively. Of the PTB patients, 14/40 (35 %) (95 % CI: 24.4-45.6) were co-infected with HIV/AIDS. Married patients were 70 % less likely than unmarried individuals (AOR = 0.3 CI; 0.07-0.98) to have MTB/HIV co-infection. Patients who had contact history with MDR-TB patients (AOR = 5 CI; 1.37-18.00), and those who had a history of alcohol use (AOR = 12.2 CI; 2.56-57.8) were more likely to have MTB-HIV co-infection than their peers.

Conclusion

Our findings showed that MTB-HIV co-infection is one of the most important community health concerns in the study area. Therefore, MTB/HIV cooperation activities should be fully in place to prevent co-infection and its impact on the population.

Novel automated AIMLAM for diagnosis of Mycobacterium tuberculosis

Aim: A rapid and precise diagnostic method is crucial for timely intervention and management of tuberculosis. The present study compared the diagnostic accuracy of a novel lipoarabinomannan (LAM) antigen test, AIMLAM, for tuberculosis in urine samples. Methodology: The study subjected 106 TB suspects to smear microscopy, MGIT, GeneXpert and AIMLAM. Results: Among 106, smear microscopy identified 36 as positive (33%) (sensitivity; 70.93%, 95% CI (60.14-80.22%), while MGIT showed 38 positive (36.8%). GeneXpert detected 59 positives (sensitivity; 96.83, 95% CI (89.00-99.61%)). AIMLAM declared 61 as positive (57.5%) (sensitivity; 100.00, 95% CI (94.13-100.00%) and 45 as negative (42.5%). Conclusion: Overall, AIMLAM demonstrated better diagnostic accuracy than GeneXpert Assay, smear microscopy and MGIT liquid culture in urine samples.

Performance of metagenomic next-generation sequencing in cerebrospinal fluid for diagnosis of tuberculous meningitis

Purpose. Metagenomic next-generation sequencing (mNGS) has been widely used in the diagnosis of infectious diseases, while its performance in diagnosis of tuberculous meningitis (TBM) is incompletely characterized. The aim of this study was to assess the performance of mNGS in the diagnosis of TBM, and illustrate the sensitivity and specificity of different methods.Methods. We retrospectively recruited TBM patients between January 2021 and March 2023 to evaluate the performance of mNGS on cerebrospinal fluid (CSF) samples, in comparison with conventional microbiological testing, including culturing of Mycobacterium tuberculosis (MTB), acid-fast bacillus (AFB) stain, reverse transcription PCR and Xpert MTB/RIF.Results. Of the 40 enrolled, 34 participants were diagnosed with TBM, including 15(44.12 %) definite and 19(55.88 %) clinical diagnosis based upon clinical manifestations, CSF parameters, brain imaging, pathogen evidence and treatment response. The mNGS method identified sequences of Mycobacterium tuberculosis complex (MTBC) in 11 CSF samples. In patients with definite TBM, the sensitivity, specificity, positive predictive value, negative predictive value and accuracy of mNGS were 78.57, 100, 100, 66.67 and 85 %, respectively. Compared to conventional diagnostic methods, the sensitivity of mNGS (78.57 %) was higher than AFB (0 %), culturing (0 %), RT-PCR (60 %) and Xpert MTB/RIF (14.29 %).Conclusions. Our study indicates that mNGS of CSF exhibited an overall improved sensitivity over conventional diagnostic methods for TBM and can be considered a front-line CSF test.

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.

Pulmonary tuberculosis and multidrug-resistant Mycobacterium tuberculosis in northwestern Ethiopia: a hospital-based cross-sectional study among presumptive pulmonary tuberculosis patients

Introduction

Border areas are important sites for disseminating Mycobacterium tuberculosis among individuals living in such areas. This study examined patients with suspected pulmonary tuberculosis (PTB) visiting the Abrihajira and Metema hospitals in northwest Ethiopia to investigate the prevalence of rifampicin-resistant Mycobacterium tuberculosis (RR-MTB), multidrug-resistant Mycobacterium tuberculosis (MDR-MTB), and risk factors related to Mycobacterium tuberculosis infection.

Methods

A hospital-based cross-sectional study was conducted from February to August 2021 among 314 PTB presumptive patients. Xpert MTB/RIF and line probe assays (LPA) were used to process sputum samples. Data were imported into the Epi-Data 3.1 program and exported to Statistical Package for the Social Sciences (SPSS) version 20.0 (SPSS, Chicago, IL, United States) to conduct the analysis. A logistic regression analysis was used to investigate the relationship between the dependent and independent variables. A value of p of <0.05 denoted statistical significance.

Results

Of the total (314) PTB presumptive patients who participated in this study, 178 (56.69%) were men, and 165 (52.5%) were from 25 to 50 years of age with a median age of 35.00 (inter-quartile: 25-45 years). Among all patients, 12.7% had PTB by Gene Xpert and 7/314 (2.23%) were resistant to rifampicin. Among patients enrolled, 4/314 (1.27%) had MDR-MTB (resistant to RIF and INH) by LPA. Regarding the risk factors assessed, primary level of education, sputum production, night sweating, respiratory disorder, contact history of TB, history of MDR-MTB infection, history of alcohol use, and cigarette smoking showed statistical significance with the prevalence of PTB (p ≤ 0.05).

Discussion

This study observed a high prevalence of PTB, RR-MTB, and MDR-MTB compared with many other previous studies conducted in Ethiopia. Among the assessed risk factors that could be associated with the prevalence of PTB, eight were statistically significant. This prevalence, resistance, and statistically significant variables are the evidence to which more emphasis should be given to the country's border areas.

Meta-analysis of diagnostic accuracy of nucleic acid amplification tests for abdominal tuberculosis

BACKGROUND

Abdominal tuberculosis (TB) is a severe extrapulmonary TB, which can lead to serious complications. Early diagnosis and treatment are very important for the prognosis and the diagnosis of abdominal TB is still difficult.

METHODS

We searched PubMed, the Cochrane Library, Embase, China National Knowledge Infrastructure, and the Wanfang database for studies evaluating the diagnostic accuracy of NAATs for abdominal TB until August 2020. Any types of study design with full text were sought and included. The risk of bias was assessed using the Quality Assessment of Diagnostic Accuracy Studies tool. Subgroup analysis, meta-regression analysis and sensitivity analysis were used to explore the sources of heterogeneity. Stata version 15.0 with the midas command packages was used to carry out meta-analyses.

RESULTS

We included a total of 78 independent studies from 53 articles; 64 with CRS as the reference standard, and 14 with culture as the reference standard. The pooled sensitivity, specificity, and the areas under summary receiver operating characteristic (SROC) curves (AUC) were 58% (51%-64%; I2 = 87%), 99% (97%-99%; I2 = 81%), and 0.92 (0.89-0.94) compared with CRS, respectively. The pooled sensitivity, specificity, and the AUC values of the SROC were 80% (66%-90%; I2 = 56%), 96% (92%-98%; I2 = 84%), and 0.97 (0.95-0.98) compared with culture, respectively. The heterogeneity of sensitivity and specificity was significant.

CONCLUSIONS

NAATs had excellent efficacy in the diagnosis of abdominal TB regardless of the reference standard and regardless of the subtype of abdominal TB. Multiplex PCR with multiple target genes may improve diagnostic sensitivity, and stool specimens may also be used for the diagnosis of abdominal TB in addition to tissue and ascites.

Toxicity of Carboplatin-Niosomal Nanoparticles in a Brain Cancer Cell Line

OBJECTIVE

Cancer poses a significant challenge in modern medicine, standing as the primary cause of death in many countries, second only to cardiovascular diseases. Among the various treatments available, carboplatin, a chemotherapy drug, is employed for specific cancer types, including brain carcinoma. The main objective of this investigation is to enhance the therapeutic efficacy of carboplatin by utilizing niosomal nanocarriers.

METHODS

We synthesized nanoniosomal carboplatin using the reverse-phase evaporation technique and conducted an assessment of its particle size, zeta potential, and drug-release properties. Subsequently, we evaluated the cytotoxicity of nanoniosomal carboplatin using the C6 rat glioma cell line.

RESULTS

Our research revealed that these niosomal nanoparticles possessed a particle size of 290.5±5.5 nm and a zeta potential of -21.7±7.4 mV. The amount of encapsulated drug and drug loading level were found to be 60.2±2.3% and 2.5±1.1%, respectively. Importantly, the cytotoxic impact of these nanoniosomes on the C6 rat glioma cell line exhibited a significant increase compared to the free drug (P<0.05).

CONCLUSION

Based on our discoveries, it is evident that carboplatin niosomal nanocarriers hold potential as an innovative approach to chemotherapy for brain cancer therapy.

Characteristics and Cytotoxic Effects of Nano-Liposomal Paclitaxel on Gastric Cancer Cells

OBJECTIVE

Addressing both the initial treatment response and subsequent paclitaxel resistance is a pivotal concern. Nano drug delivery, an emerging approach, presents a cutting-edge alternative to conventional chemotherapy.

METHODS

This investigation synthesized PEGylated nanoparticles (NPs) via the Reverse Phase Evaporation technique for liposomal NPs. Characteristics such as zeta potential, size, drug release and polydispersity index (PDI) were subjected to evaluation. Subsequently, cytotoxicity assays were conducted on gastric cancer cells (AGS) following 24 and 48-hour incubation periods.

RESULTS

In this study, the liposomal NPs had a zeta potential of -22 mV and a particle size of 285 nm. The Entrapment efficiency was determined as 41% that occurred physically. Additionally, the liposomal NPs demonstrated a high drug retention rate (39% remained after 72 hours), and they exhibited significantly increased cytotoxicity compared to the free drug, confirming their effectiveness as a suitable carrier for paclitaxel during both incubation periods (P<0.05).

CONCLUSION

These findings collectively advocate the potential of liposomal NPs as promising contenders for effective nano-drug application in propelling chemotherapy forward.

Outlook for CRISPR-based tuberculosis assays now in their infancy

Tuberculosis (TB) remains a major underdiagnosed public health threat worldwide, being responsible for more than 10 million cases and one million deaths annually. TB diagnosis has become more rapid with the development and adoption of molecular tests, but remains challenging with traditional TB diagnosis, but there has not been a critical review of this area. Here, we systematically review these approaches to assess their diagnostic potential and issues with the development and clinical evaluation of proposed CRISPR-based TB assays. Based on these observations, we propose constructive suggestions to improve sample pretreatment, method development, clinical validation, and accessibility of these assays to streamline future assay development and validation studies.

Soft tissue tuberculosis detected by next-generation sequencing: A case report and review of literature

BACKGROUND

Soft tissue tuberculosis is rare and insidious, with most patients presenting with a localized enlarged mass or swelling, which may be factors associated with delayed diagnosis and treatment. In recent years, next-generation sequencing has rapidly evolved and has been successfully applied to numerous areas of basic and clinical research. A literature search revealed that the use of next-generation sequencing in the diagnosis of soft tissue tuberculosis has been rarely reported.

CASE SUMMARY

A 44-year-old man presented with recurrent swelling and ulcers on the left thigh. Magnetic resonance imaging suggested a soft tissue abscess. The lesion was surgically removed and tissue biopsy and culture were performed; however, no organism growth was detected. Finally, Mycobacterium tuberculosis was confirmed as the pathogen responsible for infection through next-generation sequencing analysis of the surgical specimen. The patient received a standardized anti-tuberculosis treatment and showed clinical improvement. We also performed a literature review on soft tissue tuberculosis using studies published in the past 10 years.

CONCLUSION

This case highlights the importance of next-generation sequencing for the early diagnosis of soft tissue tuberculosis, which can provide guidance for clinical treatment and improve prognosis.

Efficacy of Xpert in tuberculosis diagnosis based on various specimens: a systematic review and meta-analysis

Objective

The GeneXpert MTB/RIF assay (Xpert) is a diagnostic tool that has been shown to significantly improve the accuracy of tuberculosis (TB) detection in clinical settings, with advanced sensitivity and specificity. Early detection of TB can be challenging, but Xpert has improved the efficacy of the diagnostic process. Nevertheless, the accuracy of Xpert varies according to different diagnostic specimens and TB infection sites. Therefore, the selection of adequate specimens is critical when using Xpert to identify suspected TB. As such, we have conducted a meta-analysis to evaluate the effectiveness of Xpert for diagnosis of different TB types using several specimens.

Methods

We conducted a comprehensive search of several electronic databases, including PubMed, Embase, the Cochrane Central Register of Controlled Trials, and the World Health Organization clinical trials registry center, covering studies published from Jan 2008 to July 2022. Data were extracted using an adapted version of the Checklist for Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modeling Studies. Where appropriate, meta-analysis was performed using random-effects models. The risk of bias and level of evidence was assessed using the Quality in Prognosis Studies tool and a modified version of the Grading of Recommendations Assessment, Development, and Evaluation. RStudio was utilized to analyze the results, employing the meta4diag, robvis, and metafor packages.

Results

After excluding duplicates, a total of 2163 studies were identified, and ultimately, 144 studies from 107 articles were included in the meta-analysis based on predetermined inclusion and exclusion criteria. Sensitivity, specificity and diagnostic accuracy were estimated for various specimens and TB types. In the case of pulmonary TB, Xpert using sputum (0.95 95%CI 0.91-0.98) and gastric juice (0.94 95%CI 0.84-0.99) demonstrated similarly high sensitivity, surpassing other specimen types. Additionally, Xpert exhibited high specificity for detecting TB across all specimen types. For bone and joint TB, Xpert, based on both biopsy and joint fluid specimens, demonstrated high accuracy in TB detection. Furthermore, Xpert effectively detected unclassified extrapulmonary TB and tuberculosis lymphadenitis. However, the Xpert accuracy was not satisfactory to distinguish TB meningitis, tuberculous pleuritis and unclassified TB.

Conclusions

Xpert has exhibited satisfactory diagnostic accuracy for most TB infections, but the efficacy of detection may vary depending on the specimens analyzed. Therefore, selecting appropriate specimens for Xpert analysis is essential, as using inadequate specimens can reduce the ability to distinguish TB.

Systematic review registration

https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=370111, identifier CRD42022370111.

Xpert MTB/RIF Ultra versus Xpert MTB/RIF for diagnosis of tuberculous pleural effusion: A systematic review and comparative meta-analysis

Objective

We compared diagnostic accuracy of pleural fluid Xpert MTB/RIF (Xpert) and Xpert MTB/RIF Ultra (Ultra) assays for diagnosing tuberculous pleural effusion (TPE), through systematic review and comparative meta-analysis.

Methods

We searched PubMed and Embase databases for publications reporting diagnostic accuracy of Xpert or Ultra for TPE. We used bivariate random-effects modeling to summarize diagnostic accuracy information from individual studies using either mycobacterial culture or composite criteria as reference standard. We performed meta-regression through hierarchical summary receiver operating characteristic (HSROC) modeling to evaluate comparative performance of the two tests from studies reporting diagnostic accuracy of both in the same study population.

Results

We retrieved 1097 publications, and included 74 for review. Summary estimates for sensitivity and specificity for Xpert were 0.52 (95% CI 0.43–0.60, I² 82.1%) and 0.99 (95% CI 0.97–0.99, I² 85.1%), respectively, using culture-based reference standard; and 0.21 (95% CI 0.17–0.26, I² 81.5%) and 1.00 (95% CI 0.99–1.00, I² 37.6%), respectively, using composite reference standard. Summary estimates for sensitivity and specificity for Ultra were 0.68 (95% CI 0.55–0.79, I² 80.0%) and 0.97 (95% CI 0.97–0.99, I² 92.1%), respectively, using culture-based reference standard; and 0.47 (95% CI 0.40–0.55, I² 64.1%) and 0.98 (95% CI 0.95–0.99, I² 54.8%), respectively, using composite reference standard. HSROC meta-regression yielded relative diagnostic odds ratio of 1.28 (95% CI 0.65–2.50) and 1.80 (95% CI 0.41–7.84) respectively in favor of Ultra, using culture and composite criteria as reference standard.

Conclusion

Ultra provides superior diagnostic accuracy over Xpert for diagnosing TPE, mainly because of its higher sensitivity.

Drug resistance characteristics of Mycobacterium tuberculosis isolates obtained between 2018 and 2020 in Sichuan, China

We investigated the drug resistance of Mycobacterium tuberculosis isolates from patients with tuberculosis (TB) and HIV, and those diagnosed with only TB in Sichuan, China. TB isolates were obtained from January 2018 to December 2020 and subjected to drug susceptibility testing (DST) to 11 anti-TB drugs and to GeneXpert MTB/RIF testing. The overall proportion of drug-resistant TB (DR-TB) isolates was 32.1% (n = 10 946). HIV testing was not universally available for outpatient TB cases, only 29.5% (3227/10 946) cases had HIV testing results. The observed proportion of multidrug-resistant TB (MDR-TB) isolates was almost double than that of the national level, with approximately 1.5% and 0.1% of the isolates being extensively drug resistant and universally drug resistant, respectively. The proportions of resistant isolates were generally higher in 2018 and 2019 than in 2020. Furthermore, the sensitivities of GeneXpert during 2018–2020 demonstrated a downward trend (80.9, 95% confidence intervals (CI) 76.8–85.0; 80.2, 95% CI 76.4–84.1 and 75.4, 95% CI 70.7–80.2, respectively). Approximately 69.0% (7557/10 946) of the TB cases with DST results were subjected to GeneXpert detection. Overall, the DR-TB status and the use of GeneXpert in Sichuan have improved, but DR-TB challenges remain. HIV testing for all TB cases is recommended.

Rapid Detection and Quantification of Mycobacterium tuberculosis DNA in Paraffinized Samples by Droplet Digital PCR: A Preliminary Study

Background: Rapid and reliable diagnosis of tuberculosis (TB) represents a diagnostic challenge in compartmentalized extrapulmonary TB infection because of the small number of mycobacteria (MTB) and the frequent lack of fresh samples to perform culture. Here, we estimate the performances of homemade droplet digital PCR (ddPCR)-based assays against culture in 89 biopsies, for those fresh and formalin-fixed and paraffin-embedded (FFPE) subsamples were available.

Methods: MTB diagnosis in fresh subsamples was performed by culture. Fresh subsamples were also analyzed for acid-fast bacilli smear-microscopy (AFB) and Xpert^® MTB/RIF (Xpert). MTB examination was repeated in blind in the 89 FFPE subsamples by in-house ddPCR assays targeting the IS6110 and rpoB. Analytical sensitivity of ddPCR assays was evaluated using serial dilution of H37Rv strain. Limit of detection (LOD) was calculated by probit analysis. Results were expressed in copies/10⁶ cells.

Results: IS6110 and rpoB ddPCR assays showed a good linear correlation between expected and observed values (R²: 0.9907 and 0.9743, respectively). Probit analyses predicted a LOD of 17 and 40 copies/10⁶ cells of MTB DNA for IS6110 and rpoB, respectively. Of the 89 biopsies, 68 were culture positive and 21 were culture negative. Considering mycobacterial culture as reference method, IS6110 assay yielded positive results in 67/68 culture-positive samples with a median interquartile range (IQR) of 1,680 (550–8,444) copies/10⁶ cells (sensitivity: 98.5%; accuracy: 98.9). These performances were superior to those reported by the rpoB assay in FFPE subsamples (sensitivity: 66.20%; accuracy: 74.1) and even superior to those reported by Xpert and AFB in fresh subsamples (sensitivity: 79.4 and 33.8%, respectively; accuracy: 84.3 and 49.4, respectively). When Xpert and AFB results were stratified according to mycobacterial load detected by rpoB and IS6110 ddPCR, bacterial load was lower in Xpert and AFB negative with respect to Xpert and AFB-positive samples (p = 0.003 and 0.01 for rpoB and p = 0.01 and 0.11 for IS6110), confirming the poor sensitivity of these methods in paucibacillary disease.

Conclusion: ddPCR provides highly sensitive, accurate, and rapid MTB diagnosis in FFPE samples, as defined by the high concordance between IS6110 assay and culture results. This approach can be safely introduced in clinical routine to accelerate MTB diagnosis mainly when culture results remain unavailable.

Diagnostic accuracy of the Xpert MTB/RIF assay for tuberculous pericarditis: A systematic review and meta-analysis

Objective

The purpose of this study was to evaluate the diagnostic efficacy of Xpert MTB/RIF for tuberculous pericarditis (TBP).

Methods

We searched relevant databases for Xpert MTB/RIF for TBP diagnosis until April 2021 and screened eligible studies for study inclusion. We evaluated the effectiveness of Xpert MTB/RIF when the composite reference standard (CRS) and mycobacterial culture were the gold standards, respectively. We performed meta-analyses using a bivariate random-effects model, and when the heterogeneity was obvious, the source of heterogeneity was further discussed.

Results

We included seven independent studies comparing Xpert MTB/RIF with the CRS and six studies comparing it with culture. The pooled sensitivity, specificity, and area under the curve of Xpert MTB/RIF were 65% (95% confidence interval, 59–72%), 99% (97–100%), and 0.99 (0.97–0.99) as compared with the CRS, respectively, and 75% (53–88%), 99% (90–100%), and 0.94 (0.92–0.96) as compared with culture, respectively. There was no significant heterogeneity between studies when CRS was the gold standard, whereas heterogeneity was evident when culture was the gold standard.

Conclusions

The sensitivity of Xpert MTB/RIF for diagnosing TBP was moderate and the specificity was good; thus, Xpert MTB/RIF can be used in the initial diagnosis of TBP.

Diagnostic Efficacy of Xpert MTB/RIF Assay in Bronchoalveolar Lavage Fluid for Tracheobronchial Tuberculosis: A Retrospective Analysis

Background: The Xpert Mycobacterium tuberculosis/rifampin (MTB/RIF) assay has shown good diagnostic efficacy in brushing and biopsy tissue samples from patients with tracheobronchial tuberculosis (TBTB). However, its diagnostic value in bronchoalveolar lavage fluid (BALF) is still unclear. Therefore, the present retrospective study aimed to evaluate the diagnostic value of the Xpert MTB/RIF assay in BALF.

Methods: The clinical data of 266 patients with suspected TBTB from January 2018 to October 2020 were pooled with complete details of bronchial brush and bronchoalveolar lavage samples. Smears of the bronchial brushings were stained with Auramine O stain to detect acid-fast bacilli (AFB), and BALF samples were used for culturing MTB with the BACTEC MGIT 960 system and the Xpert MTB/RIF assay. The diagnostic performance of these methods was assessed and compared.

Results: A total of 266 patients suspected to have TBTB were enrolled in the final analysis. Of these patients, 179 patients were confirmed to have TBTB and 87 patients were non-TBTB. The sensitivity of the Xpert MTB/RIF assay in BALF (87.2%) was significantly higher than that of the brush smear for AFB (35.2%, p < 0.001). No significant difference was observed between the sensitivities of the Xpert MTB/RIF assay in BALF and MTB culture in BALF (87.2 vs. 84.9%, p = 0.542). The specificities of the Xpert MTB/RIF assay in BALF, MTB culture in BALF, and the bronchial brush smear were 97.7, 97.7, and 98.9%, respectively. The positive predictive value (PPV) and negative predictive value (NPV) of the Xpert MTB/RIF assay in BALF, MTB culture in BALF, and the bronchial brush smear were 98.7 and 78.7%, 98.7 and 75.9%, and 98.4 and 42.6%, respectively. Among the MTB culture-positive patients with TBTB detected by the Xpert assay, 27.0% (20/74) were identified to be resistant to RIF.

Conclusions: The Xpert MTB/RIF assay in BALF enables a rapid and accurate diagnosis of TBTB and identification of RIF resistance, which is crucial for timely and proper treatment. Moreover, in patients with TBTB, BALF could be used as an alternative to bronchial brushing and biopsy tissues for the Xpert MTB/RIF assay.

Diagnostic utility of GeneXpert MTB/RIF assay versus conventional methods for diagnosis of pulmonary and extra-pulmonary tuberculosis

Background

Tuberculosis (T.B) is one of the major infectious diseases in the developing countries. The diagnosis of extrapulmonary T.B (EPTB) remains problematic and emergence of resistant strains poses a significant threat. Improved diagnosis of tuberculosis is a global priority for proper control. The study aimed to assess the diagnostic accuracy of GeneXpert MTB/RIF assay for diagnosis of pulmonary TB (PTB) and EPTB and to evaluate the performance of GeneXpert system for demonstrating rifampicin resistance among the studied patients.

Methods

A total of 582 clinical samples (449 pulmonary; 430 sputum and 19 bronchoalveolar lavage (BAL) and 133 extra-pulmonary origins; 26 pleural fluid, 62 CSF, 19 ascetic fluid, 12 pus and 14 urine) were collected from patients under clinical and radiological assessment of either PTB or EPTB who were admitted to Menoufia Chest Hospital over a period of three years. Clinical samples were processed and investigated for detection of Mycobacterium tuberculosis (MTB) by both Xpert assay and the conventional methods including Ziehl-Neelsen (ZN)/acid-fast bacillus (AFB) smear microscopy and Lowenstein-Jensen (LJ) culture. Patients′ demographic, clinical characteristics and risk factors for acquiring rifampicin resistance were analyzed.

Results

The sensitivity, specificity, false- negative rate and total accuracy of AFB smear microscopy respectively were 72.1 %, 81.3 %, 27.9 and 78.8 % for PTB. However for EPTB, they were 63.2 %, 70.5 %, 36.8 and 68.4 % respectively in relation to LJ culture as the gold standard. GeneXpert MTB/RIF revealed better performance for PTB than EPTB. For PTB, it showed 90.2 % sensitivity, 86.9 % specificity, and 9.8 % false- negative rate. For EPTB, the assay showed a sensitivity of 81.6 %, specificity of 78.9 % and false- negative rate of 18.5 %. Multivariate regression analysis showed that presence of EPTB and contacts with known TB cases were independent risk factors for developing rifampicin resistance.

Conclusions

GeneXpert MTB/RIF assay is a rapid and highly sensitive technique for diagnosis of PTB or EPTB. Its simplicity and accuracy make this new method a very impressive tool for diagnosis of MTB and rifampicin resistance.

Seasonal influence of tuberculosis diagnosis in Rwanda

Background

Tuberculosis (TB) remains a major global health concern. Previous research reveals that TB may have a seasonal peak during the spring and summer seasons in temperate climates; however, few studies have been conducted in tropical climates. This study evaluates the influence of seasonality on laboratory-confirmed TB diagnosis in Rwanda, a tropical country with two rainy and two dry seasons.

Methods

A retrospective chart review was performed at the University Teaching Hospital-Kigali (CHUK). From January 2016 to December 2017, 2717 CHUK patients with TB laboratory data were included. Data abstracted included patient demographics, season, HIV status, and TB laboratory results (microscopy, GeneXpert, culture). Univariate and multivariable logistic regression (adjusted for age, gender, and HIV status) analyses were performed to assess the association between season and laboratory-confirmed TB diagnoses.

Results

Patients presenting during rainy season periods had a lower odds of laboratory-confirmed TB diagnosis compared to the dry season (aOR=0.78, 95% CI 0.63–0.97, p=0.026) when controlling for age group, gender, and HIV status. Males, adults, and people living with HIV were more likely to have laboratory-confirmed TB diagnosis. On average, more people were tested for TB during the rainy season per month compared to the dry season (120.3 vs. 103.3), although this difference was not statistically significant.

Conclusion

In Rwanda, laboratory-confirmed TB case detection shows a seasonal variation with patients having higher odds of TB diagnosis occurring in the dry season. Further research is required to further elucidate this relationship and to delineate the mechanism of season influence on TB diagnosis.

Limited role of GeneXpert in peritoneal fluid in the diagnosis of genital tuberculosis in infertile women

Background and Objectives:

Genital tuberculosis (TB) is an important cause of infertility in women that poses many challenges in diagnosis. The study is done to understand the utility of GeneXpert test in peritoneal fluid in the diagnosis of genital TB in infertile women.

Methods:

All infertile women in postmenstrual phase who were planned for laparoscopy in study period were included. Women who were already on anti-TB therapy were excluded. Peritoneal fluid/washings were retrieved during laparoscopy to test for Mycobacterium tuberculosis by GeneXpert. A note was made of laparoscopy evidence of TB. Endometrial sample was sent for microbiological testing of mycobacterium on smear and liquid culture. Histopathological test of endometrium was also done to look for granulomas.

Results:

In a total of 57 women, 8 (14.03%) women were diagnosed with TB on the basis of laparoscopy or microbiological or histopathological tests. Six women had caseating tubercles in pelvis, of them two women had presence of mycobacterium on smear, one woman also had positive liquid culture. In two women endometrial smear was positive. None of the women had a positive GeneXpert test in peritoneal fluid.

Conclusion:

Genital TB is a clinical problem in infertile women. Even in women with confirmed genital TB the peritoneal fluid/washings were negative for mycobacterium. GeneXpert did not pick Mycobacterium in peritoneal fluid in women with genital TB. Hence, it is not a sensitive and good tool for the diagnosis of female genital TB.

Development of a two-step nucleic acid amplification test for accurate diagnosis of the Mycobacterium tuberculosis complex

The Mycobacterium tuberculosis complex (MTBC) remains one of the top 10 leading causes of death globally. The early diagnosis of MTBC can reduce mortality and mitigate disease transmission. However, current nucleic acid amplification diagnostic test methods are generally time-consuming and show suboptimal diagnostic performance, especially in extrapulmonary MTBC samples or acid-fast stain (AFS)-negative cases. Thus, development of an accurate assay for the diagnosis of MTBC is necessary, particularly under the above mentioned conditions. In this study, a single-tube nested real-time PCR assay (N-RTP) was developed and compared with a newly in-house-developed high-sensitivity real-time PCR assay (HS-RTP) using 134 clinical specimens (including 73 pulmonary and 61 extrapulmonary specimens). The amplification efficiency of HS-RTP and N-RTP was 99.8% and 100.7%, respectively. The sensitivity and specificity of HS-RTP and N-RTP for the diagnosis of MTBC in these specimens were 97.5% (77/79) versus 94.9% (75/79) and 80.0% (44/55) versus 89.1% (49/55), respectively. The sensitivity and specificity of HS-RTP and N-RTP for the diagnosis of MTBC in pulmonary specimens were 96.3% (52/54) versus 96.3% (52/54) and 73.7.0% (14/19) versus 89.5% (17/19), respectively; in extrapulmonary specimens, the sensitivity and specificity of HS-RTP and N-RTP were 100% (25/25) versus 92% (23/25) and 83.3% (30/36) versus 88.9% (32/36), respectively. Among the AFS-negative cases, the sensitivity and specificity of HS-RTP and N-RTP were 97.0% (32/33) versus 90.9% (30/33) and 88.0% (44/50) versus 92.0% (46/50), respectively. Overall, the sensitivity of HS-RTP was higher than that of N-RTP, and the performance was not compromised in extrapulmonary specimens and under AFS-negative conditions. In contrast, the specificity of the N-RTP assay was higher than that of the HS-RTP assay in all types of specimens. In conclusion, the HS-RTP assay would be useful for screening patients suspected of exhibiting an MTBC infection due to its higher sensitivity, while the N-RTP assay could be used for confirmation because of its higher specificity. Our results provide a two-step method (screen to confirm) that simultaneously achieves high sensitivity and specificity in the diagnosis of MTBC.

Molecular detection of Mycobacterium tuberculosis in blood stained sputum samples using GeneXpert PCR assay

This study investigated the possibility of detecting Mycobacterium tuberculosis (MTB) in blood-stained sputa with GeneXpert assay (Xpert MTB/Rif G4 v.5) using appropriate blood lysing (distilled water and distilled water/carbon tetrachloride) and protein denaturing (guanidinium chloride and heat) agents. Blood free sputa were collected from individuals infected with MTB. Various levels of blood-spiked sputa (0%-50%) were prepared and subsequently assayed with GeneXpert analyzer. GeneXpert was found to be reproducible at less than 2% blood contamination. However, beyond 5% blood contamination, GeneXpert was unreliable with absolute PCR inhibition at 20% of blood contamination. Boiling at 95°C for 5 minutes was able to recover MTB DNA in previously undetectable levels as well as in 57% of patients' sputa with blood stains with previous negative GeneXpert results.

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

BACKGROUND

Xpert MTB/RIF and Xpert MTB/RIF Ultra (Xpert Ultra) are World Health Organization (WHO)-recommended rapid tests that simultaneously detect tuberculosis and rifampicin resistance in people with signs and symptoms of tuberculosis. This review builds on our recent extensive Cochrane Review of Xpert MTB/RIF accuracy.

OBJECTIVES

To compare the diagnostic accuracy of Xpert Ultra and Xpert MTB/RIF for the detection of pulmonary tuberculosis and detection of rifampicin resistance in adults with presumptive pulmonary tuberculosis. For pulmonary tuberculosis and rifampicin resistance, we also investigated potential sources of heterogeneity. We also summarized the frequency of Xpert Ultra trace-positive results, and estimated the accuracy of Xpert Ultra after repeat testing in those with trace-positive results.

SEARCH METHODS

We searched the Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, Web of Science, LILACS, Scopus, the WHO ICTRP, the ISRCTN registry, and ProQuest to 28 January 2020 with no language restriction.

SELECTION CRITERIA

We included diagnostic accuracy studies using respiratory specimens in adults with presumptive pulmonary tuberculosis that directly compared the index tests. For pulmonary tuberculosis detection, the reference standards were culture and a composite reference standard. For rifampicin resistance, the reference standards were culture-based drug susceptibility testing and line probe assays.

DATA COLLECTION AND ANALYSIS

Two review authors independently extracted data using a standardized form, including data by smear and HIV status. We assessed risk of bias using QUADAS-2 and QUADAS-C. We performed meta-analyses comparing pooled sensitivities and specificities, separately for pulmonary tuberculosis detection and rifampicin resistance detection, and separately by reference standard. Most analyses used a bivariate random-effects model. For tuberculosis detection, we estimated accuracy in studies in participants who were not selected based on prior microscopy testing or history of tuberculosis. We performed subgroup analyses by smear status, HIV status, and history of tuberculosis. We summarized Xpert Ultra trace results.

MAIN RESULTS

We identified nine studies (3500 participants): seven had unselected participants (2834 participants). All compared Xpert Ultra and Xpert MTB/RIF for pulmonary tuberculosis detection; seven studies used a paired comparative accuracy design, and two studies used a randomized design. Five studies compared Xpert Ultra and Xpert MTB/RIF for rifampicin resistance detection; four studies used a paired design, and one study used a randomized design. Of the nine included studies, seven (78%) were mainly or exclusively in high tuberculosis burden countries. For pulmonary tuberculosis detection, most studies had low risk of bias in all domains. Pulmonary tuberculosis detection Xpert Ultra pooled sensitivity and specificity (95% credible interval) against culture were 90.9% (86.2 to 94.7) and 95.6% (93.0 to 97.4) (7 studies, 2834 participants; high-certainty evidence) versus Xpert MTB/RIF pooled sensitivity and specificity of 84.7% (78.6 to 89.9) and 98.4% (97.0 to 99.3) (7 studies, 2835 participants; high-certainty evidence). The difference in the accuracy of Xpert Ultra minus Xpert MTB/RIF was estimated at 6.3% (0.1 to 12.8) for sensitivity and -2.7% (-5.7 to -0.5) for specificity. If the point estimates for Xpert Ultra and Xpert MTB/RIF are applied to a hypothetical cohort of 1000 patients, where 10% of those presenting with symptoms have pulmonary tuberculosis, Xpert Ultra will miss 9 cases, and Xpert MTB/RIF will miss 15 cases. The number of people wrongly diagnosed with pulmonary tuberculosis would be 40 with Xpert Ultra and 14 with Xpert MTB/RIF. In smear-negative, culture-positive participants, pooled sensitivity was 77.5% (67.6 to 85.6) for Xpert Ultra versus 60.6% (48.4 to 71.7) for Xpert MTB/RIF; pooled specificity was 95.8% (92.9 to 97.7) for Xpert Ultra versus 98.8% (97.7 to 99.5) for Xpert MTB/RIF (6 studies). In people living with HIV, pooled sensitivity was 87.6% (75.4 to 94.1) for Xpert Ultra versus 74.9% (58.7 to 86.2) for Xpert MTB/RIF; pooled specificity was 92.8% (82.3 to 97.0) for Xpert Ultra versus 99.7% (98.6 to 100.0) for Xpert MTB/RIF (3 studies). In participants with a history of tuberculosis, pooled sensitivity was 84.2% (72.5 to 91.7) for Xpert Ultra versus 81.8% (68.7 to 90.0) for Xpert MTB/RIF; pooled specificity was 88.2% (70.5 to 96.6) for Xpert Ultra versus 97.4% (91.7 to 99.5) for Xpert MTB/RIF (4 studies). The proportion of Ultra trace-positive results ranged from 3.0% to 30.4%. Data were insufficient to estimate the accuracy of Xpert Ultra repeat testing in individuals with initial trace-positive results. Rifampicin resistance detection Pooled sensitivity and specificity were 94.9% (88.9 to 97.9) and 99.1% (97.7 to 99.8) (5 studies, 921 participants; high-certainty evidence) for Xpert Ultra versus 95.3% (90.0 to 98.1) and 98.8% (97.2 to 99.6) (5 studies, 930 participants; high-certainty evidence) for Xpert MTB/RIF. The difference in the accuracy of Xpert Ultra minus Xpert MTB/RIF was estimated at -0.3% (-6.9 to 5.7) for sensitivity and 0.3% (-1.2 to 2.0) for specificity. If the point estimates for Xpert Ultra and Xpert MTB/RIF are applied to a hypothetical cohort of 1000 patients, where 10% of those presenting with symptoms have rifampicin resistance, Xpert Ultra will miss 5 cases, and Xpert MTB/RIF will miss 5 cases. The number of people wrongly diagnosed with rifampicin resistance would be 8 with Xpert Ultra and 11 with Xpert MTB/RIF. We identified a higher number of rifampicin resistance indeterminate results with Xpert Ultra, pooled proportion 7.6% (2.4 to 21.0) compared to Xpert MTB/RIF pooled proportion 0.8% (0.2 to 2.4). The estimated difference in the pooled proportion of indeterminate rifampicin resistance results for Xpert Ultra versus Xpert MTB/RIF was 6.7% (1.4 to 20.1).

AUTHORS' CONCLUSIONS

Xpert Ultra has higher sensitivity and lower specificity than Xpert MTB/RIF for pulmonary tuberculosis, especially in smear-negative participants and people living with HIV. Xpert Ultra specificity was lower than that of Xpert MTB/RIF in participants with a history of tuberculosis. The sensitivity and specificity trade-off would be expected to vary by setting. For detection of rifampicin resistance, Xpert Ultra and Xpert MTB/RIF had similar sensitivity and specificity. Ultra trace-positive results were common. Xpert Ultra and Xpert MTB/RIF provide accurate results and can allow rapid initiation of treatment for rifampicin-resistant and multidrug-resistant tuberculosis.

Rifampin resistance among individuals with extrapulmonary tuberculosis: 4 years of experience from a reference laboratory

Information is limited about the drug resistance patterns in extrapulmonary tuberculosis (EPTB) in Iran. This study aimed to determine the prevalence of EPTB and to investigate the drug-resistance pattern in Mycobacterium tuberculosis strains collected from extrapulmonary samples at the Tehran regional TB reference laboratory. Extrapulmonary specimens from individuals with suspected TB referred to the TB reference laboratories in five cities of Iran were collected. Both standard conventional methods (culture and direct smear microscopy) and Xpert MTB/RIF assay were used for the identification of mycobacteria. Drug susceptibility testing was done using Xpert MTB/RIF. The proportion method on Lowenstein–Jensen medium was performed for confirmation. Between 2016 and 2020, a total of 12 050 clinical specimens from individuals with suspected TB were collected, of which 10 380 (86%) were pulmonary specimens and 1670 (14%) were extrapulmonary. Of the extrapulmonary specimens, 85 (5.0%) were positive for M. tuberculosis, and the remaining 1585 (95.0%) samples were negative by standard methods. Of 85 M. tuberculosis isolates, drug susceptibility testing was performed for 32 isolates, of which 1 (3.1%, 95% CI 0.0%–9.4%) was rifampin resistant and 31 (96.9%, 95% CI 90.1%–100%) were pan-susceptible. The rifampin-resistant isolate was also resistant to isoniazid, so was assigned as a multidrug-resistant TB. Our study indicated the frequency of drug-resistance among EPTB in Iran. Establishing rapid diagnostic methods for detection of drug-resistance in EPTB, performing drug susceptibility testing for all EPTB cases to provide effective treatment, and continuous monitoring of drug resistance, are suggested for prevention and control of drug resistance in EPTB in Iran.

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.

Diagnostic characteristics of Xpert MTB/RIF assay for the diagnosis of tuberculous meningitis and rifampicin resistance in Southern Brazil

BACKGROUND

The timely diagnosis of tuberculous meningitis (TBM) is challenging. Molecular diagnostic tools are necessary for TBM, particularly in low- and middle-income countries.

OBJECTIVES

We aimed to calculate the diagnostics characteristics of Xpert MTB/RIF for the detection of Mycobacterium tuberculosis in the cerebrospinal fluid (CSF) and the frequency of rifampicin (RIF)-resistance in the CSF samples.

METHODS

A total of 313 consecutive CSF samples were studied and categorized into TBM definite, probable, possible, or not TBM cases based on the clinical, laboratory, and imaging data.

RESULTS

For the definite TBM cases (n=7), the sensitivity, specificity, efficiency, and positive likelihood ratio were 100, 97, 97, and 38%, respectively. However, for the TBM definite associated with the probable cases (n=24), the sensitivity decreased to 46%. All CSF samples that were Xpert MTB/RIF-positive were RIF susceptible.

CONCLUSION

Xpert MTB/RIF showed high discriminating value among the microbiology-proven TBM cases, although the values for the probable and possible TBM cases were reduced. Xpert MTB/RIF contributes significantly to the diagnosis of TBM, mainly when coupled with the conventional microbiological tests and clinical algorithms.

Diagnostic accuracy of the Xpert MTB/RIF assay for abdominal tuberculosis: a systematic review and meta-analysis

BACKGROUND

We performed a meta-analysis to determine diagnostic accuracy of Xpert MTB/RIF for diagnosis of abdominal (intestinal or peritoneal) tuberculosis (TB) in various tissues (intestinal, omental/peritoneal tissue or ascitic fluid).

METHODS

Electronic databases were searched for observational studies on use of Xpert MTB/RIF in ascitic fluid, peritoneal, or omental tissue for diagnosis of peritoneal and intestinal TB. We calculated the pooled sensitivity, specificity and diagnostic odds ratio of Xpert MTB/RIF for diagnosis of peritoneal TB in comparison to composite reference standard (CRS) and culture, and in comparison to CRS for intestinal TB.

RESULTS

Twenty-five observational studies were included. The pooled sensitivity and specificity as assessed with peritoneal culture from ascites as an Index test was 64% (95% Confidence Interval [C.I.] 49-76%) and 97% (95% C.I., 95-99%) respectively and with peritoneal CRS was 30% (95% C.I., 22-40%) and 100% (95% C.I., 98-100%) respectively. In the intestinal group, the pooled sensitivity and specificity of Xpert MTB/RIF was 23% (95% C.I., 16-32%) and 100% (95% C.I., 52-100%). The AUC of peritoneal culture and intestinal tissue was 0.935 and 0.499.

CONCLUSION

Xpert MTB/RIF has modest sensitivity for diagnosis of peritoneal and intestinal tuberculosis but has a good specificity.

PROSPERO REGISTRATION

CRD42020140545.

Comparison of metagenomic next-generation sequencing technology, culture and GeneXpert MTB/RIF assay in the diagnosis of tuberculosis

Background

With a high incidence rate and mortality rate, tuberculosis (TB) is a major public health concern worldwide. There is an urgent need to develop the rapid, reliable and affordable diagnostic test for the detection of Mycobacterium tuberculosis (Mtb). Metagenomic next-generation sequencing (mNGS) showed promising values in the rapid diagnosis of clinical TB, while studies on the application of mNGS in pulmonary and extrapulmonary TB remain scarce.

Methods

In this study, we collected the results of both mNGS and culture of 70 specimens from suspected TB patients at the Shanghai Pulmonary Hospital of Tongji University. Results of GeneXpert MTB/RIF assay (Xpert) were obtained from 19 patients. We also assessed the diagnostic performance, relationship and consistency between mNGS, traditional culture method, and Xpert.

Results

Overall, 36 of 70 suspected patients were finally diagnosed with TB. The sensitivity, specificity, positive predictive value, negative predictive value and the Youden index of mNGS in all clinical TB specimens were calculated as 66.7% (95% CI: 0.489–0.809), 97.1% (95% CI: 0.829–0.998), 96.0% (95% CI: 0.777–0.998), 73.3% (95% CI: 0.578–0.849), 63.8%, respectively. The sensitivity of mNGS was much superior to that of conventional culture method (66.7%, 95% CI: 0.489–0.809 vs. 36.1%, 95% CI: 0.213–0.538) and Xpert (76.9%, 95% CI: 0.460–0.938 vs. 61.5%, 95% CI: 0.323–0.849). In pulmonary TB cases, mNGS, culture, and Xpert all demonstrated better diagnostic capacity for TB when compared with extrapulmonary TB cases. Among all methods and sample classifications, the Youden index of parallel diagnostic test in pulmonary samples was outstanding (mNGS/culture 88.2%; mNGS/Xpert 100%). Furthermore, the correlation and concordance between mNGS and culture method in all types of specimens was statistically significant (both P<0.001).

Conclusions

With high sensitivity and specificity, mNGS showed remarkable diagnostic performance in various samples from suspected TB patients. Combining mNGS and culture or Xpert method had the potential for clinical application in TB.

Diagnostic test accuracy of Xpert MTB/RIF for tuberculous pericarditis: a systematic review and meta-analysis

Introduction: Xpert MTB/RIF is a rapid diagnostic instrument for pulmonary tuberculosis (TB). However, studies reported varied accuracy of Xpert MTB/RIF in detecting Mycobacterium tuberculosis in pericardial effusion. Methods: We performed a systematic review of literature in PubMed, published up to February 1, 2020, according to PRISMA guidelines. We screened cross-sectional studies, observational cohort studies, and randomized control trials that evaluated the accuracy of Xpert MTB/RIF in diagnosing TB pericarditis. Papers with noninterpretable results of sensitivity and specificity, non-English articles, and unpublished studies were excluded. The primary outcomes were the sensitivity and specificity of Xpert MTB/RIF. We conducted a quality assessment using QUADAS-2 to evaluate the quality of the studies. A bivariate model pooled the overall sensitivity, specificity, positive likelihood ratios (PLRs), and negative likelihood ratios (NLRs) of included studies. Results: In total, 581 subjects from nine studies were analyzed in this meta-analysis. Our pooled analysis showed that the overall sensitivity, specificity, PLRs and NLRs of included studies were 0.676 (95% CI: 0.580-0.759), 0.994 (95% CI: 0.919-1.000), 110.11 (95% CI: 7.65-1584.57) and 0.326 (95% CI: 0.246-0.433), respectively. Conclusions: Xpert MTB/RIF had a robust specificity but unsatisfactory sensitivity in diagnosing TB pericarditis. These findings indicated that although positive Xpert MTB/RIF test results might be valuable in swiftly distinguishing the diagnosis of TB pericarditis, negative test results might not be able to rule out TB pericarditis. Registration: PROSPERO CRD42020167480 28/04/2020.

Metagenomic Next-Generation Sequencing (mNGS) in cerebrospinal fluid for rapid diagnosis of Tuberculosis meningitis in HIV-negative population

OBJECTIVE

Metagenomic Next-Generation Sequencing (mNGS) has been applied as a novel method of detection pathogens for infectious diseases, but its value in the rapid diagnosis of tuberculous meningitis(TBM)has not been clarified based on large samples.

METHODS

A retrospective analysis was conducted on 51 inpatients with suspected TBM who underwent mNGS and four other tests in cerebrospinal fluid (CSF).

RESULTS

Among 51 included patients, 45 cases were diagnosed as TBM (38 definite, 5 probable, 2 possible) and 6 cases as non-TBM. Using final diagnosis as reference standard, the sensitivity, specificity, PPV (positive predictive value), and NPV (negative predictive value) of mNGS in CSF for TBM were 84.44%(38/45, 69.94%-93.01%), 100%(6/6, 51.68%-100%), 100%(40/40, 88.57%-100%) and 46.15%(6/13, 20.40%-73.88%). The diagnostic sensitivity of mNGS(84.4%)was significantly higher than that of AFB (0%, P = 0.000), MGIT960 culture(22.2%, P = 0.000), MTB PCR(24.4%, P = 0.000) and Xpert MTB/RIF(40%, P = 0.000). The ROC curve showed that CSF protein quantification and CSF cell count might be valuable in the prediction of NGS positive detection of MTB (Mycobacterium tuberculosis).

CONCLUSION

CSF mNGS had high sensitivity, specificity and PPV in the diagnosis of TBM. Patients with a significant increase in CSF cell number and protein quantification might have a higher likelihood of positive MTB detection of NGS.