Use of GeneXpert Mycobacterium tuberculosis/rifampicin for rapid detection of rifampicin resistant Mycobacterium tuberculosis strains of clinically suspected multi-drug resistance tuberculosis cases

Factors associated with tuberculosis drug resistance among presumptive multidrug resistance tuberculosis patients identified in a DRTB surveillance study in western Kenya

Multidrug-resistant tuberculosis (MDR-TB) is caused by M. tuberculosis (Mtb) with resistance to the first-line anti-TB medicines isoniazid (INH) and rifampicin (RIF). In Western Kenya, there is reported low prevalence of drug resistant strains among HIV tuberculosis patients, creating a need to determine factors associated with drug resistance patterns among presumptive MDR-TB patients. To determine factors associated with drug resistance patterns among presumptive MDR-TB patients in western Kenya. Three hundred and ninety (3 9 0) sputum sample isolates from among presumptive multidrug TB patients, were analyzed for TB drug resistance as per Ministry of Health (MoH) TB program diagnostic algorithm. Frequency and percentages were used to summarize categorical data while median and interquartile range (IQR) were used for continuous data. Multivariable logistic regression was carried out to identify factors associated with TB drug resistance. Out of 390 participants enrolled, 302/390 (77.4 %) were males, with a median age of 34 years. The HIV-infected were 118/390 (30.3 %). Samples included 322 (82.6 %) from presumptive patients, while 68/390 (17.4 %) were either lost to follow-up patients, failures to first-line treatment or newly diagnosed cases. A total of 64/390 (16.4 %) of the isolates had at least some form of drug resistance. Out of 390, 14/390 (3.6 %) had MDR, 12 (3.1 %) were RIF mono-resistance, 34 (8.7 %) had INH, while 4 (1 %) had ethambutol resistance. The category of previously treated patients (those who received or are currently on TB treatment) had a 70 % reduced likelihood of resistance (aOR: 0.30; 95 % CI: 0.13-0.70). In contrast, older age was associated with an increased likelihood of resistance to INH and RIF, with an adjusted odds ratio of 1.04 per year (95 % CI: 1.00-1.08). Prompt MDR-TB diagnosis is essential for appropriate patient care, management, and disease prevention and control. We recommend active surveillance on drug resistant TB in these regions to detect drug resistance patterns for rapid disease management.

Comprehensive Drug Resistance Characterization of Pulmonary Tuberculosis in Algeria: Insights on Mycobacterium tuberculosis Strains by Whole-Genome Sequencing

In this study, we aimed to characterize drug-resistant strains by whole-genome sequencing (WGS), to describe the spreading lineages and the history of transmission. Drug susceptibility testing was performed by 96-well broth microdilution plates. The genomic DNA was extracted and purified; libraries were prepared and run on the Illumina NextSeq500 System. Among 82 isolates, 21 tuberculosis (TB) isolates (25.6%) were drug resistant, including 10 MDR and 4 pre-extensively drug-resistant (XDR)-TB. The mutation Ser315Thr in the katG gene was confirmed in 15 isolates. In rpoB, Ser450Leu and His445Asp mutations were the most common. Asp94Asn and Ala90Val mutations were reported in gyrA. The LAM family, the most TB drug resistant, was widely predominant in the north and the T sublineage in the south of the country. This study provides the first insight on TB drug resistance using WGS in Algeria and clearly describes the first pre-XDR-TB cases and lineage distribution across the country.

Study the prevalence of rifampicin resistance among pulmonary tuberculosis patients by genexpert assay from a tertiary care hospital of North India

Background

Rifampicin (RIF) resistance (RR) tuberculosis (TB) has posed a great challenge to TB control programs globally. Evidence of RIF-RR can help as a surrogate marker to find out multidrug-resistance cases. The study aimed to determine the prevalence of RIF-RR in pulmonary TB (PTB) patients over the 4 years at Dr. RPGMC, Tanda, from the year 2018 to 2021.

Methods

This was a retrospective study conducted at Dr. RPGMC, Tanda at Kangra, where we checked (from January 2018 to December 2021) clinically suspected PTB patients, whose samples were sent to the laboratory for GeneXpert assay to identify Mycobacterium TB/RIF (MTB/RIF) testing.

Results

Of the total 11,774 clinically suspected PTB specimens were collected, and identified by GeneXpert MTB/RIF assay, in which 2358 samples were MTB positive and 9416 were MTB negative. Among 2358 MTB-positive samples, 2240 (95%) samples were RIF sensitive, in which 1553 (65.9%) were males and 687 (29.1%) were females, 76 (3.2%) samples were RIF-RR, in which 51 (2.2%) were males and 25 (1%) were females, and 42 (1.8%) samples were RIF indeterminate, in which 25 (1%) were males and 17 (0.8%) were females.

Conclusion

The rate of RIF-RR was found 3.2% of total samples which was more in males. The overall positivity rate was 20%, and the rate of positivity decreased from 32% to 14% over the 4 years in sputum samples. Hence, the GeneXpert assay was found to be very important tool to detect RIF-RR among suspected PTB patients.

The Value of GeneXpert MTB/RIF for Detection in Tuberculosis: A Bibliometrics-Based Analysis and Review

With the continuous development of medical science and technology, especially with the advent of the era of precision diagnosis and treatment, molecular biology detection technology is widely valued and applied as an aid to early diagnosis of tuberculosis. The GeneXpert Mycobacterium tuberculosis Branching (MTB) technology is a suite of semi-nested real-time fluorescent quantitative PCR in vitro diagnostic technologies developed by Cepheid Inc. It targets the rifampicin resistance gene, rpoB, and can detect both MTB and resistance to rifampicin within 2 h. This review analyzed the papers related to GeneXpert using bibliometric software CiteSpace and Bibliometrix. A total of 151 articles were analyzed, spanning from 2011 to 2021. This bibliometrics-based review summarizes the history of the development of GeneXpert in tuberculosis diagnosis and its current status. Contributions of different countries to the topic, journal analysis, key paper analysis, and clustering of keywords were used to analyze this topic.

Determining the Prevalence of Rifampicin Resistant Tuberculosis in A Tertiary Care Centre of North India by using Rapid Culture Method and Gene Xpert

The objective of the present study is to find the prevalence of Mycobacterium tuberculosis from respiratory samples like sputum, BAL and pleural fluid, compare conventional LJ culture with rapid culture method i.e Mycobacterium growth indicator tube (MGIT) and to determine the pattern of drug resistance by automated methods i.e Gene Xpert. Respiratory samples were collected in sterile, wide-mouth, disposable, leak proof containers without any preservatives. Specimens were inoculated into MGIT for primary isolation of Mycobacteria. The specimen was processed according to the SOP manual provided by Becton Dickinson Company. The tubes were read for increasing fluorescence by MGIT reader. Reported results only when a MGIT tube was positive by the MGIT reader and smear made from the positive broth is also positive for AFB. For further identification, TBcID card test was put from MGIT positive tube and the result was given accordingly as mentioned in the procedure for TBcID kit insert. Polymerase chain reaction (PCR) was done in all 17 positive cases. The drug sensitivity test (CB-NAAT) was done at State Intermediate Reference Laboratory, Chandan Nagar, Dehradun, Uttrakhand as per RNTCP laboratory operational guidelines. In our study total number of samples received from the clinically suspected cases of pulmonary tuberculosis were 156, out of which 11% were positive and 89% were negative. The predominant age group involved was 51-60 years 24%, followed by 61-70 years 22%. In young children and adolescent age group very less number of samples were received i.e. 0-5%. Out of 17 positive samples, 94.11% (16/17) were detected as sensitive for Rifampicin and 5.89% (1/17) were resistant. On the statistical analysis of our data for MGIT, Positive Predictive Value (PPV) was 29% against Negative Predictive Value (NPV) of 100%. The specificity of MGIT was 92% against a sensitivity of 100%. Culture is still needed for species identification, confirmation and drug susceptibility testing. The diagnostic superiority of MGIT, both in terms of sensitivity and specificity has been proven better as compared to LJ in previous other studies and supported by our study as well. In our study, the diagnostic efficacy of MGIT culture was found to be superior as compared to the conventional LJ culture. The positivity rate was 10.89% (17/156) in MGIT & 3.2% (5/156) in LJ culture.

Rifampicin resistance in Mycobacterium tuberculosis in Iran: a two-centre study

Multidrug-resistant tuberculosis remains a challenge. In this study, we investigated the incidence of rifampicin (RIF) resistance in Mycobacterium tuberculosis in a large number of pulmonary specimens. A two-center study in Tehran, the capital of Iran, was performed with 6624 pulmonary samples of patients with tuberculosis (TB) who were subjected to detection of RIF-resistant TB by GeneXpert MTB/RIF assay between May 2014 and July 2018. Conventional drug susceptibility testing was performed to confirm the results. Xpert MTB/RIF identified a total of 96 positives for M. tuberculosis, of which 5 (5.3%) samples were found to be RIF-resistant TB. All RIF-resistant and sensitive isolates detected by GeneXpert were phenotypically confirmed by drug susceptibility testing. These results indicated that the Xpert MTB/RIF test can be used as a rapid diagnostic method and can potentially decrease the morbidity associated with diagnostic delay and mistreatment.

Value of Xpert MTB/RIF Using Bronchoalveolar Lavage Fluid for the Diagnosis of Pulmonary Tuberculosis: a Systematic Review and Meta-analysis

The performance of Xpert MTB/RIF using bronchoalveolar lavage fluid (BAL) for the diagnosis of pulmonary tuberculosis (PTB) remains unclear. Therefore, a systematic review/meta-analysis was conducted. Studies published before 31 December 2019 were retrieved from the PubMed, Embase, and Web of Science databases using the keywords "pulmonary tuberculosis," "Xpert MTB/RIF," and "BAL." Two independent evaluators extracted the data and assessed the bias risk of the included studies. A random-effects model was used to calculate the overall sensitivity, specificity, positive and negative likelihood ratios (PLR and NLR, respectively), diagnostic odds ratio (DOR), and the area under the curve (AUC), as well as the respective 95% confidence intervals (CIs). Nineteen trials involving 3,019 participants met the inclusion criteria. Compared to the culture method, the pooled sensitivity, specificity, PLR, NLR, DOR, and the AUC with 95% CIs of Xpert MTB/RIF were 0.87 (0.84 to 0.90), 0.92 (0.91 to 0.93), 10.21 (5.78 to 18.02), 0.16 (0.12 to 0.22), 78.95 (38.59 to 161.53), and 0.9467 (0.9462 to 0.9472), respectively. Relative to the composite reference standard, the observed values were 0.69 (0.65 to 0.72), 0.98 (0.98 to 0.99), 37.50 (18.59 to 75.62), 0.30 (0.21 to 0.43), 171.98 (80.82 to 365.96), and 0.9691 (0.9683 to 0.9699), respectively. All subgroups, except children, showed high sensitivity and specificity. In conclusion, the use of Xpert MTB/RIF in the context of BAL samples has a high diagnostic performance for PTB (except for children) and may serve as an alternative rapid diagnostic tool.

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.

Comparing the impact of genotypic based diagnostic algorithm on time to treatment initiation and treatment outcomes among drug-resistant tuberculosis patients in Amhara region, Ethiopia

Background

To end Tuberculosis (TB) by 2030, early detection and timely treatment of Drug-Resistant Tuberculosis (DR-TB) is vital. The role of rapid, accurate, and sensitive DR-TB diagnostic tool is indispensable to accelerate the TB control program. There are evidence breaks in the time difference and its effect on treatment outcomes among different DR-TB diagnostic tools in Ethiopia. This article aimed to compare the different DR-TB diagnostic tools with time pointers and evaluate their effect on the treatment outcomes.

Method

We performed a retrospective chart review of 574 DR-TB patients from September 2010 to December 2017 to compare the impact of molecular DR-TB diagnostic tests (Xpert MTB/RIF, Line Probe Assay (LPA), and solid culture-based Drug Susceptibility Testing (DST)) on time to diagnosis, treatment initiation, and treatment Outcomes. Kruskual-Wallis test was employed to assess the presence of a significant difference in median time among the DR-TB diagnostic tests. Chi-Square and Fisher exact tests were used to test the presence of relations between treatment outcome and diagnostic tests.

Result

The data of 574 DR-TB patients were included in the analysis. From these, 321, 173, and 80 patients were diagnosed using Xpert MTB/RIF, Line Probe Assay (LPA), and solid culture-based DST, respectively. The median time in a day with (Interquartile range (IQR)) for Xpert MTB/RIF, LPA, and solid culture-based DST was from a first care-seeking visit to diagnosis: 2(0, 9), 4(1, 55), and 70(18, 182), from diagnosis to treatment initiation: 3(1, 8), 33(4, 76), and 44(9, 145), and from a first care-seeking visit to treatment initiation: 4(1, 11), 3(1, 12) and 76(3.75, 191) respectively. The shorter median time was observed in the Xpert MTB/RIF followed by the LPA, and this was statistically significant with a p-value <0.001. There was no statistically significant difference concerning treatment outcomes among the three DST tests.

Conclusion

Xpert MTB/RIF can mitigate the transmission of DR-TB significantly via quick diagnosis and treatment initiation followed by LPA as equating to the solid culture base DST, particularly in smear-positive patients. However, we didn’t see a statistically significant impact in terms of treatment outcomes. Xpert MTB/RIF can be used as the first test to diagnose DR-TB by further complimenting solid culture base DST to grasp the drug-resistance profile.

A recent update of the diagnostic methods for tuberculosis and their applicability in Indonesia: a narrative review

Tuberculosis (TB) is a major global problem, especially with the high prevalence of HIV-TB co-infection. Delayed diagnosis and continual transmission contribute to high mortality in Indonesia, which has the third highest incidence of TB in the world, after China and India. Therefore, early diagnosis is needed to reduce the number of cases and to administer therapy to prevent the transmission of bacteria. The diagnosis of TB remains a challenge in clinical practice due to poor sensitivity and the requirement of skilled staff in microscopic tests, the slow growth Mycobacterium in culture, and the low number of bacilli present in extrapulmonary TB. Despite being the golden standard for TB diagnosis, cultures require 2–8 weeks to grow. Other methods for diagnosing TB include interferon-gamma release assays and serologic tests such as the tuberculin skin test. Recently, the World Health Organization recommended the GeneXpert MTB/RIF assay for diagnosing TB. This review presents the current state of TB epidemiology and various methods for TB diagnosis. In particular, the paper provides an in-depth discussion about the GeneXpert MTB/RIF assay that has been made available recently in selected tertiary hospitals in Indonesia.

Xpert MTB/RIF assay for the diagnosis of rifampicin resistance in different regions: a meta-analysis

Background

To estimate the diagnostic accuracy of Xpert MTB/RIF for rifampicin resistance in different regions, a meta-analysis was carried out.

Methods

Several databases were searched for relevant studies up to March 3, 2019. A bivariate random-effects model was used to estimate the diagnostic accuracy.

Results

We identified 97 studies involving 26,037 samples for the diagnosis of rifampicin resistance. The pooled sensitivity, specificity and AUC of Xpert MTB/RIF for rifampicin resistance detection were 0.93 (95% CI 0.90–0.95), 0.98 (95% CI 0.96–0.98) and 0.99 (95% CI 0.97–0.99), respectively. For different regions, the pooled sensitivity were 0.94(95% CI 0.89–0.97) and 0.92 (95% CI 0.88–0.94), the pooled specificity were 0.98 (95% CI 0.94–1.00) and 0.98 (95% CI 0.96–0.99), and the AUC were 0.99 (95% CI 0.98–1.00) and 0.99 (95% CI 0.97–0.99) in high and middle/low income countries, respectively. The pooled sensitivity were 0.91 (95% CI 0.87–0.94) and 0.91 (95% CI 0.86–0.94), the pooled specificity were 0.98 (95% CI 0.96–0.99) and 0.98 (95% CI 0.96–0.99), and the AUC were 0.98 (95% CI 0.97–0.99) and 0.99 (95% CI 0.97–0.99) in high TB burden and middle/low prevalence countries, respectively.

Conclusions

The diagnostic accuracy of Xpert MTB/RIF for rifampicin resistance detection was excellent.

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.

First genetic characterisation of multidrug-resistant Mycobacterium tuberculosis isolates from Algeria

OBJECTIVES

To characterise the genotypes of multidrug-resistant (MDR) Mycobacterium tuberculosis (MTB) isolated in Algeria, where there is a low MDR-MTB incidence rate.

METHODS

Ten MDR isolates and one resistant to isoniazid were investigated by PCR-Sanger sequencing for 10 loci involved in resistance. Amplicon-based next generation sequencing (NGS) of 15 loci was additionally performed on isolates harbouring novel mutations.

RESULTS

Sanger and amplicon-NGS provided the same results as with GenoType kits. Mutations known to be associated with resistance were described for most isolates: rpoB S531L in seven of 10 rifampicin-R MTB isolates, katG S315T in nine of 11 isoniazid-R, and promoter inhA c-15t in three of 11, embB M306V or M306I in two of two ethambutol-R, rpsL K43R in four of eight or rrs a514c associated with gidB L16R in streptomycin-R, gyrA A90V in the ofloxacin-R pre-XDR isolate. New and rare mutations were also described in rpoB (deletion 512-513-514), katG (S315R, M126I/ R496L), gidB (V124G, E92A, V139A, G37V), and gyrA (P8A). Mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) profiles were similar for three isolates (lineage Cameroon), indicating a possible clonal diffusion in epidemiologically unrelated patients.

CONCLUSIONS

Resistant MTB isolates in Algeria harbour resistance genotypes similar to other countries, but some rare patterns may result from selection and transmission processes inherent to the country.

Influence of single-nucleotide polymorphisms in the IFNG towards susceptibility to tuberculosis in a Pakistani population

Tuberculosis (TB) is a global issue as one-third of the population worldwide is considered to be infected. TB has become a critical public health problem as a result of increasing drug resistance, which poses a challenge to current control strategies. Similar to environmental factors, genetic makeup of the host equally contributes to disease onset. We performed genotypic analysis to examine the relationship between IFNG and TB onset and drug resistance in a Pakistani population comprising 689 subjects. Notable differences were observed in the IFNG polymorphism (+874T/A) between the case and control groups. The frequency of the wild-type genotype (TT) in the controls (43.2%) was significantly higher than in the cases (25.3%) (odds ratio [OR] = 0.77, p < 0.0001), while the mutant genotype frequency (AA) (38.57%) in the cases was significantly higher than in the controls (22.6%) (OR = 1.46, p < 0.0001). The heterozygous genotype frequency (TA) did not significantly differ between the control and case groups. Compared with the controls, the variant allele (A) was approximately twice as frequent in the cases. Females and older people have a higher chance of disease development. Finally, the IFNG (+874T/A) polymorphism was not associated with drug sensitivity or resistance. However, a genotypic polymorphism of IFNG (+874T/A) was significantly associated with susceptibility to TB, and the T allele conferred protection against TB. Additional studies involving larger cohorts are needed to further explore this relationship between genetics and disease vulnerability.

Clinical risk factors associated with multidrug-resistant tuberculosis (MDR-TB) in Mali

Background

MDR-TB is a major threat to global TB control. In 2015, 580,000 were treated for MDR-TB worldwide. The worldwide roll-out of GeneXpert MTB/RIF^® has improved diagnosis of MDR-TB; however, in many countries laboratories are unable to assess drug resistance and clinical predictors of MDR-TB could help target suspected patients. In this study, we aimed to determine the clinical factors associated with MDR-TB in Bamako, Mali.

Methods

We performed a cross-sectional study of 214 patients with presumed MDR-TB admitted to University of Bamako Teaching Hospital, Point-G between 2007 and 2016. We calculated crude and adjusted odds ratios for MDR-TB disease diagnosis using SPSS.

Results

We found that age ≤40years (OR = 2.56. 95% CI: 1.44–4.55), two courses of prior TB treatment (OR = 3.25,95% CI: 1.44–7.30), TB treatment failure (OR = 3.82,95% CI 1.82–7.79), sputum microscopy with 3+ bacilli load (OR = 1.98, 95% CI: 1.13–3.48) and a history of contact with a TB patient (OR = 2.48, 95% CI: 1.11–5.50) were significantly associated with confirmation of MDR-TB disease. HIV was not a risk factor for MDR-TB (aOR = 0.88, 95% CI: 0.34–1.94).

Conclusion

We identified several risk factors that could be used to identify MDR-TB suspects and prioritize them for laboratory confirmation. Prospective studies are needed to understand factors associated with TB incidence and clinical outcomes of TB treatment and disease.

Meta-narrative review of molecular methods for diagnosis and monitoring of multidrug-resistant tuberculosis treatment in adults

Early and accurate diagnosis and rigorous clinical and microbiological monitoring of multidrug-resistant tuberculosis (MDR-TB) treatment can curb morbidity and mortality. While others are still under evaluation, the World Health Organization has recommended few novel molecular methods for MDR-TB diagnosis only. We present current molecular methods for diagnosis and monitoring of MDR-TB treatment in TB-endemic settings. A systematic meta-narrative review was conducted according to the RAMESES recommendations. Electronic databases were searched for relevant articles published in English language from January 2013 to June 2018. Based on predefined criteria, two independent reviewers extracted the key messages from relevant articles. Disagreement between them was resolved through discussion and the involvement of a third reviewer, if needed. Key messages were synthesized to create the meta-narratives for method's accuracy, drug-susceptibility capability, and laboratory infrastructure required. We included 33 articles out of 1213 records retrieved, of which 16 (48%) and 12 (36%) were conducted in high- and low-TB-endemic settings, respectively. Xpert® MTB/RIF, GenoType MTBDRplus, GenoType MTBDRsl, FlouroType™ MTBDR, TB TaqMan® array card, and DNA sequencers can accurately guide effective treatment regimens. Molecular bacterial load assay quantifies mycobactericidal impact of these regimens. Although they present inherent advantages compared to the current standard of care, they carry important limitations to implementation and/or scale-up. Therefore, considerable effort must now be directed to implementation and health systems research to maximize these forecasted benefits for individual patient's health outcomes.

Comparison of GeneXpert MTB/RIF assay and LED-FM microscopy for the diagnosis of extra pulmonary tuberculosis in Khyber Pakhtunkhwa, Pakistan

GeneXpert is one of the recent technological instruments used to diagnose tuberculosis in a short span of time. In this study, the performance of GeneXpert MTB/RIF assay for the diagnosis of extrapulmonary tuberculosis (EPTB) was compared with light-emitting diode Fluorescent Microscopy (LED-FM) in Khyber Pakhtunkhwa, Pakistan. A total of 737 EPTB samples were collected from tuberculosis (TB) suspected patients. Out of these samples, male to female ratio was 53% (n = 390) to 47% (n = 347) respectively. The sensitivity and specificity was 73% and 100% for GeneXpert, while 40% and 100% for LED-FM microscopy. This shows that the sensitivity of GeneXpert is 40–50%, higher than LED-FM microscopy. GeneXpert also detected low number of bacilli as compared to LED-FM microscopy.

Evaluating the diagnostic accuracy of the Xpert MTB/RIF assay on bronchoalveolar lavage fluid: A retrospective study

OBJECTIVE

Limited data on the diagnostic accuracy of the Xpert MTB/RIF assay using bronchoalveolar lavage fluid from patients with suspected pulmonary tuberculosis (PTB) have been reported in China. Therefore, a retrospective study was designed to evaluate the diagnostic accuracy of this assay.

METHODS

Clinical, radiological, and microbiological characteristics of 238 patients with suspected PTB were reviewed retrospectively. The sensitivity, specificity, positive predictive value, and negative predictive value for the diagnosis of active PTB were calculated for the Xpert MTB/RIF assay using TB culture or final diagnosis based on clinical and radiological evaluation as the reference standard.

RESULTS

The sensitivity and specificity of the Xpert MTB/RIF assay were 84.5% and 98.9%, respectively, and those for smear microscopy were 36.2% and 100%, respectively, when compared to the culture method. However, compared with the sensitivity and specificity of final diagnosis based on clinical and radiological evaluation, the sensitivity and specificity of the assay were 72.9% and 98.7%, respectively, which were significantly higher than those for smear microscopy.

CONCLUSIONS

The Xpert MTB/RIF assay on bronchoalveolar lavage fluid could serve as an additional rapid diagnostic tool for PTB in a high TB-burden country and improve the time to TB treatment initiation in patients with PTB.