Equivalence of the GeneXpert System and GeneXpert Omni System for tuberculosis and rifampicin resistance detection.
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ABSTRACT:
SUBMITTER: Georghiou SB
PROVIDER: S-EPMC8682871 | biostudies-literature | 2021
REPOSITORIES: biostudies-literature
Publications
Equivalence of the GeneXpert System and GeneXpert Omni System for tuberculosis and rifampicin resistance detection.
Georghiou Sophia B SB Alagna Riccardo R Cirillo Daniela M DM Carmona Sergio S Ruhwald Morten M Schumacher Samuel G SG
PloS one 20211217 12
A laboratory validation study was conducted to assess the equivalence of Xpert MTB/RIF Ultra testing on the GeneXpert System and the GeneXpert Omni System ('Omni') for tuberculosis and rifampicin resistance. High concordance of the two devices was demonstrated for well-characterized clinical samples as well as control materials, with controls tested on Omni at normal and challenging environmental conditions (i.e. 35°C, 90% relative humidity). Equivalence of the Cts for all probes was also shown. ...[more]
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Project description:BackgroundThe dual challenge of low diagnostic sensitivity of microscopy test and technical challenge of performing a TB culture test poses a problem for case detection and initiation of Tuberculosis (TB) second-line treatment. There is thus need for a rapid, reliable and easily accessible assay. This comparative analysis was performed to assess diagnostic performance characteristics of GeneXpert MTB/RIF and Line Probe Assay (LPA).MethodsThree hundred twenty nine sputum samples of patients across the 47 counties in Kenya suspected to have drug resistant TB were picked and subjected to GeneXpert, LPA and Culture MGIT at the National TB Reference Laboratory. Sensitivity, specificity and predictive values were then determined to assess the performance characteristics of the various assays.ResultsAgainst culture MGIT as the gold standard for TB diagnosis, GeneXpert had a sensitivity, specificity, positive predictive value, and negative predictive value of 78.5, 64.9, 59.4 and 82.2% respectively while LPA had 98.4, 66.0, 65.4 and 98.4%. For diagnosis of rifampicin mono-resistance GeneXpert had a moderate agreement (Kappa 0.59, P < 0.01) (sensitivity 62.50%, specificity 96.50%) while LPA that had almost perfect agreement (Kappa = 0.89, p < 0.01) with a (sensitivity 90.0% and specificity 99.1%).ConclusionLPA has a better performance characteristic to GeneXpert and an alternative to culture with regards to detection of RIF's mono-resistance.
| S-EPMC6794895 | biostudies-literature
Project description:Despite a Mycobacterium tuberculosis control programme and anti-tuberculosis drugs, drug-resistant tuberculosis (DR-TB) is one of the most serious public health issues worldwide. Rapid laboratory diagnosis of M. tuberculosis is needed for the diagnosis of multidrug-resistant (MDR) TB and to find the optimal treatment protocol. The purpose of this study was to detect resistance to rifampicin in new cases of TB using the GeneXpert MTB/RIF (M. tuberculosis/rifampicin) assay and the standard proportional method in west and northwest Iran. In this descriptive cross-sectional study, sputum samples were enrolled and screened for M. tuberculosis using Ziehl-Neelsen stain and mycobacterial culture. Samples from individuals with smear-positive TB were cultured on Lowenstein-Jensen medium; afterwards, the presence of resistance to rifampicin was examined by the GeneXpert MTB/RIF and standard proportional methods. A total of 400 new cases of suspected TB were collected, 162 (40.5%) of which were smear- and culture-positive for M. tuberculosis. The frequencies of rifampicin resistance in new smear-positive TB cases were 3.1% and 4.3% for GeneXpert and standard proportional method, respectively. Sensitivity and specificity of GeneXpert were 71% and 100%, respectively, compared with the proportional method. GeneXpert can be a quick and helpful method for the diagnosis of rifampicin-resistant TB in regions with high rates of DR-TB or MDR-TB. GeneXpert MTB-RIF assay must be used as an early diagnostic method whose results must be confirmed by the standard proportional method. The GeneXpert and proportional methods complement but do not replace each other.
| S-EPMC5547232 | biostudies-other
Project description:IntroductionAntimicrobial resistance in Mycobacterium tuberculosis (MTB) poses a significant challenge to tuberculosis (TB) management worldwide. Rifampicin resistance (RR) has been associated with the rpoB gene mutation. No study was conducted in Tanzania to determine the commonest mutation. The inconsistent findings from various studies support the need to determine whether reported mutation patterns are applicable in our setting. We determined the frequency of rpoB gene mutation and factors associated with RR, which were detected using GeneXpert MTB/RIF assay.MethodsWe conducted a retrospective cross-sectional study involving data from the National Tuberculosis and Leprosy Program database from 2020 to 2022 for cases investigated using GeneXpert MTB/RIF assay. Descriptive analysis was performed to determine the frequency of categorical variables. The chi-square test and logistic regression analysis assessed the relationship between the independent variables and outcome. The 95% confidence interval and a significance level of p<0.05 were used to assess the strength of association.ResultsA total of 56,004 participants had a status of MTB and RR, where 38,705/56,004 (69.11%) were males. Probe E mutation (codon 529-533), 89/219 (40.64%) was predominant. Human immunodeficiency virus (HIV)-positive patients had a higher gene mutation, 134/10601 (1.26%) than HIV-negative, 306/45016 (0.68%) (p<0.001). Patients with both pulmonary and extra-pulmonary TB had about four times greater odds of developing rifampicin resistance (AOR 3.88, 95%CI: 1.80-8.32). RR was nearly nine times higher in previously treated patients than new patients (AOR 8.66, 95% CI: 6.97-10.76). HIV-positive individuals had nearly twice the odds of developing RR than HIV-negative individuals (AOR 1.91, 95%CI: 1.51-2.42).ConclusionThe rate of RR was lower compared to other studies in Tanzania, with probe E mutations the most prevalent. Patients with disseminated TB, HIV co-infection and those with prior exposure to anti-TB had more risk of RR. The findings highlight the need to strengthen surveillance of multidrug-resistant TB among high risk patients.
| S-EPMC11346956 | biostudies-literature
Project description:IntroductionMycobacterium tuberculosis strains with phenotypically susceptible rpoB mutations (rifampicin discordant) have emerged following implementation of rapid molecular drug resistance testing for tuberculosis. Whilst rifampicin resistance is known to be associated with resistance to other rifamycins (rifapentine and rifabutin) as well as isoniazid and pyrazinamide, rifampicin discordant strains have shown high rates of susceptibility to isoniazid and rifabutin. However, pyrazinamide susceptibly testing results have not been reported.Materials and methodsWe evaluated pyrazinamide resistance in 80 rifampicin discordant and 25 rifampicin and isoniazid susceptible isolates from KwaZulu-Natal in South Africa using Mycobacteria Growth Indicator Tube method and sequencing of the pncA. We also compared susceptibility of pyrazinamide with that of isoniazid.ResultsPyrazinamide resistance was found in 6/80 (7.5%) rifampicin discordant isolates. All pyrazinamide resistant isolates were also resistant to isoniazid and pyrazinamide resistance was found to be associated with isoniazid resistance. No pyrazinamide resistance was found among the isoniazid susceptible isolates.ConclusionGiven the low prevalence of pyrazinamide resistance in rifampicin discordant TB, this anti-TB drug still has a significant role in the treatment of these patients. Performing pyrazinamide susceptibility testing remains a challenge, our findings show that isoniazid susceptible isolates are unlikely to be resistant to pyrazinamide among the discordant TB isolates.
| S-EPMC9491533 | biostudies-literature
Project description:BackgroundDrug-resistant tuberculosis continues to be a global public health threat. Ethiopia is one of the high-burden countries for tuberculosis and multi-drug resistant tuberculosis. The estimated annual incidents of tuberculosis were 119 per 100,000 populations in 2021 and the prevalence of multi-drug resistance tuberculosis is about 0.7% among newly diagnosed cases in Ethiopia. On time detection of rifampicin resistance is essential for the management of the disease and earlier treatment initiation. Among the different diagnostic tests; Xpert is widely used for the rapid detection of Mycobacterium tuberculosis and rifampicin resistant in the country. The prevalence of rifampicin resistance-pulmonary tuberculosis varied from locality to locality and the estimated national prevalence of rifampicin resistance pulmonary tuberculosis is not available in the country. Therefore, the aim of this meta-analysis was to summarize the results of available studies and generate pooled prevalence estimate of rifampicin resistance pulmonary tuberculosis in Ethiopia.MethodsLiterature search was carried out using PubMed and Scopus public databases. Original articles conducted in Ethiopia and those containing a prevalence report of rifampicin resistance pulmonary tuberculosis diagnosed by Xpert Mycobacterium tuberculosis/rifampicin resistance assay were included in the meta-analysis. All retrospective and prospective studies published until May 2022 were screened in the study. The methodological qualities of included article were assessed using Joanna Briggs Institute quality assessment tool for cross-sectional studies. Random effect model was used to determine the pooled prevalence of rifampicin resistance pulmonary tuberculosis. Subgroup analysis and regression were carried out across regional states and study designs. Heterogeneity across studies was assessed using I2 test. The data were analyzed using STATA version 14.ResultA total of 1570 titles were identified and 34 studies met the inclusion criteria. Of the total 17,292 pulmonary tuberculosis patients who were identified from the included articles, 1669 were rifampicin resistance pulmonary tuberculosis. The pooled prevalence of rifampicin resistant among pulmonary tuberculosis patients diagnosed with Xpert Mycobacterium tuberculosis/rifampicin resistance assay was 9.67% (95% CI: 8.11-11.24). The highest pooled prevalence was from Oromia11.84% (95% CI: 4.49-19.2%) and the lowest rifampicin resistance was identified in Amhara Regional State, 8.51% (95% CI: 5.96-11.06%). The pooled prevalence rates of rifampicin resistant among pulmonary tuberculosis patients were 10.18% (95% CI: 6.85-13.51) and 9.57% (95% CI: 7.68-11.47) in prospective and retrospective types of cross-sectional studies.ConclusionOur study showed that the pooled prevalence of rifampicin resistance among pulmonary tuberculosis patients was 9.67%. This showed that the occurrence of rifampicin resistance pulmonary tuberculosis among Mycobacterium tuberculosis patients remains high in Ethiopia. Regional state wise, rifampicin resistance variation was small. Further meta-analysis of factors associated with rifampicin resistance among pulmonary tuberculosis patients as well as among extrapulmonary Mycobacterium tuberculosis cases should be carried out.
| S-EPMC10558782 | biostudies-literature
Project description:BackgroundThe increasing prevalence of drug-resistant tuberculosis (TB) infection represents a global public health emergency. We evaluated the usefulness of a newly developed multiplexed, bead-based bioassay (Quantamatrix Multiplexed Assay Platform [QMAP], QuantaMatrix, Seoul, Korea) to rapidly identify the Mycobacterium tuberculosis complex (MTBC) and detect rifampicin (RIF) and isoniazid (INH) resistance-associated mutations.MethodsA total of 200 clinical isolates from respiratory samples were used. Phenotypic anti-TB drug susceptibility testing (DST) results were compared with those of the QMAP system, reverse blot hybridization (REBA) MTB-MDR assay, and gene sequencing analysis.ResultsCompared with the phenotypic DST results, the sensitivity and specificity of the QMAP system were 96.4% (106/110; 95% confidence interval [CI] 0.9072-0.9888) and 80.0% (72/90; 95% CI 0.7052-0.8705), respectively, for RIF resistance and 75.0% (108/144; 95% CI 0.6731-0.8139) and 96.4% (54/56; 95% CI 0.8718-0.9972), respectively, for INH resistance. The agreement rates between the QMAP system and REBA MTB-MDR assay for RIF and INH resistance detection were 97.6% (121/124; 95% CI 0.9282-0.9949) and 99.1% (109/110; 95% CI 0.9453-1.0000), respectively. Comparison between the QMAP system and gene sequencing analysis showed an overall agreement of 100% for RIF resistance (110/110; 95% CI 0.9711-1.0000) and INH resistance (124/124; 95% CI 0.9743-1.0000).ConclusionsThe QMAP system may serve as a useful screening method for identifying and accurately discriminating MTBC from non-tuberculous mycobacteria, as well as determining RIF- and INH-resistant MTB strains.
| S-EPMC6056394 | biostudies-literature
Project description:Control of the global epidemic tuberculosis is severely hampered by the emergence of drug-resistant Mycobacterium tuberculosis strains. Molecular methods offer a more rapid means of characterizing resistant strains than phenotypic drug susceptibility testing. We have developed a molecular method for detection of rifampicin-resistant M. tuberculosis based on padlock probes and magnetic nanobeads. Padlock probes were designed to target the most common mutations associated with rifampicin resistance in M. tuberculosis, i.e. at codons 516, 526 and 531 in the gene rpoB. For detection of the wild type sequence at all three codons simultaneously, a padlock probe and two gap-fill oligonucleotides were used in a novel assay configuration, requiring three ligation events for circularization. The assay also includes a probe for identification of the M. tuberculosis complex. Circularized probes were amplified by rolling circle amplification. Amplification products were coupled to oligonucleotide-conjugated magnetic nanobeads and detected by measuring the frequency-dependent magnetic response of the beads using a portable AC susceptometer.
| S-EPMC3632517 | biostudies-literature
Project description:The disease tuberculosis, caused by Mycobacterium tuberculosis (MTB), remains a major cause of morbidity and mortality in developing countries. The evolution of drug-resistant tuberculosis causes a foremost threat to global health. Most drug-resistant MTB clinical strains are showing resistance to isoniazid and rifampicin (RIF), the frontline anti-tuberculosis drugs. Mutation in rpoB, the beta subunit of DNA-directed RNA polymerase of MTB, is reported to be a major cause of RIF resistance. Amongst mutations in the well-defined 81-base-pair central region of the rpoB gene, mutation at codon 450 (S450L) and 445 (H445Y) is mainly associated with RIF resistance. In this study, we modeled two resistant mutants of rpoB (S450L and H445Y) using Modeller9v10 and performed a docking analysis with RIF using AutoDock4.2 and compared the docking results of these mutants with the wild-type rpoB. The docking results revealed that RIF more effectively inhibited the wild-type rpoB with low binding energy than rpoB mutants. The rpoB mutants interacted with RIF with positive binding energy, revealing the incapableness of RIF inhibition and thus showing resistance. Subsequently, this was verified by molecular dynamics simulations. This in silico evidence may help us understand RIF resistance in rpoB mutant strains.
| S-EPMC4330266 | biostudies-literature
Project description:BackgroundActive tuberculosis (TB) case finding is important as it helps detect pulmonary TB cases missed by the other active screening methods. It requires periodic mass screening in risk population groups such as prisoners and refugees. Unfortunately, in these risk population groups periodic mass screening can be challenging due to lengthy turnaround time (TAT), cost and implementation constraints. The aim of this study was to evaluate a diagnostic algorithm that can reduce the TAT and cost for TB and Rifampicin resistance (RR) detection. The algorithm involves testing with TB-LAMP followed by Xpert MTB/RIF for positive TB-LAMP cases to diagnose TB during mass campaigns in prisons and refugee camps.MethodsThe National Tuberculosis Control Program (NTCP) organized routine TB mass-screening campaigns in 34 prisons and 3 villages with refugees camps in Cameroon in 2019. TB LAMP was used for initial TB diagnosis and all TB-LAMP positive cases tested with the Xpert MTB/RIF assay to determine RR. TAT and cost benefits analysis of the combined use of TB-LAMP and Xpert MTB/RIF assays was determined and compared to the Xpert MTB/RIF assay when used only.ResultsA total of 4075 sputum samples were collected from TB presumptive, 3672 cases in 34 prisons and 403 samples in 3 villages. Of the 4,075 samples screened with TB-LAMP, 135 were TB positive (3.31%) and run on the Xpert MTB/RIF. Of the 135 positives cases, Xpert MTB/RIF revealed 3 were RR (2.22%). The use of TB-LAMP followed by testing with Xpert MTB/RIF for TB and RR detection reduced the TAT by 73.23% in prisons and 74.92% in villages. In addition to a reduced TAT, the two molecular tests used in synergy is cost benefit from year 2 onwards.ConclusionThis study demonstrates the advantages of a diagnostic algorithm based on an initial testing with TB-LAMP followed by testing with Xpert MTB/RIF for TB diagnosis. This approach improved early and rapid TB detection with an added advantage of providing RR status. The proposed algorithm is effective and less costly from the second year of implementation and should be used by TB control programs.
| S-EPMC8895851 | biostudies-literature
Project description:ObjectiveTo determine the cost-effectiveness of Xpert Omni compared with Xpert MTB/Rif for point-of-care diagnosis of tuberculosis among presumptive cases in a low-resource, high burden facility.DesignCost-effectiveness analysis from the provider's perspective.SettingA low-resource, high tuberculosis burden district in Eastern Uganda.ParticipantsA provider's perspective was used, and thus, data were collected from experts in the field of tuberculosis diagnosis purposively selected at the local, subnational and national levels.MethodsA decision analysis model was contracted from TreeAge comparing Xpert MTB/Rif and Xpert Omni. Cost estimation was done using the ingredients' approach. One-way deterministic sensitivity analyses were performed to identify the most influential model parameters.Outcome measureThe outcome measure was incremental cost per additional test diagnosed expressed as the incremental cost-effectiveness ratio.ResultsThe total cost per test for Xpert MTB/Rif was US$14.933. Cartridge and reagent kits contributed to 67% of Xpert MTB/Rif costs. Sample transport costs increased the cost per test of Xpert MTB/Rif by $1.28. The total cost per test for Xpert Omni was $16.153. Cartridge and reagent kits contributed to over 71.2% of Xpert Omni's cost per test. The incremental cost-effectiveness ratio for using Xpert Omni as a replacement for Xpert MTB/Rif was US$30.73 per additional case detected. There was no dominance noted in the cost-effectiveness analysis, meaning no strategy was dominant over the other.ConclusionThe use of Xpert Omni at the point-of-care health facility was more effective but with an increased cost compared with Xpert MTB/Rif at the centralised referral testing facility.
| S-EPMC9403108 | biostudies-literature