Performance evaluation of Truenat MTB and Truenat MTB-RIF DX assays in comparison to gene XPERT MTB/RIF ultra for the diagnosis of pulmonary tuberculosis in Uganda.

BACKGROUND: The World Health Organization endorsed Truenat MTB rapid molecular assay in 2020 and recommended additional in-country evaluation studies before uptake. We evaluated the accuracy and operational feasibility of Truenat MTB assay (Truenat) in comparison with GeneXpert Ultra and culture. METHODS: In a cross-sectional study of 250 presumptive TB patients, participants were requested to provide a sputum sample on the day of their visit to the clinic. The sputum sample was homogenized and a portion was tested using GeneXpert Ultra as per the routine standard procedure and the other portion was tested using Truenat assay at the clinic laboratory. The second sample portion was processed for Concentrated Fluorescent smear Microscopy (CFM), LJ, and MGIT cultures. Truenat sensitivity and specificity were compared to GeneXpert Ultra and culture. Test performance characteristics and operational feasibility assessment data through interview of the study laboratory staff were also collected and summarized as proportions and percentages. RESULTS: Of the 250 participants recruited in the study, the sensitivity and specificity of Truenat was n/N (%, 95%CI); 66/82 (80.5, 70.2-88.4) and 156/159 (98.1, 94.5-99.6) when compared with Ultra, 50/64 (89.3, 66.0-87.4) and 166/180 (92.2, 87.2-95.6) when compared with LJ, 58/71 (81.7,70.7-89.8) and 131/138 (94.9, 89.8-97.9) when compared to MGIT culture and 59/73 (80.8, 69.9-89.1) and 159/169 (94.1,89.3-97.1) when compared to LJ and/or MGIT culture. The sensitivity of Truenat was lower, 14/23 (60.9, 40.6-82.8) among smear-negative compared to 45/50 (90.0, 78.1-96.6) among smear-positive participants but not different by HIV status. There were no special training needs especially among laboratory personnel with previous GeneXpert /molecular test experience, 19/242 (7.8%) error/invalid, and 12 (17,4%) uninterpretable/indeterminate results mainly for rifampicin resistance determination. However, there were 3 (3.5%) of GeneXpert Ultra indeterminate results. CONCLUSION: Among presumptive TB patients in Uganda, the Truenat assay has high sensitivity and specificity. The Truenat assay has acceptable operational feasibility attributes when compared with the GeneXpert Assay.

Evaluation of Xpert MTB/XDR test for susceptibility testing of Mycobacterium tuberculosis to first and second-line drugs in Uganda.

BACKGROUND: Drug-Resistant Tuberculosis (DR-TB) is one of the major challenges to TB control. DESIGN AND METHODS: This was a blinded, laboratory-based cross-sectional study using sputum samples or culture isolates. Samples were from patients with rifampicin-resistant-TB and/or with high risk for isoniazid (INH) resistance and/or 2nd line fluoroquinolones (FQ) and injectable agents (IAs). The diagnostic accuracy of the Xpert® MTB/XDR test was compared to MGIT960 and the Hain Genotype® MTBDRplus and MDRsl assays (LPA) as reference DST methods. Factors for laboratory uptake of the Xpert® MTB/XDR test were also evaluated. RESULTS: Of the 100 stored sputum samples included in this study, 65/99 (65.6%) were resistant to INH, 5/100 (5.0%) were resistant to FQ and none were resistant to IAs using MGIT960. The sensitivity and specificity, n (%; 95% Confidence Interval, CI) of Xpert® MTB/XDR test for; INH was 58 (89.2; 79.1-95.5) and 30 (88.2; 72.5-96.6) and for FQ; 4 (80.0; 28.3-99.4) and 95 (100; 96.2-100), respectively. Using LPA as a reference standard, a total of 52/98 (53.1%) were resistant to INH, 3/100 (3.0%) to FQ, and none to IA. The sensitivity and specificity, n (%; 95%CI) of Xpert® MTB/XDR test compared to LPA for; INH was 50 (96.1; 86.7-99.5) and 34 (74.0; 58.8-85.7) for FQ 3 (100; 29.2-100) and 96 (99.0; 94.3-99.9) respectively. The factors for laboratory uptake and roll-out of the Xpert® MTB/XDR test included: no training needed for technicians with, and one day for those without, previous Xpert-ultra experience, recording and reporting needs were not different from those of Xpert-ultra, the error rate was 4/100 (4%), one (1%) indeterminate rate and test turn-around-time were 1hr/45 minutes. CONCLUSION: There is high sensitivity and specificity of Xpert® MTB/XDR test for isoniazid and fluoroquinolones. There are acceptable Xpert® MTB/XDR test attributes for the test uptake and roll-out.

Evaluation of Xpert ® MTB/XDR test for susceptibility testing of Mycobacterium tuberculosis to first and second-line drugs in Uganda.

Background: Drug-Resistant Tuberculosis (DR-TB) is one of the key challenges toward TB control. There is an urgent need for rapid and accurate drug susceptibility tests (DST) for the most commonly used 1 st and 2 nd line TB drugs. Design and Methods: In a blinded, laboratory-based cross-sectional study, we set out to validate the performance of the Xpert ® MTB/XDR test for DST of M. tuberculosis . Sputum samples or culture isolates collected between January 2020 and December 2021 from patients with rifampicin resistance -TB and/or with higher suspicion index for isoniazid (INH) resistance and/or 2 nd line fluoroquinolones (FQ) and injectable agents (IAs) were tested using the Xpert ® MTB/XDR test from 11/September 2021 to 26/May /2022. Diagnostic accuracy and factors for laboratory uptake of Xpert ® MTB/XDR test were compared to MGIT960 and the Hain Genotype® MTBDR plus and MDRsl assays (LPA) as reference DST methods. Results: A total of 100 stored sputum samples were included in this study. Of the samples tested using MGIT960, 65/99 (65.6%) were resistant to INH, 5/100 (5.0%) resistant to FQ and none were resistant to IAs. The sensitivity and specificity, n (%; 95%Confidence Interval, CI) of Xpert ® MTB/XDR test for; INH were 58 (89.2; 79.1-95.5) and 30 (88.2; 72.5-96.6), FQ; 4 (80.0; 28.3-99.4) and 95 (100; 96.2-100), respectively. The specificity for AIs was 100 (100; 96.3-100). Using LPA as a reference standard, a total of 52/98 (53.1%) were resistant to INH, 3/100 (3.0%) to FQ, and none to IA. The sensitivity and specificity, n (%; 95%CI) of Xpert ® MTB/XDR test compared to LPA for; INH was 50 (96.1; 86.7-99.5) and 34 (74.0; 58.8-85.7) and FQ 3 (100; 29.2-100) and 96 (99.0; 94.3-99.9) respectively. The specificity of IAs was 96 (100; 96.2-100). The factors for laboratory uptake and roll-out included; no training needed for technicians with previous Xpert-ultra experience and one day for those without, recording and reporting needs were not different from those of Xpert ultra, the error rate was 4/100 (4%), no uninterpretable results reported, test turn-around-time was 1hr/45 minutes and workflow similar to that of the Xpert-ultra test. Conclusion: There is high sensitivity and specificity of Xpert ® MTB/XDR test for isoniazid, fluoroquinolones, and Injectable agents. There are acceptable Xpert ® MTB/XDR test attributes for test uptake and roll-out.

Efficacy of Face Masks Used in Uganda: A Laboratory-Based Inquiry during the COVID-19 Pandemic.

With shortages of face masks being reported worldwide, it is critical to consider alternatives to commercially manufactured face masks. This study aimed to test and compare the efficacy of various makes of locally made or homemade cloth face masks obtained from face-mask vendors in Kampala, Uganda, during the COVID-19 pandemic. The testing was performed to assess the bacterial filtration efficiency (BFE), breathability, distance-dependent fitness, and reusability of the locally made or homemade cloth face masks, while considering the most commonly used non-published face-mask decontamination approaches in Uganda. During laboratory experimentation, modified protocols from various face-mask testing organizations were adopted. Ten different face-mask types were experimented upon; each face-mask type was tested four times for every single test, except for the decontamination protocols involving washing where KN95 and surgical face masks were not included. Among the locally made or homemade cloth face masks, the double-layered cloth face masks (described as F) had better BFE and distance-dependent fitness characteristics, they could be reused, and had good breathability, than the other locally made or homemade cloth face masks. Despite these good qualities, the certainty of these face masks protecting wearers against COVID-19 remains subject to viral filtration efficiency testing.

High prevalence of phenotypic pyrazinamide resistance and its association with pncA gene mutations in Mycobacterium tuberculosis isolates from Uganda.

INTRODUCTION: Susceptibility testing for pyrazinamide (PZA), a cornerstone anti-TB drug is not commonly done in Uganda because it is expensive and characterized with technical difficulties thus resistance to this drug is less studied. Resistance is commonly associated with mutations in the pncA gene and its promoter region. However, these mutations vary geographically and those conferring phenotypic resistance are unknown in Uganda. This study determined the prevalence of PZA resistance and its association with pncA mutations. MATERIALS AND METHODS: Using a cross-sectional design, archived isolates collected during the Uganda national drug resistance survey between 2008-2011 were sub-cultured. PZA resistance was tested by BACTEC Mycobacterial Growth Indicator Tube (MGIT) 960 system. Sequence reads were downloaded from the NCBI Library and bioinformatics pipelines were used to screen for PZA resistance-conferring mutations. RESULTS: The prevalence of phenotypic PZA resistance was found to be 21%. The sensitivity and specificity of pncA sequencing were 24% (95% CI, 9.36-45.13%) and 100% (73.54% - 100.0%) respectively. We identified four mutations associated with PZA phenotypic resistance in Uganda; K96R, T142R, R154G and V180F. CONCLUSION: There is a high prevalence of phenotypic PZA resistance among TB patients in Uganda. The low sensitivity of pncA gene sequencing confirms the already documented discordances suggesting other mechanisms of PZA resistance in Mycobacterium tuberculosis.