Shaheed Vally Omar
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View article: Characterizing the performance of an antibiotic resistance prediction tool, gnomonicus, using a diverse test set of 2,663 Mycobacterium tuberculosis samples
Characterizing the performance of an antibiotic resistance prediction tool, gnomonicus, using a diverse test set of 2,663 Mycobacterium tuberculosis samples Open
Tuberculosis remains a global health problem. Making it easier and quicker to identify which antibiotics an infection is likely to be susceptible to will be a key part of the solution. Whilst whole-genome sequencing offers many advantages,…
View article: Clinical evaluation of a commercial culture-free targeted next-generation sequencing test for diagnosis of drug-resistant tuberculosis
Clinical evaluation of a commercial culture-free targeted next-generation sequencing test for diagnosis of drug-resistant tuberculosis Open
Rapid molecular diagnostics have significantly improved access to tuberculosis (TB) drug resistance detection and reduced turnaround times. However, these tools remain limited in their capacity to generate comprehensive resistance profiles…
View article: Comparing end-user diagnostic outputs from a commercial tNGS pipeline for <i>Mycobacterium tuberculosis</i> drug resistance detection
Comparing end-user diagnostic outputs from a commercial tNGS pipeline for <i>Mycobacterium tuberculosis</i> drug resistance detection Open
BACKGROUNDTargeted next-generation sequencing has emerged as a rapid solution for diagnosing drug-resistant TB (DR-TB) directly from clinical specimens. Updating the bioinformatics software component can lead to rapid improvements in diagn…
View article: Targeted next-generation sequencing for drug-resistant tuberculosis diagnosis: implementation considerations for bacterial load, regimen selection and diagnostic algorithm placement
Targeted next-generation sequencing for drug-resistant tuberculosis diagnosis: implementation considerations for bacterial load, regimen selection and diagnostic algorithm placement Open
Introduction Early and accurate diagnosis of drug-resistant tuberculosis (DR-TB) is essential for improving treatment outcomes. Phenotypic drug susceptibility testing (pDST) is comprehensive but slow, while rapid molecular assays provide r…
Rapidly and reproducibly building a comprehensive catalogue of resistance-associated variants for <i>M. tuberculosis</i> Open
Background Catalogues of genetic variants associated with resistance underpin whole-genome sequencing (WGS)-based predictions of drug susceptibility in Mycobacterium tuberculosis , and are essential for molecular diagnostics and surveillan…
<i>In vitro</i> exposure to clofazimine can select for delamanid and pretomanid resistance in <i>Mycobacterium tuberculosis</i> Open
In vitro experiments with Mycobacterium tuberculosis showed that clofazimine exposure selected for delamanid and pretomanid resistance and mutations in fbiA , fbiC , or fbiD —after the acquisition of Rv0678 mutations where this could be de…
Cost-effectiveness of Targeted Next-Generation Sequencing for Tuberculosis Drug-resistance Testing as an Alternative to the Standard of Care in South Africa Open
Background South Africa faces emerging resistance to tuberculosis drugs like bedaquiline. Phenotypic drug-susceptibility testing (DST), the current reference standard for bedaquiline DST, has long turnaround times. Targeted next-generation…
TB elimination in Southern Africa: overview and critical reflection Open
Despite significant progress, TB remains a major public health challenge in Southern Africa. We highlight the key initiatives in Eswatini, Mozambique and South Africa, which have implemented various interventions, including systematic TB s…
An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance in Mycobacterium tuberculosis using a reproducible algorithmic approach Open
Bedaquiline (BDQ) has only been approved for use for just over a decade and is a key drug for treating multidrug-resistant tuberculosis; however, rising levels of resistance threaten to reduce its effectiveness. Catalogues of mutations ass…
Equitable access to diagnostic resources means one Xpert-Ultra cartridge for all inpatients with HIV being investigated for tuberculosis Open
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Cost-effectiveness of Targeted Next Generation Sequencing for TB drug-resistance testing as an alternative to the standard of care in South Africa Open
Background South Africa faces emerging resistance to key TB drugs, including bedaquiline. Phenotypic drug susceptibility testing (pDST), the current reference standard for bedaquiline DST, while accurate has long turnaround times. Targeted…
View article: Field evaluation of nanopore targeted next-generation sequencing to predict drug-resistant tuberculosis from native sputum in South Africa and Zambia
Field evaluation of nanopore targeted next-generation sequencing to predict drug-resistant tuberculosis from native sputum in South Africa and Zambia Open
Rapid and comprehensive drug susceptibility testing (DST) is essential for diagnosing and treating drug-resistant tuberculosis effectively, and next-generation sequencing can be an effective genotypic DST method. We implemented and evaluat…
An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance in <i>M. tuberculosis</i> using a reproducible algorithmic approach Open
Objectives Bedaquiline (BDQ) has only been approved for use for a little over a decade yet is a key drug for treating multi-drug resistant tuberculosis. Rising levels of resistance threaten, however, to reduce its effec-tiveness. Catalogue…
Systematic review and meta-analysis of protocols and yield of direct from sputum sequencing of<i>Mycobacterium tuberculosis</i> Open
Direct sputum whole genome sequencing (dsWGS) can revolutionize Mycobacterium tuberculosis ( Mtb ) diagnosis by enabling rapid detection of drug resistance and strain diversity without the biohazard of culture. We searched PubMed, Web of S…
Investigating the causal links between inflammatory cytokines and scoliosis through bidirectional Mendelian randomization analysis Open
Background Scoliosis, characterized by a lateral curvature of the spine, affects millions globally. The role of inflammatory cytokines in the pathogenesis of scoliosis is increasingly acknowledged, yet their causal relationships remain poo…
View article: Characterising the performance of an antibiotic resistance prediction tool, gnomonicus, using a diverse testset of 2,663 <i>Mycobacterium tuberculosis</i> samples
Characterising the performance of an antibiotic resistance prediction tool, gnomonicus, using a diverse testset of 2,663 <i>Mycobacterium tuberculosis</i> samples Open
Tuberculosis remains a global health problem. Making it easier and quicker to identify which antibiotics an infection is likely to be susceptible to will be a key part of the solution. Whilst whole-genome sequencing offers many advantages,…
View article: Evaluating culture-free targeted next-generation sequencing for diagnosing drug-resistant tuberculosis: a multicentre clinical study of two end-to-end commercial workflows
Evaluating culture-free targeted next-generation sequencing for diagnosing drug-resistant tuberculosis: a multicentre clinical study of two end-to-end commercial workflows Open
Unitaid.
Extended clinical sample incubation in the cepheid Xpert MTB/XDR test sample reagent: Enhancing flexibility and workflows in high-volume laboratories Open
Cepheid Xpert MTB/RIF ULTRA (ULTRA) and Xpert MTB/XDR are tests for detecting Mycobacterium tuberculosis (MTB) and drug resistance. Both tests involve a sample pre-processing step using the test's sample reagent (SR). The manufacturer reco…
Performance evaluation of the Xpert MTB/XDR test for the detection of drug resistance to <i>Mycobacterium tuberculosis</i> among people diagnosed with tuberculosis in South Africa Open
Drug-resistant tuberculosis (TB) poses a significant public health concern in South Africa due to its complexity in diagnosis, treatment, and management. This study assessed the diagnostic performance of the Xpert MTB/XDR test for detectin…
View article: A composite reference standard is needed for bedaquiline antimicrobial susceptibility testing for<i>Mycobacterium tuberculosis</i>complex
A composite reference standard is needed for bedaquiline antimicrobial susceptibility testing for<i>Mycobacterium tuberculosis</i>complex Open
A composite reference standard minimises false-susceptible AST results for bedaquiline https://bit.ly/3wAVvFm
Missed rifampicin and isoniazid resistance by commercial molecular assays Open
Drug-resistant tuberculosis (TB) has poor outcomes unless resistance is detected early, ideally by commercially available molecular tests. We present a case of occult multidrug-resistant TB where both rifampicin and isoniazid resistance we…
MmpR5 protein truncation and bedaquiline resistance in Mycobacterium tuberculosis isolates from South Africa: a genomic analysis Open
US Centers for Disease Control and Prevention.
Xpert MTB/XDR implementation in South Africa: cost outcomes of centralised vs. decentralised approaches Open
INTRODUCTIONIn South Africa, Xpert ® MTB/RIF Ultra (Ultra) is the recommended diagnostic assay for TB with line-probe assays for first- (LPAfl) and second-line drugs (LPAsl) providing additional drug susceptibility testing (DST) for sample…
45 Evaluation of Drug-Resistant Tuberculosis Guidelines and Outcomes by Treatment Site in South Africa Open
OBJECTIVES/GOALS: DR-TB care in South Africa includes decentralized treatment with shorter, all-oral regimens. Treatment guidelines direct regular clinical and laboratory evaluation to assess patient improvement. We therefore measured sput…