Anzaan Dippenaar
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View article: Mycobacterium tuberculosis cultured in MGIT media for whole-genome sequencing application: a systematic literature review and meta-analysis
Mycobacterium tuberculosis cultured in MGIT media for whole-genome sequencing application: a systematic literature review and meta-analysis Open
Whole-genome sequencing (WGS) holds promise for accurate and comprehensive diagnosis of drug resistance in Mycobacterium tuberculosis and identification of transmission events. ‘Early positive cultures’ (EPC) are increasingly used when WGS…
View article: Correction: Assessing the propensity of TB clinical isolates to form viable but non-replicating subpopulations
Correction: Assessing the propensity of TB clinical isolates to form viable but non-replicating subpopulations Open
View article: Targeted and whole genome sequencing for drug resistance and genetic relatedness inference of rifampicin resistant <i>Mycobacterium tuberculosis –</i> an in-depth comparison
Targeted and whole genome sequencing for drug resistance and genetic relatedness inference of rifampicin resistant <i>Mycobacterium tuberculosis –</i> an in-depth comparison Open
Background Challenges in tuberculosis (TB) control have fuelled interest in routine Next-Generation Sequencing (NGS). However, the comparative performance of targeted NGS (tNGS) and whole genome sequencing (WGS) for drug resistance and gen…
View article: Phylogenetic typing of Mycobacterium tuberculosis using WGS and tNGS
Phylogenetic typing of Mycobacterium tuberculosis using WGS and tNGS Open
Background: Strain typing plays a crucial role in understanding transmission dynamics, allowing national TB programs to better “know their epidemic”. Both tNGS and WGS technologies have the potential to provide information regarding strain…
View article: Whole genomic analysis uncovers high genetic diversity of rifampicin-resistant Mycobacterium tuberculosis strains in Botswana
Whole genomic analysis uncovers high genetic diversity of rifampicin-resistant Mycobacterium tuberculosis strains in Botswana Open
Background The emergence of drug-resistant Mycobacterium tuberculosis ( M. tb ) strains remains a threat to tuberculosis (TB) prevention and care. Understanding the drug resistance profiles of circulating strains is crucial for effective T…
View article: Implications of serological, genomic, and epidemiological insights into Mycobacterium tuberculosis mixed infection in a human-managed African elephant (Loxodonta africana)
Implications of serological, genomic, and epidemiological insights into Mycobacterium tuberculosis mixed infection in a human-managed African elephant (Loxodonta africana) Open
Zoonotic and reverse zoonotic tuberculosis pose a risk to human and animal health, especially when individuals are in close contact. Whole genome sequencing (WGS) has led to significant advancements in our comprehension of bacterial diseas…
View article: The DREstimator - Automated Interpretation of Variants in Candidate Resistance Genes in Mycobacterium Tuberculosis to Move Whole Genome Sequencing Towards Clinical Actionability
The DREstimator - Automated Interpretation of Variants in Candidate Resistance Genes in Mycobacterium Tuberculosis to Move Whole Genome Sequencing Towards Clinical Actionability Open
View article: Assessing the propensity of TB clinical isolates to form viable but non-replicating subpopulations
Assessing the propensity of TB clinical isolates to form viable but non-replicating subpopulations Open
Current tuberculosis (TB) treatment is typically effective against drug-susceptible Mycobacterium tuberculosis, but can fail due to acquired drug resistance or phenotypic resistance. M. tuberculosis persisters, a subpopulation of viable bu…
View article: Collaborative learning in the digital age: empowering tuberculosis researchers through virtual training
Collaborative learning in the digital age: empowering tuberculosis researchers through virtual training Open
Integrating whole genome sequencing (WGS) of the Mycobacterium tuberculosis complex into routine care, surveillance, and research in high tuberculosis burden settings remains challenging due to limited resources and skills. While technolog…
View article: A Genome-Focused Investigation Reveals the Emergence of a Mycobacterium tuberculosis Strain Related to Multidrug-Resistant Tuberculosis in the Amazon Region of Brazil
A Genome-Focused Investigation Reveals the Emergence of a Mycobacterium tuberculosis Strain Related to Multidrug-Resistant Tuberculosis in the Amazon Region of Brazil Open
A previous study in Pará, Northern Brazil, described a strain of Mycobacterium tuberculosis with a unique genotype (SIT2517/T1) associated with multidrug-resistant tuberculosis (MDR-TB). To improve our understanding of MDR-TB transmission …
View article: Bridging the gap between molecular and genomic epidemiology in tuberculosis: inferring MIRU-VNTR patterns from genomic data
Bridging the gap between molecular and genomic epidemiology in tuberculosis: inferring MIRU-VNTR patterns from genomic data Open
The transition from MIRU-VNTR-based epidemiology studies in tuberculosis (TB) to genomic epidemiology has transformed how we track transmission. However, short-read sequencing is poor at analyzing repetitive regions such as the MIRU-VNTR l…
View article: Exploring the potential of Oxford Nanopore Technologies sequencing for Mycobacterium tuberculosis sequencing: An assessment of R10 flowcells and V14 chemistry
Exploring the potential of Oxford Nanopore Technologies sequencing for Mycobacterium tuberculosis sequencing: An assessment of R10 flowcells and V14 chemistry Open
Oxford Nanopore Technologies (ONT) sequencing is a promising technology. We assessed the performance of the new ONT R10 flowcells and V14 rapid sequencing chemistry for Mtb whole genome sequencing of Mycobacterium tuberculosis ( Mtb ) DNA …
View article: Droplet based whole genome amplification for sequencing minute amounts of purified Mycobacterium tuberculosis DNA
Droplet based whole genome amplification for sequencing minute amounts of purified Mycobacterium tuberculosis DNA Open
View article: Droplet-based whole genome amplification: a novel approach for sequencing minute amounts of Mycobacterium tuberculosis DNA
Droplet-based whole genome amplification: a novel approach for sequencing minute amounts of Mycobacterium tuberculosis DNA Open
Implementation of whole genome sequencing (WGS) for patient care is hindered by limited Mycobacterium tuberculosis (Mtb) in clinical specimens and slow Mtb growth. We evaluated droplet multiple displacement amplification (dMDA) for amplifi…
View article: Whole genome sequencing improves the discrimination between Mycobacterium bovis strains on the southern border of Kruger National Park, South Africa
Whole genome sequencing improves the discrimination between Mycobacterium bovis strains on the southern border of Kruger National Park, South Africa Open
Mycobacterium bovis isolates from MP were hypothesized to be directly linked to KNP wildlife, based on spoligotyping. However, WGS indicated more complex epidemiology. The presence of two distinct clades which were genetically disti…
View article: Bedaquiline resistance in patients with drug-resistant tuberculosis in Cape Town, South Africa: a retrospective longitudinal cohort study
Bedaquiline resistance in patients with drug-resistant tuberculosis in Cape Town, South Africa: a retrospective longitudinal cohort study Open
Doris Duke Charitable Foundation, US National Institute of Allergy and Infectious Diseases, South African Medical Research Council, National Research Foundation, Research Foundation Flanders, Stellenbosch University Faculty of Medicine Hea…
View article: The Detection of Mutations and Genotyping of Drug-Resistant Mycobacterium tuberculosis Strains Isolated from Patients in the Rural Eastern Cape Province
The Detection of Mutations and Genotyping of Drug-Resistant Mycobacterium tuberculosis Strains Isolated from Patients in the Rural Eastern Cape Province Open
Drug-resistant tuberculosis (DR-TB) is still a major public health concern in South Africa. Mutations in M. tuberculosis can cause varying levels of phenotypic resistance to anti-TB medications. There have been no prior studies on gene mut…
View article: Microfluidic Capture of Mycobacterium tuberculosis from Clinical Samples for Culture-Free Whole-Genome Sequencing
Microfluidic Capture of Mycobacterium tuberculosis from Clinical Samples for Culture-Free Whole-Genome Sequencing Open
Diagnosis of tuberculosis is effective using molecular methods; however, a comprehensive characterization of the resistance profile of Mycobacterium tuberculosis often requires culturing and phenotypic drug susceptibility testing or cultur…
View article: Detection of Mutations and Genotyping of Drug-Resistant <em>Mycobacterium tuberculosis</em> Strains Isolated from Patients in Rural Eastern Cape Province
Detection of Mutations and Genotyping of Drug-Resistant <em>Mycobacterium tuberculosis</em> Strains Isolated from Patients in Rural Eastern Cape Province Open
Drug-resistant tuberculosis (DR-TB) is still a major public health concern in South Africa. Mutations in M. tuberculosis can cause varying levels of phenotypic resistance to anti-TB medications. There have been no prior studies on gene mut…
View article: Effect of compensatory evolution in the emergence and transmission of rifampicin-resistant Mycobacterium tuberculosis in Cape Town, South Africa: a genomic epidemiology study
Effect of compensatory evolution in the emergence and transmission of rifampicin-resistant Mycobacterium tuberculosis in Cape Town, South Africa: a genomic epidemiology study Open
View article: The impact of genotype on the phenotype of Mycobacterium tuberculosis ΔsufR mutants
The impact of genotype on the phenotype of Mycobacterium tuberculosis ΔsufR mutants Open
Iron-sulphur (FeS) cluster biogenesis is a tightly regulated process in vivo. In Mycobacterium tuberculosis (Mtb), SufR functions as a transcriptional repressor of the operon encoding the primary FeS cluster biogenesis system. Previously, …
View article: Detection of Mutations and Genotyping of Drug-Resistant <em>Mycobacterium tuberculosis</em> Strains Isolated from Patients in Rural Eastern Cape Province
Detection of Mutations and Genotyping of Drug-Resistant <em>Mycobacterium tuberculosis</em> Strains Isolated from Patients in Rural Eastern Cape Province Open
In South Africa, drug-resistant tuberculosis (DR-TB) continues to be a serious public health issue. Gene mutations and the genotyping of DR-TB in a rural Eastern Cape Province have not previously been studied. We detected prevalent mutatio…
View article: Detection of Mutations and Genotyping of Drug-Resistant Mycobacterium Tuberculosis Strains Isolated From Patients in Rural Eastern Cape Province
Detection of Mutations and Genotyping of Drug-Resistant Mycobacterium Tuberculosis Strains Isolated From Patients in Rural Eastern Cape Province Open
Drug-resistant tuberculosis (DR-TB) remains a major public health problem in South Africa. Gene mu-tations and the genotyping of DR-TB in a rural Eastern Cape Province have not previously been studied. Hence, we sought to detect prevalent …
View article: Spatial Distribution of Drug-Resistant Mycobacterium tuberculosis Infections in Rural Eastern Cape Province of South Africa
Spatial Distribution of Drug-Resistant Mycobacterium tuberculosis Infections in Rural Eastern Cape Province of South Africa Open
Tuberculosis (TB), an infectious airborne disease caused by Mycobacterium tuberculosis (Mtb), is a serious public health threat reported as the leading cause of morbidity and mortality worldwide. South Africa is a high-TB-burden country wi…
View article: Emergence of Canonical and Noncanonical Genomic Variants following <i>In Vitro</i> Exposure of Clinical Mycobacterium tuberculosis Strains to Bedaquiline or Clofazimine
Emergence of Canonical and Noncanonical Genomic Variants following <i>In Vitro</i> Exposure of Clinical Mycobacterium tuberculosis Strains to Bedaquiline or Clofazimine Open
In Mycobacterium tuberculosis , bedaquiline and clofazimine resistance occurs primarily through Rv0678 variants, a gene encoding a repressor protein that regulates mmpS5 / mmpL5 efflux pump gene expression. Despite the shared effect of bot…
View article: New insights on tuberculosis transmission dynamics and drug susceptibility profiles among the prison population in Southern Brazil based on whole-genome sequencing
New insights on tuberculosis transmission dynamics and drug susceptibility profiles among the prison population in Southern Brazil based on whole-genome sequencing Open
WGS demonstrated the recent transmission of TB within prisons in Brazil. The high movement among prisoners seems to be related to the transmission of the same M. tuberculosis strain within the prison system. Screening for TB before and aft…
View article: New insights on tuberculosis transmission dynamics and drug susceptibility profiles among the prison population in Southern Brazil based on whole-genome sequencing
New insights on tuberculosis transmission dynamics and drug susceptibility profiles among the prison population in Southern Brazil based on whole-genome sequencing Open
Background: The rate of tuberculosis (TB) infection among the prison population (PP) in Brazil is 28 times higher than that in the general population, and prison environment favors the spread of TB. Objective: To describe TB transmission d…
View article: Spatial Distribution and Clustering of Drug-Resistant <em>Mycobacterium Tuberculosis</em> Infections in Rural Eastern Cape Province of South Africa
Spatial Distribution and Clustering of Drug-Resistant <em>Mycobacterium Tuberculosis</em> Infections in Rural Eastern Cape Province of South Africa Open
Tuberculosis (TB), an infectious airborne disease caused by Mycobacterium tuberculosis (Mtb), is a serious public health threat reported as the leading cause of morbidity and mortality worldwide. South Africa is a high TB burden country wi…
View article: Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis
Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis Open
View article: Bedaquiline resistance probability to guide treatment decision making for rifampicin-resistant tuberculosis: insights from a qualitative study
Bedaquiline resistance probability to guide treatment decision making for rifampicin-resistant tuberculosis: insights from a qualitative study Open