Robin M. Warren

DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University

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JoVE Journal Publications

ArticleTotal : 2	Year
Publication title	2025
Publication title	2026

Other Publications

Article	Year
Multiple Mycobacterium tuberculosis strains in early cultures from patients in a high-incidence community setting. Journal of clinical microbiology\| PubMed ID: 12149324	2002
Stability of variable-number tandem repeats of mycobacterial interspersed repetitive units from 12 loci in serial isolates of Mycobacterium tuberculosis. Journal of clinical microbiology\| PubMed ID: 12454152	2002
Patients with active tuberculosis often have different strains in the same sputum specimen. American journal of respiratory and critical care medicine\| PubMed ID: 14701710	2004
Proportion of tuberculosis transmission that takes place in households in a high-incidence area. Lancet (London, England)\| PubMed ID: 14738796	2004
Stability of polymorphic GC-rich repeat sequence-containing regions of Mycobacterium tuberculosis. Journal of clinical microbiology\| PubMed ID: 15004103	2004
Transmission of tuberculosis in a high incidence urban community in South Africa. International journal of epidemiology\| PubMed ID: 15082639	2004
Rate of reinfection tuberculosis after successful treatment is higher than rate of new tuberculosis. American journal of respiratory and critical care medicine\| PubMed ID: 15831840	2005
Reinfection and mixed infection cause changing Mycobacterium tuberculosis drug-resistance patterns. American journal of respiratory and critical care medicine\| PubMed ID: 15947286	2005
Recurrent culture-confirmed tuberculosis in human immunodeficiency virus-infected children. The Pediatric infectious disease journal\| PubMed ID: 16094221	2005
Drug resistance in Mycobacterium tuberculosis. Current issues in molecular biology\| PubMed ID: 16878362	2006
Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. BMC evolutionary biology\| PubMed ID: 17105670	2006
Antimicrobial resistance in tuberculosis: an international perspective. Expert review of anti-infective therapy\| PubMed ID: 17140353	2006
Absence of an association between Mycobacterium tuberculosis genotype and clinical features in children with tuberculous meningitis. The Pediatric infectious disease journal\| PubMed ID: 17195699	2007
The role of IS6110 in the evolution of Mycobacterium tuberculosis. Tuberculosis (Edinburgh, Scotland)\| PubMed ID: 17627889	2007
A threshold value for the time delay to TB diagnosis. PloS one\| PubMed ID: 17712405	2007
Creation and characterisation of a high-copy-number version of the pAL5000 mycobacterial replicon. Tuberculosis (Edinburgh, Scotland)\| PubMed ID: 17888739	2007
Pulmonary infection due to the dassie bacillus (Mycobacterium tuberculosis complex sp.) in a free-living dassie (rock hyrax-Procavia capensis) from South Africa. Tuberculosis (Edinburgh, Scotland)\| PubMed ID: 17933586	2008
Application of sensitive and specific molecular methods to uncover global dissemination of the major RDRio Sublineage of the Latin American-Mediterranean Mycobacterium tuberculosis spoligoty... Journal of clinical microbiology\| PubMed ID: 18234868	2008
Detection of natural infection with Mycobacterium intracellulare in healthy wild-caught Chacma baboons (Papio ursinus) by ESAT-6 and CFP-10 IFN-gamma ELISPOT tests following a tuberculosis o... BMC microbiology\| PubMed ID: 18254982	2008
Pulmonary infection due to Mycobacterium goodii in a spotted hyena (Crocuta crocuta) from South Africa. Journal of wildlife diseases\| PubMed ID: 18263830	2008
Detection of Mycobacterium tuberculosis infection in chacma baboons (Papio ursinus) using the QuantiFERON-TB gold (in-tube) assay. Journal of medical primatology\| PubMed ID: 19627435	2009
Multiple, independent, identical IS6110 insertions in Mycobacterium tuberculosis PPE genes. Tuberculosis (Edinburgh, Scotland)\| PubMed ID: 19734099	2009
Evidence for a rapid rate of molecular evolution at the hypervariable and immunogenic Mycobacterium tuberculosis PPE38 gene region. BMC evolutionary biology\| PubMed ID: 19769792	2009
Emergence of increased resistance and extensively drug-resistant tuberculosis despite treatment adherence, South Africa. Emerging infectious diseases\| PubMed ID: 20113557	2010
Using a label-free proteomics method to identify differentially abundant proteins in closely related hypo- and hypervirulent clinical Mycobacterium tuberculosis Beijing isolates. Molecular & cellular proteomics : MCP\| PubMed ID: 20190197	2010
Detection of Mycobacterium kansasii infection in a rhesus macaque (Macaca mulatta) using a modified QuantiFERON-TB Gold assay. Veterinary immunology and immunopathology\| PubMed ID: 20394987	2010
Insertion element IS6110-based restriction fragment length polymorphism genotyping of Mycobacterium tuberculosis. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 20560064	2009
Novel Mycobacterium tuberculosis complex pathogen, M. mungi. Emerging infectious diseases\| PubMed ID: 20678329	2010
Rifampicin Resistant Tuberculosis in Lesotho: Diagnosis, Treatment Initiation and Outcomes. Scientific reports\| PubMed ID: 32024860	2020
Molecular detection of mixed infections of Mycobacterium tuberculosis strains in sputum samples from patients in Karonga District, Malawi. Journal of clinical microbiology\| PubMed ID: 20962138	2010
Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database. Molecular & cellular proteomics : MCP\| PubMed ID: 21030493	2011
The non-clonality of drug resistance in Beijing-genotype isolates of Mycobacterium tuberculosis from the Western Cape of South Africa. BMC genomics\| PubMed ID: 21110864	2010
Rifampicin reduces susceptibility to ofloxacin in rifampicin-resistant Mycobacterium tuberculosis through efflux. American journal of respiratory and critical care medicine\| PubMed ID: 21512166	2011
Modification of the QuantiFERON-TB Gold (In-Tube) assay for the diagnosis of Mycobacterium bovis infection in African buffaloes (Syncerus caffer). Veterinary immunology and immunopathology\| PubMed ID: 21561669	2011
Mutations in the rrs A1401G gene and phenotypic resistance to amikacin and capreomycin in Mycobacterium tuberculosis. Microbial drug resistance (Larchmont, N.Y.)\| PubMed ID: 21732736	2012
Treatment outcomes of isoniazid-resistant tuberculosis patients, Western Cape Province, South Africa. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America\| PubMed ID: 21810750	2011
Emergence and treatment of multidrug resistant (MDR) and extensively drug-resistant (XDR) tuberculosis in South Africa. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases\| PubMed ID: 21839855	2012
Xpert MTB/RIF for rapid diagnosis of tuberculous lymphadenitis from fine-needle-aspiration biopsy specimens. Journal of clinical microbiology\| PubMed ID: 21880965	2011
SNP/RD typing of Mycobacterium tuberculosis Beijing strains reveals local and worldwide disseminated clonal complexes. PloS one\| PubMed ID: 22162765	2011
Population structure of multi- and extensively drug-resistant Mycobacterium tuberculosis strains in South Africa. Journal of clinical microbiology\| PubMed ID: 22170931	2012
gyrA mutations and phenotypic susceptibility levels to ofloxacin and moxifloxacin in clinical isolates of Mycobacterium tuberculosis. The Journal of antimicrobial chemotherapy\| PubMed ID: 22357804	2012
Comparative analysis of Mycobacterium tuberculosis pe and ppe genes reveals high sequence variation and an apparent absence of selective constraints. PloS one\| PubMed ID: 22496726	2012
Development of a diagnostic gene expression assay for tuberculosis and its use under field conditions in African buffaloes (Syncerus caffer). Veterinary immunology and immunopathology\| PubMed ID: 22683147	2012
Characterization of Mycobacterium orygis. Emerging infectious diseases\| PubMed ID: 23017199	2012
Mixed-strain mycobacterium tuberculosis infections and the implications for tuberculosis treatment and control. Clinical microbiology reviews\| PubMed ID: 23034327	2012
Infection of African buffalo (Syncerus caffer) by oryx bacillus, a rare member of the antelope clade of the Mycobacterium tuberculosis complex. Journal of wildlife diseases\| PubMed ID: 23060486	2012
Implementation of genotype MTBDRplus reduces time to multidrug-resistant tuberculosis therapy initiation in South Africa. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America\| PubMed ID: 23090928	2013
embB306 mutations as molecular indicators to predict ethambutol susceptibility in Mycobacterium tuberculosis. Chemotherapy\| PubMed ID: 23171739	2012
The rationale for using rifabutin in the treatment of MDR and XDR tuberculosis outbreaks. PloS one\| PubMed ID: 23527189	2013
Epidemic spread of multidrug-resistant tuberculosis in Johannesburg, South Africa. Journal of clinical microbiology\| PubMed ID: 23554196	2013
Emergence and spread of extensively and totally drug-resistant tuberculosis, South Africa. Emerging infectious diseases\| PubMed ID: 23622714	2013
Sulfatase-activated fluorophores for rapid discrimination of mycobacterial species and strains. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 23878250	2013
Population structure of mixed Mycobacterium tuberculosis infection is strain genotype and culture medium dependent. PloS one\| PubMed ID: 23936157	2013
Associations between human leukocyte antigen class I variants and the Mycobacterium tuberculosis subtypes causing disease. The Journal of infectious diseases\| PubMed ID: 23945374	2014
Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nature genetics\| PubMed ID: 23995135	2013
Programmatically selected multidrug-resistant strains drive the emergence of extensively drug-resistant tuberculosis in South Africa. PloS one\| PubMed ID: 24058399	2013
Characterization of W-Beijing isolates of Mycobacterium tuberculosis from the Western Cape. Vaccine\| PubMed ID: 24144471	2013
Proposal of a consensus set of hypervariable mycobacterial interspersed repetitive-unit-variable-number tandem-repeat loci for subtyping of Mycobacterium tuberculosis Beijing isolates. Journal of clinical microbiology\| PubMed ID: 24172154	2014
Novel cause of tuberculosis in meerkats, South Africa. Emerging infectious diseases\| PubMed ID: 24274183	2013
Alcohol, hospital discharge, and socioeconomic risk factors for default from multidrug resistant tuberculosis treatment in rural South Africa: a retrospective cohort study. PloS one\| PubMed ID: 24349518	2013
Moxifloxacin retains antimycobacterial activity in the presence of gyrA mutations. Antimicrobial agents and chemotherapy\| PubMed ID: 24514091	2014
Energy metabolism and drug efflux in Mycobacterium tuberculosis. Antimicrobial agents and chemotherapy\| PubMed ID: 24614376	2014
The temporal dynamics of relapse and reinfection tuberculosis after successful treatment: a retrospective cohort study. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America\| PubMed ID: 24647020	2014
Agreement between assays of cell-mediated immunity utilizing Mycobacterium bovis-specific antigens for the diagnosis of tuberculosis in African buffaloes (Syncerus caffer). Veterinary immunology and immunopathology\| PubMed ID: 24794136	2014
Rapid sequencing of the Mycobacterium tuberculosis pncA gene for detection of pyrazinamide susceptibility. Journal of clinical microbiology\| PubMed ID: 25165081	2014
Rapid diagnosis of pediatric mycobacterial lymphadenitis using fine needle aspiration biopsy. The Pediatric infectious disease journal\| PubMed ID: 25361020	2014
The evaluation of candidate biomarkers of cell-mediated immunity for the diagnosis of Mycobacterium bovis infection in African buffaloes (Syncerus caffer). Veterinary immunology and immunopathology\| PubMed ID: 25464825	2014
Genetic diversity of Mycobacterium tuberculosis isolated from tuberculosis patients in the Serengeti ecosystem in Tanzania. Tuberculosis (Edinburgh, Scotland)\| PubMed ID: 25522841	2015
Phosphoproteomics analysis of a clinical Mycobacterium tuberculosis Beijing isolate: expanding the mycobacterial phosphoproteome catalog. Frontiers in microbiology\| PubMed ID: 25713560	2015
Fighting an old disease with next-generation sequencing. eLife\| PubMed ID: 25732038	2015
Association of toll-like receptors with susceptibility to tuberculosis suggests sex-specific effects of TLR8 polymorphisms. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases\| PubMed ID: 26160538	2015
A Global Perspective on Pyrazinamide Resistance: Systematic Review and Meta-Analysis. PloS one\| PubMed ID: 26218737	2015
Mycobacterium tuberculosis pncA Polymorphisms That Do Not Confer Pyrazinamide Resistance at a Breakpoint Concentration of 100 Micrograms per Milliliter in MGIT. Journal of clinical microbiology\| PubMed ID: 26292310	2015
Efflux pump inhibitors: targeting mycobacterial efflux systems to enhance TB therapy. The Journal of antimicrobial chemotherapy\| PubMed ID: 26472768	2016
Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates. BMC genomics\| PubMed ID: 26496891	2015
Whole genome sequence analysis of Mycobacterium suricattae. Tuberculosis (Edinburgh, Scotland)\| PubMed ID: 26542221	2015
MDR tuberculosis control: time to change the dogma? The Lancet. Respiratory medicine\| PubMed ID: 26597129	2015
Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value. American journal of respiratory and critical care medicine\| PubMed ID: 26910495	2016
Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages. BMC genomics\| PubMed ID: 26923687	2016
The plasmid-mediated evolution of the mycobacterial ESX (Type VII) secretion systems. BMC evolutionary biology\| PubMed ID: 26979252	2016
The stability of plasma IP-10 enhances its utility for the diagnosis of Mycobacterium bovis infection in African buffaloes (Syncerus caffer). Veterinary immunology and immunopathology\| PubMed ID: 27090621	2016
Mapping of Mycobacterium tuberculosis Complex Genetic Diversity Profiles in Tanzania and Other African Countries. PloS one\| PubMed ID: 27149626	2016
Prevalence of pyrazinamide resistance across the spectrum of drug resistant phenotypes of Mycobacterium tuberculosis. Tuberculosis (Edinburgh, Scotland)\| PubMed ID: 27450014	2016
Implementation of new tools for multidrug-resistant tuberculosis detection and control. International journal of mycobacteriology\| PubMed ID: 28043620	2016
Outcomes, infectiousness, and transmission dynamics of patients with extensively drug-resistant tuberculosis and home-discharged patients with programmatically incurable tuberculosis: a pros... The Lancet. Respiratory medicine\| PubMed ID: 28109869	2017
Implications of Failure to Routinely Diagnose Resistance to Second-Line Drugs in Patients With Rifampicin-Resistant Tuberculosis on Xpert MTB/RIF: A Multisite Observational Study. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America\| PubMed ID: 28199520	2017
The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis. The Lancet. Respiratory medicine\| PubMed ID: 28344011	2017
Progenitor strain introduction of Mycobacterium bovis at the wildlife-livestock interface can lead to clonal expansion of the disease in a single ecosystem. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases\| PubMed ID: 28412523	2017
Exploring the potential of T7 bacteriophage protein Gp2 as a novel inhibitor of mycobacterial RNA polymerase. Tuberculosis (Edinburgh, Scotland)\| PubMed ID: 28802409	2017
Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates. Journal of proteome research\| PubMed ID: 28820946	2017
Mycobacterium tuberculosis Subculture Results in Loss of Potentially Clinically Relevant Heteroresistance. Antimicrobial agents and chemotherapy\| PubMed ID: 28893776	2017
Isoniazid Resistance and Dosage as Treatment for Patients with Tuberculosis. Current drug metabolism\| PubMed ID: 29086682	2017
Mycobacterial genomic DNA from used Xpert MTB/RIF cartridges can be utilised for accurate second-line genotypic drug susceptibility testing and spoligotyping. Scientific reports\| PubMed ID: 29093504	2017
A standardised method for interpreting the association between mutations and phenotypic drug resistance in . The European respiratory journal\| PubMed ID: 29284687	2017
Mutations in ppe38 block PE_PGRS secretion and increase virulence of Mycobacterium tuberculosis. Nature microbiology\| PubMed ID: 29335553	2018
Genetic diversity and potential routes of transmission of Mycobacterium bovis in Mozambique. PLoS neglected tropical diseases\| PubMed ID: 29346413	2018
Mycobacterial nucleoid associated proteins: An added dimension in gene regulation. Tuberculosis (Edinburgh, Scotland)\| PubMed ID: 29523320	2018
Papanicolaou induced fluorescence, Ziehl-Neelsen and Auramine O stains on lymph node fine needle aspiration biopsy specimens from children: A comparative study. Diagnostic cytopathology\| PubMed ID: 29722172	2018
Accuracy of whole genome sequencing versus phenotypic (MGIT) and commercial molecular tests for detection of drug-resistant Mycobacterium tuberculosis isolated from patients in Brazil and Mo... Tuberculosis (Edinburgh, Scotland)\| PubMed ID: 29779775	2018
Drug-Penetration Gradients Associated with Acquired Drug Resistance in Patients with Tuberculosis. American journal of respiratory and critical care medicine\| PubMed ID: 29877726	2018
IP-10: A potential biomarker for detection of Mycobacterium bovis infection in warthogs (Phacochoerus africanus). Veterinary immunology and immunopathology\| PubMed ID: 29914681	2018
Diagnostic Accuracy and Utility of FluoroType MTBDR, a New Molecular Assay for Multidrug-Resistant Tuberculosis. Journal of clinical microbiology\| PubMed ID: 29976588	2018
Rv1460, a SufR homologue, is a repressor of the suf operon in Mycobacterium tuberculosis. PloS one\| PubMed ID: 29979728	2018
The potential use of rifabutin for treatment of patients diagnosed with rifampicin-resistant tuberculosis. The Journal of antimicrobial chemotherapy\| PubMed ID: 29982641	2018
Unexpected Genomic and Phenotypic Diversity of Mycobacterium africanum Lineage 5 Affects Drug Resistance, Protein Secretion, and Immunogenicity. Genome biology and evolution\| PubMed ID: 30010947	2018
Geospatial distribution of Mycobacterium tuberculosis genotypes in Africa. PloS one\| PubMed ID: 30067763	2018
Mixed Mycobacterium tuberculosis-Strain Infections Are Associated With Poor Treatment Outcomes Among Patients With Newly Diagnosed Tuberculosis, Independent of Pretreatment Heteroresistance. The Journal of infectious diseases\| PubMed ID: 30085153	2018
Using routinely collected laboratory data to identify high rifampicin-resistant tuberculosis burden communities in the Western Cape Province, South Africa: A retrospective spatiotemporal ana... PLoS medicine\| PubMed ID: 30130377	2018
Impact of alcohol consumption on tuberculosis treatment outcomes: a prospective longitudinal cohort study protocol. BMC infectious diseases\| PubMed ID: 30268101	2018
Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase. Scientific reports\| PubMed ID: 30337678	2018
Transmission of drug-resistant tuberculosis in HIV-endemic settings. The Lancet. Infectious diseases\| PubMed ID: 30554996	2019
Parallel testing increases detection of Mycobacterium bovis-infected African buffaloes (Syncerus caffer). Veterinary immunology and immunopathology\| PubMed ID: 30596379	2018
Linezolid Pharmacokinetics in South African Patients with Drug-Resistant Tuberculosis and a High Prevalence of HIV Coinfection. Antimicrobial agents and chemotherapy\| PubMed ID: 30617089	2019
Spatial Network Mapping of Pulmonary Multidrug-Resistant Tuberculosis Cavities Using RNA Sequencing. American journal of respiratory and critical care medicine\| PubMed ID: 30694692	2019
Prevalence, Predictors, and Successful Treatment Outcomes of Xpert MTB/RIF-identified Rifampicin-resistant Tuberculosis in Post-conflict Eastern Democratic Republic of the Congo, 2012-2017: ... Clinical infectious diseases : an official publication of the Infectious Diseases Society of America\| PubMed ID: 30759187	2019
The microbiome and tuberculosis: state of the art, potential applications, and defining the clinical research agenda. The Lancet. Respiratory medicine\| PubMed ID: 30910543	2019
Deciphering Within-Host Microevolution of through Whole-Genome Sequencing: the Phenotypic Impact and Way Forward. Microbiology and molecular biology reviews : MMBR\| PubMed ID: 30918049	2019
Genetic diversity of Mycobacterium tuberculosis strains circulating in Botswana. PloS one\| PubMed ID: 31063472	2019
Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nature reviews. Microbiology\| PubMed ID: 31209399	2019
Recovery of from positive mycobacterium growth indicator tubes stored at room temperature for up to 6 years in low-income and High-Tuberculosis-Burden Country. International journal of mycobacteriology\| PubMed ID: 31210164	2019
Evolution of rifampicin treatment for tuberculosis. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases\| PubMed ID: 31247337	2019
Whole genome sequencing provides additional insights into recurrent tuberculosis classified as endogenous reactivation by IS6110 DNA fingerprinting. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases\| PubMed ID: 31276801	2019
On the Impact of the Pangenome and Annotation Discrepancies While Building Protein Sequence Databases for Bacteria Proteogenomics. Frontiers in microbiology\| PubMed ID: 31281302	2019
Parallel measurement of IFN-γ and IP-10 in QuantiFERON®-TB Gold (QFT) plasma improves the detection of Mycobacterium bovis infection in African buffaloes (Syncerus caffer). Preventive veterinary medicine\| PubMed ID: 31311648	2019
Xpert MTB/RIF performance to diagnose tuberculosis and rifampicin resistance in a reference centre in southern Brazil. ERJ open research\| PubMed ID: 31404338	2019
Utility of Targeted, Amplicon-Based Deep Sequencing To Detect Resistance to First-Line Tuberculosis Drugs in Botswana. Antimicrobial agents and chemotherapy\| PubMed ID: 31405858	2019
Distinct serum biosignatures are associated with different tuberculosis treatment outcomes. Tuberculosis (Edinburgh, Scotland)\| PubMed ID: 31434026	2019
Impact of Mycobacterium bovis-induced pathology on interpretation of QuantiFERON®-TB Gold assay results in African buffaloes (Syncerus caffer). Veterinary immunology and immunopathology\| PubMed ID: 31470250	2019
The Lancet Respiratory Medicine Commission: 2019 update: epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant and incurable tuberculosis. The Lancet. Respiratory medicine\| PubMed ID: 31486393	2019
Switching to bedaquiline for treatment of rifampicin-resistant tuberculosis in South Africa: A retrospective cohort analysis. PloS one\| PubMed ID: 31622366	2019
Detection of Second Line Drug Resistance among Drug Resistant Mycobacterium Tuberculosis Isolates in Botswana. Pathogens (Basel, Switzerland)\| PubMed ID: 31661825	2019
Cytokine gene expression assay as a diagnostic tool for detection of Mycobacterium bovis infection in warthogs (Phacochoerus africanus). Scientific reports\| PubMed ID: 31712604	2019
Test Characteristics of Assays to Detect Infection in High-Prevalence African Buffalo () Herds. Journal of wildlife diseases\| PubMed ID: 31750773	2020
Minority Genotypic Populations as an Indicator of Subsequent Phenotypic Resistance. American journal of respiratory cell and molecular biology\| PubMed ID: 31774334	2019
A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic. BMC medicine\| PubMed ID: 32014024	2020
Discordances between molecular assays for rifampicin resistance in Mycobacterium tuberculosis: frequency, mechanisms and clinical impact. The Journal of antimicrobial chemotherapy\| PubMed ID: 32016320	2020
Extract from used Xpert MTB/RIF Ultra cartridges is useful for accurate second-line drug-resistant tuberculosis diagnosis with minimal rpoB-amplicon cross-contamination risk. Scientific reports\| PubMed ID: 32060311	2020
Phylogenomic assessment of drug-resistant Mycobacterium tuberculosis strains from Beira, Mozambique. Tuberculosis (Edinburgh, Scotland)\| PubMed ID: 32063558	2020
Xpert MTB/RIF Ultra and Xpert MTB/RIF for diagnosis of tuberculosis in an HIV-endemic setting with a high burden of previous tuberculosis: a two-cohort diagnostic accuracy study. The Lancet. Respiratory medicine\| PubMed ID: 32066534	2020
Author Correction: Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase. Scientific reports\| PubMed ID: 32081980	2020
Tuberculosis research in South Africa over the past 30 years: From bench to bedside. South African medical journal = Suid-Afrikaanse tydskrif vir geneeskunde\| PubMed ID: 32252868	2019
Identifying nucleic acid-associated proteins in Mycobacterium smegmatis by mass spectrometry-based proteomics. BMC molecular and cell biology\| PubMed ID: 32293251	2020
Spatial distribution of Mycobacterium Tuberculosis in metropolitan Harare, Zimbabwe. PloS one\| PubMed ID: 32315335	2020
Molecular epidemiology of drug resistant Mycobacterium tuberculosis in Africa: a systematic review. BMC infectious diseases\| PubMed ID: 32404119	2020
Evidence for the Effect of Vaccination on Host-Pathogen Interactions in a Murine Model of Pulmonary Tuberculosis by . Frontiers in immunology\| PubMed ID: 32508826	2020
Xpert Mycobacterium tuberculosis/Rifampicin-Detected Rifampicin Resistance is a Suboptimal Surrogate for Multidrug-resistant Tuberculosis in Eastern Democratic Republic of the Congo: Diagnos... Clinical infectious diseases : an official publication of the Infectious Diseases Society of America\| PubMed ID: 32590841	2021
The VetMAX™ M. tuberculosis complex PCR kit detects MTBC DNA in antemortem and postmortem samples from white rhinoceros (Ceratotherium simum), African elephants (Loxodonta africana) and Afri... BMC veterinary research\| PubMed ID: 32600471	2020
The Xpert MTB/RIF Ultra assay detects Mycobacterium tuberculosis complex DNA in white rhinoceros (Ceratotherium simum) and African elephants (Loxodonta africana). Scientific reports\| PubMed ID: 32879401	2020
Genetic Diversity in Clinical Isolates and Resulting Outcomes of Tuberculosis Infection and Disease. Annual review of genetics\| PubMed ID: 32926793	2020
Use of the MILLIPLEX bovine cytokine/chemokine multiplex assay to identify Mycobacterium bovis-infection biomarkers in African buffaloes (Syncerus caffer). Veterinary immunology and immunopathology\| PubMed ID: 33227620	2021
MDR M. tuberculosis outbreak clone in Eswatini missed by Xpert has elevated bedaquiline resistance dated to the pre-treatment era. Genome medicine\| PubMed ID: 33239092	2020
Optimized interferon-gamma release assays for detection of Mycobacterium bovis infection in African buffaloes (Syncerus caffer). Veterinary immunology and immunopathology\| PubMed ID: 33276277	2021
Cytokine biomarker discovery in the white rhinoceros (Ceratotherium simum). Veterinary immunology and immunopathology\| PubMed ID: 33373875	2021
Diagnosis of Mycobacterium bovis infection in free-ranging common hippopotamus (Hippopotamus amphibius). Transboundary and emerging diseases\| PubMed ID: 33423384	2022
Human whole genome sequencing in South Africa. Scientific reports\| PubMed ID: 33436733	2021
Optimisation of the tuberculin skin test for detection of Mycobacterium bovis in African buffaloes (Syncerus caffer). Preventive veterinary medicine\| PubMed ID: 33465641	2021
Face masks in the post-COVID-19 era: a silver lining for the damaged tuberculosis public health response? The Lancet. Respiratory medicine\| PubMed ID: 33493446	2021
Development of a cytokine gene expression assay for the relative quantification of the African elephant (Loxodonta africana) cell-mediated immune responses. Cytokine\| PubMed ID: 33548797	2021
Identification of gene fusion events in that encode chimeric proteins. NAR genomics and bioinformatics\| PubMed ID: 33575588	2020
Review of Diagnostic Tests for Detection of Infection in South African Wildlife. Frontiers in veterinary science\| PubMed ID: 33585615	2021
Decentralized Care for Rifampin-Resistant Tuberculosis, Western Cape, South Africa. Emerging infectious diseases\| PubMed ID: 33622466	2021
Cell-Mediated Immunological Biomarkers and Their Diagnostic Application in Livestock and Wildlife Infected With . Frontiers in immunology\| PubMed ID: 33746980	2021
Novel molecular transport medium used in combination with Xpert MTB/RIF ultra provides rapid detection of Mycobacterium bovis in African buffaloes. Scientific reports\| PubMed ID: 33782515	2021
A multi-phenotype genome-wide association study of clades causing tuberculosis in a Ghanaian- and South African cohort. Genomics\| PubMed ID: 33862184	2021
Melting the : Nondetection of Kanamycin Resistance Markers by Routine Diagnostic Tests and Identification of New Promoter Variants. Antimicrobial agents and chemotherapy\| PubMed ID: 33903113	2021
Diagnostic accuracy of the FluoroType MTB and MTBDR VER 2.0 assays for the centralized high-throughput detection of Mycobacterium tuberculosis complex DNA and isoniazid and rifampicin resist... Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases\| PubMed ID: 33933566	2021
Anaerobe-enriched gut microbiota predicts pro-inflammatory responses in pulmonary tuberculosis. EBioMedicine\| PubMed ID: 33975252	2021
Alcohol and Tobacco Use in a Tuberculosis Treatment Cohort during South Africa's COVID-19 Sales Bans: A Case Series. International journal of environmental research and public health\| PubMed ID: 34069737	2021
Directly Observed Therapy to Measure Adherence to Tuberculosis Medication in Observational Research: Protocol for a Prospective Cohort Study. JMIR research protocols\| PubMed ID: 34132642	2021
COVID-19 cough classification using machine learning and global smartphone recordings. Computers in biology and medicine\| PubMed ID: 34182331	2021
Improved detection of and in African wildlife samples using cationic peptide decontamination and mycobacterial culture supplementation. Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc\| PubMed ID: 34510986	2022
Drug resistant tuberculosis cases from the Copperbelt province and Northern regions of Zambia: Genetic diversity, demographic and clinical characteristics. Tuberculosis (Edinburgh, Scotland)\| PubMed ID: 34517268	2021
Potential contribution of HIV during first-line tuberculosis treatment to subsequent rifampicin-monoresistant tuberculosis and acquired tuberculosis drug resistance in South Africa: a retros... The Lancet. Microbe\| PubMed ID: 34766068	2021
Comprehensive and accurate genetic variant identification from contaminated and low-coverage whole genome sequencing data. Microbial genomics\| PubMed ID: 34793294	2021
Optimizing liquefaction and decontamination of sputum for DNA extraction from Mycobacterium tuberculosis. Tuberculosis (Edinburgh, Scotland)\| PubMed ID: 34906896	2022
COVID-19 detection in cough, breath and speech using deep transfer learning and bottleneck features. Computers in biology and medicine\| PubMed ID: 34954610	2022
CYTOKINE-RELEASE ASSAY FOR THE DETECTION OF INFECTION IN CHEETAH (). Journal of zoo and wildlife medicine : official publication of the American Association of Zoo Veterinarians\| PubMed ID: 34998280	2021
Transmission Of Tuberculosis Among illicit drug use Linkages (TOTAL): A cross-sectional observational study protocol using respondent driven sampling. PloS one\| PubMed ID: 35167586	2022
A treatment recommender clinical decision support system for personalized medicine: method development and proof-of-concept for drug resistant tuberculosis. BMC medical informatics and decision making\| PubMed ID: 35236355	2022
Ancient and recent differences in the intrinsic susceptibility of Mycobacterium tuberculosis complex to pretomanid. The Journal of antimicrobial chemotherapy\| PubMed ID: 35260883	2022
Localization of EccA at the growing pole in Mycobacterium smegmatis. BMC microbiology\| PubMed ID: 35590245	2022
Spatial heterogeneity of extensively drug resistant-tuberculosis in Western Cape Province, South Africa. Scientific reports\| PubMed ID: 35760977	2022
Adaptation and Diagnostic Potential of a Commercial Cat Interferon Gamma Release Assay for the Detection of Infection in African Lions (). Pathogens (Basel, Switzerland)\| PubMed ID: 35890010	2022
Identification and Characterisation of Nontuberculous Mycobacteria in African Buffaloes (), South Africa. Microorganisms\| PubMed ID: 36144463	2022
Comparison of interferon gamma release assay and gene expression assay for the detection of infection in African lions (). Frontiers in cellular and infection microbiology\| PubMed ID: 36189358	2022
Methods for handling missing data in serially sampled sputum specimens for mycobacterial culture conversion calculation. BMC medical research methodology\| PubMed ID: 36402979	2022
Variation in missed doses and reasons for discontinuation of anti-tuberculosis drugs during hospital treatment for drug-resistant tuberculosis in South Africa. PloS one\| PubMed ID: 36780443	2023
New insights on tuberculosis transmission dynamics and drug susceptibility profiles among the prison population in Southern Brazil based on whole-genome sequencing. Revista da Sociedade Brasileira de Medicina Tropical\| PubMed ID: 36820651	2023
A machine-learning based model for automated recommendation of individualized treatment of rifampicin-resistant tuberculosis. Research square\| PubMed ID: 36824956	2023
Comparison of two diagnostic intervention packages for community-based active case finding for tuberculosis: an open-label randomized controlled trial. Nature medicine\| PubMed ID: 36894651	2023
Site-directed mutagenesis of Mycobacterium tuberculosis and functional validation to investigate potential bedaquiline resistance-causing mutations. Scientific reports\| PubMed ID: 37280265	2023
The impact of genotype on the phenotype of Mycobacterium tuberculosis ΔsufR mutants. Tuberculosis (Edinburgh, Scotland)\| PubMed ID: 37295353	2023
Effect of compensatory evolution in the emergence and transmission of rifampicin-resistant Mycobacterium tuberculosis in Cape Town, South Africa: a genomic epidemiology study. The Lancet. Microbe\| PubMed ID: 37295446	2023
Microfluidic Capture of Mycobacterium tuberculosis from Clinical Samples for Culture-Free Whole-Genome Sequencing. Microbiology spectrum\| PubMed ID: 37358439	2023
The HesB Protein, MSMEG_4272, Is Required for In Vitro Growth and Iron Homeostasis. Microorganisms\| PubMed ID: 37375075	2023
The Detection of Mutations and Genotyping of Drug-Resistant Strains Isolated from Patients in the Rural Eastern Cape Province. Infectious disease reports\| PubMed ID: 37489395	2023
"Spotting" infection in leopards () - novel application of diagnostic tools. Frontiers in immunology\| PubMed ID: 37727792	2023
The MAGMA pipeline for comprehensive genomic analyses of clinical Mycobacterium tuberculosis samples. PLoS computational biology\| PubMed ID: 38019772	2023
Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing. Frontiers in microbiology\| PubMed ID: 38075895	2023
Whole genome sequencing improves the discrimination between strains on the southern border of Kruger National Park, South Africa. One health (Amsterdam, Netherlands)\| PubMed ID: 38283183	2023
Detection of in nasal swabs from communal goats () in rural KwaZulu-Natal, South Africa. Frontiers in microbiology\| PubMed ID: 38419629	2024
Identification and molecular characterization of DNA in GeneXpert® MTB/RIF ultra-positive, culture-negative sputum from a rural community in South Africa. One health (Amsterdam, Netherlands)\| PubMed ID: 38487729	2024
Point-of-care C-reactive protein and Xpert MTB/RIF Ultra for tuberculosis screening and diagnosis in unselected antiretroviral therapy initiators: a prospective, cross-sectional, diagnostic ... The Lancet. Global health\| PubMed ID: 38583458	2024
Latent tuberculosis infection is associated with an enrichment of short chain fatty acid producing bacteria in the stool of women living with HIV. Research square\| PubMed ID: 38645218	2024
Droplet based whole genome amplification for sequencing minute amounts of purified Mycobacterium tuberculosis DNA. Scientific reports\| PubMed ID: 38689002	2024
Integrating molecular and radiological screening tools during community-based active case-finding for tuberculosis and COVID-19 in southern Africa. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases\| PubMed ID: 38701914	2024
Exploring the potential of Oxford Nanopore Technologies sequencing for Mycobacterium tuberculosis sequencing: An assessment of R10 flowcells and V14 chemistry. PloS one\| PubMed ID: 38843147	2024
Latent Tuberculosis Infection Is Associated with an Enrichment of Short-Chain Fatty Acid-Producing Bacteria in the Stool of Women Living with HIV. Microorganisms\| PubMed ID: 38930430	2024
The Hidden Epidemic of Isoniazid-Resistant Tuberculosis in South Africa. Annals of the American Thoracic Society\| PubMed ID: 38935769	2024
The impact of alcohol and illicit substance use on the pharmacokinetics of first-line TB drugs. The Journal of antimicrobial chemotherapy\| PubMed ID: 38985541	2024
Bedaquiline: what might the future hold? The Lancet. Microbe\| PubMed ID: 39074472	2024
Insights into mycobacteriome composition in Mycobacterium bovis-infected African buffalo (Syncerus caffer) tissue samples. Scientific reports\| PubMed ID: 39080347	2024
Bridging the gap between molecular and genomic epidemiology in tuberculosis: inferring MIRU-VNTR patterns from genomic data. Journal of clinical microbiology\| PubMed ID: 39136450	2024
PneumoniaCheck, a novel aerosol collection device, permits capture of airborne Mycobacterium tuberculosis and characterisation of the cough aeromicrobiome in people with tuberculosis. Annals of clinical microbiology and antimicrobials\| PubMed ID: 39175010	2024
A machine-learning based model for automated recommendation of individualized treatment of rifampicin-resistant tuberculosis. PloS one\| PubMed ID: 39241084	2024
Subtracting the background by reducing cell-free DNA's confounding effects on Mycobacterium tuberculosis quantitation and the sputum microbiome. Scientific reports\| PubMed ID: 39333362	2024
A Genome-Focused Investigation Reveals the Emergence of a Strain Related to Multidrug-Resistant Tuberculosis in the Amazon Region of Brazil. Microorganisms\| PubMed ID: 39338491	2024
Understanding the impact of pandemics on long-term medication adherence: directly observed therapy in a tuberculosis treatment cohort pre- and post-COVID-19 lockdowns. BMC infectious diseases\| PubMed ID: 39396938	2024
Comprehensive genomic surveillance reveals transmission profiles of extensively drug-resistant tuberculosis cases in Pará, Brazil. Frontiers in microbiology\| PubMed ID: 39911713	2024
Patient Determinants and Effects on Adherence of Adverse Drug Reactions to Tuberculosis Treatment: A Prospective Cohort Analysis. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America\| PubMed ID: 39973802	2025
A new rapid lipoarabinomannan urine assay for tuberculosis: a two-centre diagnostic accuracy evaluation in outpatients with and without HIV. Research square\| PubMed ID: 40034451	2025
Efficacy and Safety of Higher Doses of Levofloxacin for MDR-TB: A Randomized Placebo-controlled Phase 2 Trial. American journal of respiratory and critical care medicine\| PubMed ID: 40080768	2025
Evidence of DNA in shared water sources at livestock-wildlife-human interfaces in KwaZulu-Natal, South Africa. Frontiers in veterinary science\| PubMed ID: 40093619	2025
Unpacking bedaquiline hetero-resistance: the importance of intermediate profiles for phenotypic drug-susceptibility testing. bioRxiv : the preprint server for biology\| PubMed ID: 40161652	2025
Oral washes and tongue swabs for Xpert MTB/RIF Ultra-based tuberculosis diagnosis in people with and without the ability to make sputum. Research square\| PubMed ID: 40166039	2025
Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species. Bioinformatics (Oxford, England)\| PubMed ID: 40341387	2025