2021

Ismail N, Riviere E, Limberis J, Huo S, Metcalfe JZ, Warren RW, Van Rie A. Genetic variants and their association with phenotypic resistance to bedaquiline in Mycobacterium tuberculosis: a systematic review and individual isolate data analysis. Lancet Microbe 2021.
https://doi.org/10.1016/S2666-5247(21)00175-0

Dippenaar A, Goossens SN, Grobbelaar M, Oostvogels S, Cuypers B, Laukens K, Meehan CJ, Warren RM, van Rie A. Nanopore sequencing for Mycobacterium tuberculosis: a critical review of the literature, new developments and future opportunities. Journal of Clinical Microbiology 2021.
https://journals.asm.org/doi/10.1128/JCM.00646-21

Van Rie A, de Viedma DG, Meehan C, Comas I, Heupink TH, De Vos E, de Oñate WA, Mathys V, Ceyssens PJ, Groenen G, González-Candelas F, Forier A, Juengst E. Whole-genome sequencing for TB source investigations: principles of ethical precision public health. International Journal of Tuberculosis and Lung Disease 2021; 25:222-227.
https://doi.org/10.5588/ijtld.20.0886

De Vos E, Scott L, Voss De Lima Y, Warren RM, Stevens W, Hayes C, da Silva P, Van Rie A. Management of rifampicin-resistant TB: programme indicators and care cascade analysis in South Africa. International Journal of Tuberculosis and Lung Disease 2021; 25:134-141.
https://doi.org/10.5588/ijtld.20.0598

Dippenaar A, Derendinger B, Dolby T, Beylis N, van Helden PD, Theron G, Warren RM, de Vos M. 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 resistance. Clinical Microbiology and Infection 2021.
https://doi.org/10.1016/j.cmi.2021.04.022

Ley SD*, Pillay S*, Streicher EM, van der Heijden YF, Sirgel F, Derendinger B, de Kock M, Gagneux S., Warren RM, Theron G, de Vos M. Melting the eis: Nondetection of Kanamycin Resistance Markers by Routine Diagnostic Tests and Identification of New eis Promoter Variants. Antimicrobial Agents and Chemotherapy 2021;65(7):e0250220.
https://doi.org/10.1128/AAC.02502-20

2020

Whitfield MG, Marras SAE, Warren RM, Van Rie A, Rice J, Wangh LJ, Kreiswirth BN Rapid Pyrazinamide Drug Susceptibility Testing using a Closed-Tube PCR Assay of the Entire pncA gene. Scientific Reports 2020; 10:4234.
https://doi.org/10.1038/s41598-020-61286-7

Juengst ET, Van Rie A. Transparency, trust, and community welfare: towards a precision public health ethics framework for the genomics era. Genome Medicine 2020; 20;12:98.
https://doi.org/10.1186/s13073-020-00800-y

Goossens SN, Sampson SL, Van Rie A. Mechanisms of Drug-Induced Tolerance in Mycobacterium tuberculosis. Clinical Microbiology Reviews 2020; 34:e00141-20.
https://doi.org/10.1128/CMR.00141-20

Van Rie A, Whitfield MG, De Vos E, Scott L, Da Silva P, Hayes C, Heupink TH, Sirgel FA, Stevens W, Warren RM. Discordances between molecular assays for rifampicin resistance in Mycobacterium tuberculosis: frequency, mechanisms and clinical impact. J Antimicrob Chemother. 2020; 75:1123-1129.
https://doi.org/10.1093/jac/dkz564

Riviere E, Heupink TH, Ismail N, Dippenaar A, Clarke C, Abebe G, Heusden P, Warren R, Meehan CJ, Van Rie A. 2020. Capacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countries. Briefings in Bioinformatics 2020.
https://doi.org/10.1093/bib/bbaa246

Klopper M, Heupink TH, Hill-Cawthorne G, Streicher EM, Dippenaar A, de Vos M, Abdallah AM, Limberis J, Merker M, Burns S, Niemann S, Dheda K, Posey J, Pain A, Warren RM. 2020. A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic. BMC Medicine 2020; 18:24.
https://doi.org/10.1186/s12916-019-1487-2

Rivière E, Whitfield MG, Nelen J, Heupink TH, Van Rie A. Identifying isoniazid resistance markers to guide inclusion of high-dose isoniazid in tuberculosis treatment regimens. Clinical Microbiolology and Infection 2020 ;26:1332-1337.
https://doi.org/10.1016/j.cmi.2020.07.004

Van Rie A, Meehan C. The devil is in the diversity: Exploring within-person evolution of Mycobacterium tuberculosis. EBioMedicine. 2020; 55:102758.
https://doi.org/10.1016/j.ebiom.2020.102758

Peters JS, Ismail N, Dippenaar A, Ma S, Sherman DR, Warren RM, Kana BD. Genetic Diversity in Mycobacterium tuberculosis Clinical Isolates and Resulting Outcomes of Tuberculosis Infection and Disease. Annual Review of Genetics 2020; 54:511-537.
https://doi.org/10.1146/annurev-genet-022820-085940

Katende B, Esterhuizen TM, Dippenaar A, Warren RM. 2020. Rifampicin Resistant Tuberculosis in Lesotho: Diagnosis, Treatment Initiation and Outcomes. Scientific Reports 2020; 10:1917.
https://doi.org/10.1038/s41598-020-58690-4

2019

Meehan C, Serrano GAG, Kohl T, Verboven L, Dippenaar A, Ezewudo M, Farhat M, Guthrie J, Laukens K, Miotto P, Ofori-Anyinam B, Dreyer V, Supply P, Suresh A, Utpatel C, van Soolingen D, Zhou Y, Ashton P, Brites D, Cabibbe A, de Jong B, De Vos M, Fabrizio M, Gagneux S, Gao Q, Heupink T, Liu Q, Loiseau CM, Rigouts L, Rodwell T, Tagliani E, Walker T, Warren R, Zhao Y, Zignol M, Schioto M, Gardy J, Cirillo D, Niemann S, Comas I, Van Rie A. Whole genome sequencing of Mycobacterium tuberculosis: current standard and open issues. Nature Reviews Microbiology 2019; 17:533-545.
https://doi.org/10.1038/s41579-019-0214-5

de Vos M, Ley SD, Wiggins KB, Derendinger B, Dippenaar A, Grobbelaar M, Reuter A, Dolby T, Burns S, Schito M, Engelthaler DM, Metcalfe J, Theron G, van Rie A, Posey J, Warren R, Cox H. 2019. Bedaquiline Micro-heteroresistance after Cessation of Tuberculosis Treatment. New England Journal of Medicine 2019; 380:2178-2180.
https://doi.org/10.1056/NEJMc1815121

Ley SD, de Vos M, Van Rie A, Warren RM. Deciphering Within-Host Micro-evolution of Mycobacterium tuberculosis through Whole-Genome Sequencing: the Phenotypic Impact and Way Forward. Microbiology and Molecular Biology Reviews 2019; 83(2):e00062-18.
https://doi.org/10.1128/MMBR.00062-18

Dippenaar A, De Vos M, Marx FM, Adroub SA, van Helden PD, Pain A, Sampson SL, Warren RM. 2019. Whole genome sequencing provides additional insights into recurrent tuberculosis classified as endogenous reactivation by IS6110 DNA fingerprinting. Infection, Genetics and Evolution 2019; 75:103948.
https://doi.org/10.1016/j.meegid.2019.103948

2018

Whitfield MG, Warren RM, Mathys V, Scott L, De Vos E, Stevens W, Streicher EM, Groenen G, Sirgel FA, Van Rie A The potential use of rifabutin for treatment of patients diagnosed with rifampicin-resistant tuberculosis. Journal of Antimicrobial Chemotherapy 2018; 73(10):2667-2674.
https://doi.org/10.1093/jac/dky248