TB Genomics
Welcome to Stellenbosch University

Division of Molecular Biology and Human Genetics

​TB Genomics​

​Publications

 

​Publications 2018

Feliciano CS, Namburete EA, Plaça JR, Peronni K, Dippenaar A, Warren RM, Silva Jr. WA, Bollela VR. (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 Mozambique." Tuberculosis (Edinb) 110: 59-67. http://dx.doi.org/10.1016/j.tube.2018.04.003


Ates LS, Dippenaar A, Ummels R, Piersma SR, van der Woude AD, van der Kuij K, Le Chevalier F, Mata-Espinosa D, Barrios-Payán J, Marquina-Castillo B, Guapillo C, Jiménez CR, Pain A, Houben ENG, Warren RM, Brosch R, Hernández-Pando R, Bitter W (2018). “Mutations in ppe38 block PE_PGRS secretion and increase virulence of Mycobacterium tuberculosis." Nat Microbiol. https://www.ncbi.nlm.nih.gov/pubmed/29335553


de Vos M, Derendinger B, Nathavitharana RR, Dolby T, Simpson JA, van Helden PD, Warren RM, Theron G.Widespread use of incorrect PCR ramp rate negatively impacts multidrug-resistant tuberculosis diagnosis (MTBDRplus). Sci Rep. 2018 Feb 16; 8(1):3206. https://www.nature.com/articles/s41598-018-21458-y


de Vos M, Derendinger B, Dolby T, Simpson J, van Helden P, Rice J, Wangh L, Theron G, Warren R. Diagnostic accuracy and utility of a new molecular assay for multidrug-resistant tuberculosis: FluoroType MTBDR. Journal of Clinical Microbiology Jul 2018, JCM.00531-18; DOI: 10.1128/JCM.00531-18


Dekhil N, Skhairia MA, Mhenni B, Ben Fradj S, Warren R, Mardassi H. Automated IS6110-based fingerprinting of Mycobacterium tuberculosis: Reaching unprecedented discriminatory power and versatility. PLoS One. 2018 Jun 1;13(6):e0197913. doi: 10.1371/journal.pone.0197913


Olayanju O, Limberis J, Esmail A, Oelofse S, Gina P, Pietersen E, Fadul M, Warren R, Dheda K. Long-term bedaquiline-related treatment outcomes in patients with extensively drug-resistant tuberculosis from South Africa. Eur Respir J. 2018 May 30;51(5). pii: 1800544. doi: 10.1183/13993003.00544-2018


Botha GHR, Theron G, Warren RM, Klopper M, Dheda K, van Helden PD, Niesler TR. Detection of tuberculosis by automatic cough sound analysis. Physiological Measurement. 2018 Mar 15 (epub ahead of print). PMID: 29543189. http://iopscience.iop.org/article/10.1088/1361-6579/aab6d0

 

Publications 2017

Hoal EG, Dippenaar A, Kinnear C, van Helden PD, Möller M (2017). “The arms race between man and Mycobacterium tuberculosis: time to regroup." Infect Genet Evol. https://www.ncbi.nlm.nih.gov/pubmed/28843547


Dippenaar A, Heunis T, Warren RM, van Helden PD, van der Merwe RG, Gey van Pittius NC, Pain A, Sampson SL, Tabb DL (2017). “Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates." J Proteome Res. https://www.ncbi.nlm.nih.gov/pubmed/28820946


Dippenaar, A., S. D. C. Parsons, M. A. Miller, T. Hlokwe, N. C. G. van Pittius, S. A. Adroub, A. M. Abdallah, A. Pain, R. M. Warren, A. L. Michel and P. D. van Helden (2017). "Progenitor strain introduction of Mycobacterium bovis at the wildlife-livestock interface can lead to clonal expansion of the disease in a single ecosystem." Infect Genet Evol. https://www.ncbi.nlm.nih.gov/pubmed/28412523


A van Rie, M de Vos, The role of line probe assays in the Xpert MTB/RIF Ultra era. Journal of Laboratory and Precision Medicine. 2017 http://jlpm.amegroups.com/article/view/3686

Venter R, Derendinger B, de Vos M, Pillay S, Dolby T, Simpson J, Kitchin N, Ruiters A, van Helden PD, Warren RM, Theron G.Mycobacterial genomic DNA from used Xpert MTB/RIF cartridges can be utilised for accurate second-line genotypic drug susceptibility testing and spoligotyping. Sci Rep. 2017 Nov 1; 7(1):14854. https://www.nature.com/articles/s41598-017-14385-x

 

Metcalfe JZ, Streicher E, Theron G, Colman RE, Allender C, Lemmer D, Warren R, Engelthaler DM. Cryptic Microheteroresistance Explains Mycobacterium tuberculosis Phenotypic Resistance. Am J Respir Crit Care Med. 2017 Nov 1;196(9):1191-1201. doi: 10.1164/rccm.201703-0556OC
Nagel S, Streicher EM, Klopper M, Warren RM, van Helden PD. Isoniazid Resistance and Dosage as Treatment for Patients with Tuberculosis. Curr Drug Metab. 2017 Oct 31; 18 (11) pp1030 – 1039 PMID: 29086682. http://www.eurekaselect.com/156686/article

 

Publications 2015

6Black, P. A., M. de Vos, G. E. Louw, R. G. van der Merwe, A. Dippenaar, E. M. Streicher, A. M. Abdallah, S. L. Sampson, T. C. Victor, T. Dolby, J. A. Simpson, P. D. van Helden, R. M. Warren and A. Pain (2015). "Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates." BMC Genomics 16: 857. https://www.ncbi.nlm.nih.gov/pubmed/26496891

Dippenaar, A., S. D. Parsons, S. L. Sampson, R. G. van der Merwe, J. A. Drewe, A. M. Abdallah, K. K. Siame, N. C. Gey van Pittius, P. D. van Helden, A. Pain and R. M. Warren (2015). "Whole genome sequence analysis of Mycobacterium suricattae." Tuberculosis (Edinb) 95(6): 682-688. https://www.ncbi.nlm.nih.gov/pubmed/26542221

Dippenaar, A. and R. M. Warren (2015). "Fighting an old disease with next-generation sequencing." Elife 4. https://www.ncbi.nlm.nih.gov/pubmed/25732038

de Vos M, Black PA, Louw GE, van der Merwe RG, Dippenaar A, Streicher EM, Abdallah AM, Sampson SL, Victor TC, Dolby T, Simpson JA, van Helden PD, Warren RM, Pain A.Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates. BMC Genomics. 2015 Oct 24; 16:857. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-2067-2