​​​​​Division of Molecular Biology & Human Genetics

 

​Mycobacteriology​​​: Host-pathogen Mycobactomics​​

 

​Peer reviewed publications


2020

Goossens SN, Sampson SL, Van Rie A. Mechanisms of Drug-Induced Tolerance in Mycobacterium tuberculosis. Clin Microbiol Rev. 2020 Oct 14;34(1):e00141-20.
doi: 10.1128/CMR.00141-20. PMID: 33055230; PMCID: PMC7566​895.​


Gallant JL, Heunis T, Sampson SL, Bitter W. ProVision: A web based platform for rapid analysis of proteomics data processed by MaxQuant. Bioinformatics. 2020 Jul 8:btaa620. doi: 10.1093/bioinformatics/btaa620. PMID: 32638008​; PMCID: PMC7723325​.


​Parbhoo T, Sampson SL, Mouton JM. Recent Developments in the Application of Flow Cytometry to Advance our Understanding of Mycobacterium tuberculosis Physiology and Pathogenesis. Cytometry A. 2020 May 21. doi:10.1002/cyto.a.24030. PMID: 32437069; PMCID: PMC7496436.​


Gallant J, Mouton J, Ummels R, ten Hagen-Jongman C, Kriel N, Pain A, Warren RM, Bitter W, Heunis T, Sampson SL. Identification of gene fusion events in Mycobacterium tuberculosis that encode chimeric proteins. NAR Genomics and Bioinformatics. 2020 2(2):1-15. doi: 10.1093/nargab/lqaa033.


Chisompola NK, Streicher EM, Muchemwa CMK, Warren RM, Sampson SL. Molecular epidemiology of drug resistant Mycobacterium tuberculosis in Africa: a systematic review.  BMC Infectious Diseases. 2020  20:344.


Chirenda J, Gwitira I, Warren RM, Sampson SL, Murwira A, Masimirembwa C,  Mateveke KM, Duri C,  Chonzi P,  Rusakaniko S, Streicher EM. Spatial Distribution of Mycobacterium tuberculosis in Metropolitan Harare, Zimbabwe. PLOS One. 2020 21:​15(4):e0231637. doi.org/10.1371/journal.pone.0231637​.


Kriel NS, Heunis T, Sampson SL, Gey van Pittius NC, Williams MJ, Warren RM. Identifying nucleic acid-associated proteins in Mycobacterium smegmatis by mass spectrometry-based proteomics.  BMC Molecular and Cell Biology. 2020 21:19. ​


2019

Mouton JM, Heunis T, Dippenaar A, Gallant JL, Kleynhans L, Sampson SL. Comprehensive Characterization of the Attenuated Double Auxotroph Mycobacterium tuberculosis ΔleuDΔpanCD as an Alternative to H37Rv. Frontiers in Microbiology. 2019 20;10:1922. doi.org/10.3389/fmicb.2019.01922.


​Chirenda J, Chipinduro M, de Kock M, Spies C, Sakubani, RM, Sampson SL, Streicher EM. Recovery of Mycobacterium tuberculosis 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. 2019 8(2):185-189.​


Grobbelaar M, Louw GE, Sampson SL, van HeldenPD, Donald PR, Warren RM.  Evolution of rifampicin treatment for tuberculosis. Infection, Genetics and Evolution. 2019 75:103948. doi.org/10.1016/j.meegid.2019.103937.​


Shahbaaz M, Cloete R, Grobbelaar M, Sampson SL, Christoffels A. Structure based identification of novel inhibitors against ATP sy​nthase of Mycobacterium tuberculosis: A combined in silico and in vitro study. International Journal of Biological Macromolecules. 2019 135:582-590​.


2018​​

Bekale RB, Du Plessis SM, Hsu NJ, Sharma JR, Sampson SL, Jacobs M, Meyer M, Morse GD, Dube A. Mycobacterium tuberculosis and Interactions with the Host Immune System: Opportunities for Nanoparticle Based Immunotherapeutics and Vaccines. Pharm Res. 2018 Nov 8;36(1):8. doi: 10.1007/s11095-018-2528-9.


Chihota VN, Niehaus A, Streicher EM, Wang X, Sampson SL, Mason P, Källenius G, Mfinanga SG, Pillay M, Klopper M, Kasongo W, Behr MA, Gey van Pittius NC, van Helden PD, Couvin D, Rastogi N, Warren RM. Geospatial distribution of Mycobacterium tuberculosis genotypes in Africa. PLoS One. 2018 1;13(8):e0200632. 
doi: 10.1371/journal.pone.0200632. eCollection 2018​.


Kriel NL, Gallant J, van Wyk N, van Helden P, Sampson SL, Warren RM, Williams MJ. Mycobacterial nucleoid associated proteins: Adding a new dimension to gene regulation. Tuberculosis. 2018 108:169-177. doi.org/10.1016/j.tube.2017.12.004.​


Kapp, Malan SF, Sampson SL. Small Molecule Efflux Pump Inhibitors in Mycobacterium tuberculosis: a Rational Drug Design Perspective. Mini-Reviews in Medicinal Chemistry. 2018 18(1):72-86. doi: 10.2174/1389557517666170510105506​.​​

 

2017

Kapp E, Visser H, Sampson SL, Malan SF, Streicher EM, Foka GB, Warner DF, Omoruyi SI, Enogieru AB, Ekpo OE, Zindo FT, Joubert J, 2017. Versatility of 7-substituted coumarin molecules as antimycobacterial agents, neuronal enzyme inhibitors and neuroprotective agents. Molecules. 2017 22(10).
doi: 10.3390/molecules22101644.​


Heunis T, Dippenaar A, Warren RM, van Helden PD, van der Merwe RG, Gey van Pittius NC, Pain A, Sampson SL, Tabb DL. Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates. J Proteome Res. 2017 16(10):3841-3851. doi.org/10.1021/acs.jproteome.7b00483.​


Fang Z, Newton-Foot M, Sampson SL, Gey van Pittius NC. Two promoters in the esx-3 gene cluster of Mycobacterium smegmatis respond inversely to different iron concentrations in vitro. BMC Res Notes. 2017 10(1):426.d​.


Du Plessis J, Cloete R, Burchell L, Sarkar P, Warren RM, Christoffels A, Wigneshweraraj R, Sampson SL. Exploring the potential of T7 bacteriophage protein Gp2 as a novel inhibitor of mycobacterial RNA polymerase. Tuberculosis. 2017 (106):82-90. doi: 10.1016/j.tube.2017.07.004.​


2016

Chingwaru W, Glashoff RH, Vidmar J, Kapewangolo P, Sampson SL. Mammalian cell cultures as models for Mycobacterium tuberculosis-human immunodeficiency virus (HIV) interaction studies: A review. Asian Pacific Journal of Tropical Medicine. 2016 (9):832-838. doi.org/10.1016/j.apjtm.2016.07.002.​


Whitfield MG, Streicher EM, Dolby T, Simpson JA, Sampson SL, Van Helden PD, Van Rie A, Warren RM. Prevalence of pyrazinamide resistance across the spectrum of drug resistant phenotypes of Mycobacterium tuberculosis. Tuberculosis. 2016 (99):128-130. doi: 10.1016/j.tube.2016.05.003.​


Mouton JM, Helaine S, Holden DW, Sampson SL. Elucidating population-wide mycobacterial replication dynamics at the single-cell level. Microbiology - SGM. 2016 (162):966-978. doi: 10.1099/mic.0.000288​​.


Newton-Foot M, Warren RM, Sampson SL, van Helden PD, Gey van Pittius NC. The plasmid-mediated evolution of the mycobacterial ESX (Type VII) secretion systems. BMC Evol Biol. 2016 16(1):62. doi: 10.1186/s12862-016-0631-2.


Phelan JE, Coll F, Bergval I, A​nthony RM, Warren RM, Sampson SL and 24 other authors. Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages. BMC Genomics. (2016). 17:151​.


Sampson SL. Strength in Diversity: Hidden Genetic Depths of Mycobacterium tuberculosis. Invited Spotlight article, Trends in Microbiology. 2016. 24(2):82-84. 
doi.org/10.1016/j.tim.2015.12.006.


Pule C, Sampson SL (corresponding author), Warren RM, Black P, Van Helden PD, Victor TC, Louw GE. Efflux pump inhibitors: targeting mycobacterial efflux systems to enhance TB therapy. Journal of Antimicrobial Chemotherapy. 2016. 71(1):17-26. doi: 10.1093/jac/dkv316​.


2015

Black P, De Vos M, Louw G, Van der Merwe R,  Dippenaar A, Streicher E, Abdallah A, Sampson S,  Victor T, Dolby T, Simpson J, Van Helden P, Warren R, Pain A. Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates. BMC Genomics. 2015. 16(1):857. doi: 10.1186/s12864-015-2067-2.


Dippenaar A, Parsons SDC, Sampson SL, Van der Merwe RG, Drewe JA, Abdallah AM, Siame KK, Gey van Pittius NC, Van Helden PD, Pain A, Warren RM.  Whole genome sequence analysis of Mycobacterium suricattae. Tuberculosis. 2015. 95(6):682-8. doi: ​10.1016/j.tube.2015.10.001.


Streicher EM, Sampson SL, Dheda K, Dolby T, Simpson J, Victor TC, Gey van Pittius NC, van Helden PD, Warren RM. Molecular epidemiological interpretation of the extensively drug resistant tuberculosis epidemic in South Africa J Clin Microbiol. 2015. 53(11):3650-3653. doi: 10.1128/JCM.01414-15.​


Whitfield MG, Warren RM, Streicher EM, Sampson SL, Sirgel F, Van Helden PD, Mercante A, Willby M, Hughes K, Birkness K, Morlock G, Van Rie A, Posey J. Mycobacterium tuberculosis pncA polymorphisms that do not confer pyrazinamide resistance at a breakpoint concentration of 100 µg/ml in MGIT. J Clin Microbiol. 2015 53(11):3633-5. doi: 10.1128/JCM.01001-15.​


Whitfield MG, Soeters HM, Warren RM, York T, Sampson SL, Streicher EM, van Helden PD, van Rie A. A Global Perspective on Pyrazinamide Resistance: Systematic Review and Meta-analysis. PLOS ONE. 2015 10(7):e0133869. doi: 10.1371/journal.pone.0133869.


Fishbein S, Van Wyk N, Warren RM, Sampson SL. Phylogeny to function: PE/PPE protein evolution and impact on Mycobacterium tuberculosis pathogenicity. Molecular Microbiology. 2015.  doi: 10.1111/mmi.12981.​ 


Fortuin S, Tomazella G, Nagayaryan N, Sampson S, Gey van Pittius N, Soares N, Wiker H, De Souza G, Warren R. Phosphoproteomics analysis of a clinical Mycobacterium tuberculosis Beijing isolate: Expanding the mycobacterial phosphoproteome catalogue. Frontiers in Microbiology, section Microbial Physiology and Metabolism. 2015. doi: 10.3389/fmicb.2015.00006.


Fang Z, Sampson SL, Warren RM, Gey van Pittius NC, Newton-Foot M. Iron acquisition Strategies in Mycobacteria. Tuberculosis. 2015. 95(2):123-130.  
doi: 10.1016/j.tube.2015.01.004.


2014

Van der Merwe RG, Van Helden PD, Warren RM, Sampson SLGey van Pittius NC. Phage-based detection of bacterial pathogens.  Analyst2014  DOI: 10.1039/C4AN00208C​.


Items in the press

What needs to be added to South Africa's anti-TB toolbox. SL Sampson. The Conversation, May 2015; http://theconversation.com/what-needs-to-be-added-to-south-africas-anti-tb-toolbox-40538 Republished under Creative Commons licence by: Biznews , The Big Issue, SciBraai

Fresh Hope for MDR-TB patients. SL Sampson. Sowetan. March 2014