​Publications

1.      Uys P, Brand H, Warren R, van der Spuy G, Hoal EG, van Helden PD. The risk of tuberculosis reinfection soon after cure of a first disease episode is extremely high in a hyperendemic community. PloS one 2015;10:e0144487.

2.      Van Rie A, Warren RM. Mdr tuberculosis control: Time to change the dogma? The Lancet Respiratory medicine 2015;3:907-909.

3.      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;95:682-688.

4.      Black PA, de Vos M, 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;16:857.

5.      Streicher EM, Sampson SL, Dheda K, Dolby T, Simpson JA, Victor TC, Gey van Pittius NC, van Helden PD, Warren RM. Molecular epidemiological interpretation of the epidemic of extensively drug-resistant tuberculosis in south africa. Journal of clinical microbiology 2015;53:3650-3653.

6.      Whitfield MG, Warren RM, Streicher EM, Sampson SL, Sirgel FA, van Helden PD, Mercante A, Willby M, Hughes K, Birkness K, Morlock G, van Rie A, Posey JE. 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 2015;53:3633-3635.

7.      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:e0133869.

8.      Salie M, Daya M, Lucas LA, Warren RM, van der Spuy GD, van Helden PD, Hoal EG, Moller M. 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 2015;34:221-229.

9.      Jubulis J, Dionne K, Osterhout G, Ayuk L, Awasom C, Achu P, Noeske J, Warren R, McArthur C, Parrish N. Mycobacterium tuberculosis resistance in pulmonary tb patients in cameroon: A phenotypic susceptibility assay. The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease 2015;19:823-827.

10.   Pietersen E, Peter J, Streicher E, Sirgel F, Rockwood N, Mastrapa B, Te Riele J, Davids M, van Helden P, Warren R, Dheda K. High frequency of resistance, lack of clinical benefit, and poor outcomes in capreomycin treated south african patients with extensively drug-resistant tuberculosis. PloS one 2015;10:e0123655.

11.   Dippenaar A, Warren RM. Fighting an old disease with next-generation sequencing. eLife 2015;4.

12.   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;96:901-916.

13.   Fortuin S, Tomazella GG, Nagaraj N, Sampson SL, Gey van Pittius NC, Soares NC, Wiker HG, de Souza GA, Warren RM. Phosphoproteomics analysis of a clinical mycobacterium tuberculosis beijing isolate: Expanding the mycobacterial phosphoproteome catalog. Frontiers in microbiology 2015;6:6.

14.   Fang Z, Sampson SL, Warren RM, Gey van Pittius NC, Newton-Foot M. Iron acquisition strategies in mycobacteria. Tuberculosis 2015;95:123-130.

15.   Merker M, Blin C, Mona S, Duforet-Frebourg N, Lecher S, Willery E, Blum MG, Rusch-Gerdes S, Mokrousov I, Aleksic E, Allix-Beguec C, Antierens A, Augustynowicz-Kopec E, Ballif M, Barletta F, Beck HP, Barry CE, 3rd, Bonnet M, Borroni E, Campos-Herrero I, Cirillo D, Cox H, Crowe S, Crudu V, Diel R, Drobniewski F, Fauville-Dufaux M, Gagneux S, Ghebremichael S, Hanekom M, Hoffner S, Jiao WW, Kalon S, Kohl TA, Kontsevaya I, Lillebaek T, Maeda S, Nikolayevskyy V, Rasmussen M, Rastogi N, Samper S, Sanchez-Padilla E, Savic B, Shamputa IC, Shen A, Sng LH, Stakenas P, Toit K, Varaine F, Vukovic D, Wahl C, Warren R, Supply P, Niemann S, Wirth T. Evolutionary history and global spread of the mycobacterium tuberculosis beijing lineage. Nature genetics 2015;47:242-249.

16.   Fang Z, van der Merwe RG, Warren RM, Schubert WD, Gey van Pittius NC. Assessing the progress of mycobacterium tuberculosis h37rv structural genomics. Tuberculosis 2015;95:131-136.

17.   Mbugi EV, Katale BZ, Siame KK, Keyyu JD, Kendall SL, Dockrell HM, Streicher EM, Michel AL, Rweyemamu MM, Warren RM, Matee MI, van Helden PD. Genetic diversity of mycobacterium tuberculosis isolated from tuberculosis patients in the serengeti ecosystem in tanzania. Tuberculosis 2015;95:170-178.

18.   Warren RM. Implementation of new tools for multidrug-resistant tuberculosis detection and control. International journal of mycobacteriology 2016;5 Suppl 1:S67.

19.   Theron G, Peter J, Richardson M, Warren R, Dheda K, Steingart KR. Genotype((r)) mtbdrsl assay for resistance to second-line anti-tuberculosis drugs. The Cochrane database of systematic reviews 2016;9:CD010705.

20.   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.

21.   Chengalroyen MD, Beukes GM, Gordhan BG, Streicher EM, Churchyard G, Hafner R, Warren R, Otwombe K, Martinson N, Kana BD. Detection and quantification of differentially culturable tubercle bacteria in sputum from patients with tuberculosis. American journal of respiratory and critical care medicine 2016;194:1532-1540.

22.   Mbugi EV, Katale BZ, Streicher EM, Keyyu JD, Kendall SL, Dockrell HM, Michel AL, Rweyemamu MM, Warren RM, Matee MI, van Helden PD, Couvin D, Rastogi N. Mapping of mycobacterium tuberculosis complex genetic diversity profiles in tanzania and other african countries. PloS one 2016;11:e0154571.

23.   Goosen WJ, van Helden PD, Warren RM, Miller MA, Parsons SD. 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 2016;173:17-20.

24.   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 evolutionary biology 2016;16:62.

25.   Phelan JE, Coll F, Bergval I, Anthony RM, Warren R, Sampson SL, Gey van Pittius NC, Glynn JR, Crampin AC, Alves A, Bessa TB, Campino S, Dheda K, Grandjean L, Hasan R, Hasan Z, Miranda A, Moore D, Panaiotov S, Perdigao J, Portugal I, Sheen P, de Oliveira Sousa E, Streicher EM, van Helden PD, Viveiros M, Hibberd ML, Pain A, McNerney R, Clark TG. Recombination in pe/ppe genes contributes to genetic variation in mycobacterium tuberculosis lineages. BMC genomics 2016;17:151.

26.   Farhat MR, Sultana R, Iartchouk O, Bozeman S, Galagan J, Sisk P, Stolte C, Nebenzahl-Guimaraes H, Jacobson K, Sloutsky A, Kaur D, Posey J, Kreiswirth BN, Kurepina N, Rigouts L, Streicher EM, Victor TC, Warren RM, van Soolingen D, Murray M. Genetic determinants of drug resistance in mycobacterium tuberculosis and their diagnostic value. American journal of respiratory and critical care medicine 2016;194:621-630.

27.   Tomasicchio M, Theron G, Pietersen E, Streicher E, Stanley-Josephs D, van Helden P, Warren R, Dheda K. The diagnostic accuracy of the mtbdrplus and mtbdrsl assays for drug-resistant tb detection when performed on sputum and culture isolates. Scientific reports 2016;6:17850.

28.   Pule CM, Sampson SL, Warren RM, Black PA, van Helden PD, Victor TC, Louw GE. Efflux pump inhibitors: Targeting mycobacterial efflux systems to enhance tb therapy. The Journal of antimicrobial chemotherapy 2016;71:17-26.

29.   Dowdy DW, Theron G, Tornheim JA, Warren R, Kendall EA. Of testing and treatment: Implications of implementing new regimens for multidrug-resistant tuberculosis. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017;65:1206-1211.

30.   Miotto P, Tessema B, Tagliani E, Chindelevitch L, Starks AM, Emerson C, Hanna D, Kim PS, Liwski R, Zignol M, Gilpin C, Niemann S, Denkinger CM, Fleming J, Warren RM, Crook D, Posey J, Gagneux S, Hoffner S, Rodrigues C, Comas I, Engelthaler DM, Murray M, Alland D, Rigouts L, Lange C, Dheda K, Hasan R, Ranganathan UDK, McNerney R, Ezewudo M, Cirillo DM, Schito M, Koser CU, Rodwell TC. A standardised method for interpreting the association between mutations and phenotypic drug resistance in mycobacterium tuberculosis. The European respiratory journal 2017;50.

31.   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. Scientific reports 2017;7:14854.

32.   Nagel S, Streicher EM, Klopper M, Warren RM, Van Helden PD. Isoniazid resistance and dosage as treatment for patients with tuberculosis. Current drug metabolism 2017;18:1030-1039.

33.   Rockwood N, Sirgel F, Streicher E, Warren R, Meintjes G, Wilkinson RJ. Low frequency of acquired isoniazid and rifampicin resistance in rifampicin-susceptible pulmonary tuberculosis in a setting of high hiv-1 infection and tuberculosis coprevalence. The Journal of infectious diseases 2017;216:632-640.

34.   Metcalfe JZ, Streicher E, Theron G, Colman RE, Penaloza R, Allender C, Lemmer D, Warren RM, Engelthaler DM. Mycobacterium tuberculosis subculture results in loss of potentially clinically relevant heteroresistance. Antimicrobial agents and chemotherapy 2017;61.

35.   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. Journal of proteome research 2017;16:3841-3851.

36.   du Plessis J, Cloete R, Burchell L, Sarkar P, Warren RM, Christoffels A, Wigneshweraraj S, Sampson SL. Exploring the potential of t7 bacteriophage protein gp2 as a novel inhibitor of mycobacterial rna polymerase. Tuberculosis 2017;106:82-90.

37.   Metcalfe JZ, Streicher E, Theron G, Colman RE, Allender C, Lemmer D, Warren R, Engelthaler DM. Cryptic microheteroresistance explains mycobacterium tuberculosis phenotypic resistance. American journal of respiratory and critical care medicine 2017;196:1191-1201.

38.   Dippenaar A, Parsons SDC, Miller MA, Hlokwe T, Gey van Pittius NC, Adroub SA, Abdallah AM, Pain A, Warren RM, Michel AL, van Helden PD. 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 2017;51:235-238.

39.   Loveday M, Ramjee A, Osburn G, Master I, Kabera G, Brust JC, Padayatchi N, Warren R, Theron G. Drug-resistant tuberculosis in patients with minimal symptoms: Favourable outcomes in the absence of treatment. The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease 2017;21:556-563.

40.   Dheda K, Gumbo T, Maartens G, Dooley KE, McNerney R, Murray M, Furin J, Nardell EA, London L, Lessem E, Theron G, van Helden P, Niemann S, Merker M, Dowdy D, Van Rie A, Siu GK, Pasipanodya JG, Rodrigues C, Clark TG, Sirgel FA, Esmail A, Lin HH, Atre SR, Schaaf HS, Chang KC, Lange C, Nahid P, Udwadia ZF, Horsburgh CR, Jr., Churchyard GJ, Menzies D, Hesseling AC, Nuermberger E, McIlleron H, Fennelly KP, Goemaere E, Jaramillo E, Low M, Jara CM, Padayatchi N, Warren RM. The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis. The Lancet Respiratory medicine 2017.

41.   Jacobson KR, Barnard M, Kleinman MB, Streicher EM, Ragan EJ, White LF, Shapira O, Dolby T, Simpson J, Scott L, Stevens W, van Helden PD, Van Rie A, Warren RM. 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 2017;64:1502-1508.

42.   Walters E, van der Zalm MM, Palmer M, Bosch C, Demers AM, Draper H, Goussard P, Schaaf HS, Friedrich SO, Whitelaw A, Warren R, Gie RP, Hesseling AC. Xpert mtb/rif on stool is useful for the rapid diagnosis of tuberculosis in young children with severe pulmonary disease. The Pediatric infectious disease journal 2017;36:837-843.

43.   Dheda K, Limberis JD, Pietersen E, Phelan J, Esmail A, Lesosky M, Fennelly KP, Te Riele J, Mastrapa B, Streicher EM, Dolby T, Abdallah AM, Ben-Rached F, Simpson J, Smith L, Gumbo T, van Helden P, Sirgel FA, McNerney R, Theron G, Pain A, Clark TG, Warren RM. Outcomes, infectiousness, and transmission dynamics of patients with extensively drug-resistant tuberculosis and home-discharged patients with programmatically incurable tuberculosis: A prospective cohort study. The Lancet Respiratory medicine 2017;5:269-281.

44.   Katale BZ, Mbugi EV, Siame KK, Keyyu JD, Kendall S, Kazwala RR, Dockrell HM, Fyumagwa RD, Michel AL, Rweyemamu M, Streicher EM, Warren RM, van Helden P, Matee MI. Isolation and potential for transmission of mycobacterium bovis at human-livestock-wildlife interface of the serengeti ecosystem, northern tanzania. Transboundary and emerging diseases 2017;64:815-825.

45.   Olivier TT, Viljoen IM, Hofmeyr J, Hausler GA, Goosen WJ, Tordiffe ASW, Buss P, Loxton AG, Warren RM, Miller MA, van Helden PD, Parsons SDC. Development of a gene expression assay for the diagnosis of mycobacterium bovis infection in african lions (panthera leo). Transboundary and emerging diseases 2017;64:774-781.

Versatility of 7-Substituted Coumarin Molecules as Antimycobacterial Agents, Neuronal Enzyme Inhibitors and Neuroprotective Agents.

Kapp E, Visser H, Sampson SL, Malan SF, Streicher EM, Foka GB, Warner DF, Omoruyi SI, Enogieru AB, Ekpo OE, Zindo FT, Joubert J.

Molecules. 2017 Sep 30;22(10):1644. doi: 10.3390/molecules22101644.

PMID: 28973990

Hoal EG, Dippenaar A, Kinnear C, van Helden PD, Möller M. The arms race between man and Mycobacterium tuberculosis: Time to regroup.Infect Genet Evol. 2018 Dec;66:361-375. doi: 10.1016/j.meegid.2017.08.021. Epub 2017 Aug 23. Review. PubMed PMID: 28843547.

Biology of clinical strains of Mycobacterium tuberculosis with varying levels of transmission.

Shanley CA, Henao-Tamayo MI, Bipin C, Mugasimangalam R, Verma D, Ordway DJ, Streicher EM, Orme IM. Tuberculosis (Edinb). 2018 Mar;109:123-133. doi: 10.1016/j.tube.2018.02.003. Epub 2018 Feb 9. PMID: 29559116

46.   Bernitz N, Goosen WJ, Clarke C, Kerr TJ, Higgitt R, Roos EO, Cooper DV, Warren RM, van Helden PD, Parsons SDC, Miller MA. Parallel testing increases detection of mycobacterium bovis-infected african buffaloes (syncerus caffer). Veterinary immunology and immunopathology 2018;204:40-43.

47.   Brites D, Loiseau C, Menardo F, Borrell S, Boniotti MB, Warren R, Dippenaar A, Parsons SDC, Beisel C, Behr MA, Fyfe JA, Coscolla M, Gagneux S. A new phylogenetic framework for the animal-adapted mycobacterium tuberculosis complex. Frontiers in microbiology 2018;9:2820.

48.   Roos EO, Olea-Popelka F, Buss P, Hausler GA, Warren R, van Helden PD, Parsons SDC, de Klerk-Lorist LM, Miller MA. Measuring antigen-specific responses in mycobacterium bovis-infected warthogs (phacochoerus africanus) using the intradermal tuberculin test. BMC veterinary research 2018;14:360.

49.   Miller MA, Buss P, Parsons SDC, Roos E, Chileshe J, Goosen WJ, van Schalkwyk L, de Klerk-Lorist LM, Hofmeyr M, Hausler G, Rossouw L, Manamela T, Mitchell EP, Warren R, van Helden P. Conservation of white rhinoceroses threatened by bovine tuberculosis, south africa, 2016-2017. Emerging infectious diseases 2018;24:2373-2375.

50.   Ezewudo M, Borens A, Chiner-Oms A, Miotto P, Chindelevitch L, Starks AM, Hanna D, Liwski R, Zignol M, Gilpin C, Niemann S, Kohl TA, Warren RM, Crook D, Gagneux S, Hoffner S, Rodrigues C, Comas I, Engelthaler DM, Alland D, Rigouts L, Lange C, Dheda K, Hasan R, McNerney R, Cirillo DM, Schito M, Rodwell TC, Posey J. Integrating standardized whole genome sequence analysis with a global mycobacterium tuberculosis antibiotic resistance knowledgebase. Scientific reports 2018;8:15382.

51.   Myers B, Bouton TC, Ragan EJ, White LF, McIlleron H, Theron D, Parry CDH, Horsburgh CR, Warren RM, Jacobson KR. Impact of alcohol consumption on tuberculosis treatment outcomes: A prospective longitudinal cohort study protocol. BMC infectious diseases 2018;18:488.

52.   McIntosh AI, Jenkins HE, White LF, Barnard M, Thomson DR, Dolby T, Simpson J, Streicher EM, Kleinman MB, Ragan EJ, van Helden PD, Murray MB, Warren RM, Jacobson KR. Using routinely collected laboratory data to identify high rifampicin-resistant tuberculosis burden communities in the western cape province, south africa: A retrospective spatiotemporal analysis. PLoS medicine 2018;15:e1002638.

53.   Shin SS, Modongo C, Baik Y, Allender C, Lemmer D, Colman RE, Engelthaler DM, Warren RM, Zetola NM. 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 2018;218:1974-1982.

54.   Chihota VN, Niehaus A, Streicher EM, Wang X, Sampson SL, Mason P, Kallenius 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;13:e0200632.

55.   Ates LS, Dippenaar A, Sayes F, Pawlik A, Bouchier C, Ma L, Warren RM, Sougakoff W, Majlessi L, van Heijst JWJ, Brossier F, Brosch R. Unexpected genomic and phenotypic diversity of mycobacterium africanum lineage 5 affects drug resistance, protein secretion, and immunogenicity. Genome biology and evolution 2018;10:1858-1874.

56.   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. The Journal of antimicrobial chemotherapy 2018;73:2667-2674.

57.   Willemse D, Weber B, Masino L, Warren RM, Adinolfi S, Pastore A, Williams MJ. Rv1460, a sufr homologue, is a repressor of the suf operon in mycobacterium tuberculosis. PloS one 2018;13:e0200145.

58.   de Vos M, Derendinger B, Dolby T, Simpson J, van Helden PD, Rice JE, Wangh LJ, Theron G, Warren RM. Diagnostic accuracy and utility of fluorotype mtbdr, a new molecular assay for multidrug-resistant tuberculosis. Journal of clinical microbiology 2018;56.

59.   Roos EO, Olea-Popelka F, Buss P, de Klerk-Lorist LM, Cooper D, Warren RM, van Helden PD, Parsons SDC, Miller MA. Ip-10: A potential biomarker for detection of mycobacterium bovis infection in warthogs (phacochoerus africanus). Veterinary immunology and immunopathology 2018;201:43-48.

60.   Clarke C, Cooper D, Goosen WJ, McFadyen R, Warren RM, van Helden PD, Parsons SDC, Miller MA. Antigen-specific interferon-gamma release is decreased following the single intradermal comparative cervical skin test in african buffaloes (syncerus caffer). Veterinary immunology and immunopathology 2018;201:12-15.

61.   Reeve BWP, McFall SM, Song R, Warren R, Steingart KR, Theron G. Commercial products to preserve specimens for tuberculosis diagnosis: A systematic review. The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease 2018;22:741-753.

62.   Dheda K, Lenders L, Magombedze G, Srivastava S, Raj P, Arning E, Ashcraft P, Bottiglieri T, Wainwright H, Pennel T, Linegar A, Moodley L, Pooran A, Pasipanodya JG, Sirgel FA, van Helden PD, Wakeland E, Warren RM, Gumbo T. Drug-penetration gradients associated with acquired drug resistance in patients with tuberculosis. American journal of respiratory and critical care medicine 2018;198:1208-1219.

63.   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;13:e0197913.

64.   Feliciano CS, Namburete EI, Rodrigues Placa J, Peronni K, Dippenaar A, Warren RM, Silva WA, Jr., Bollela VR. 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 2018;110:59-67.

65.   Selepe MM, van Wyk AC, Hoek KGP, Prince Y, van Helden PD, Warren RM, Wright CA. Papanicolaou induced fluorescence, ziehl-neelsen and auramine o stains on lymph node fine needle aspiration biopsy specimens from children: A comparative study. Diagnostic cytopathology 2018;46:589-592.

66.   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. The European respiratory journal 2018;51.

67.   Coll F, Phelan J, Hill-Cawthorne GA, Nair MB, Mallard K, Ali S, Abdallah AM, Alghamdi S, Alsomali M, Ahmed AO, Portelli S, Oppong Y, Alves A, Bessa TB, Campino S, Caws M, Chatterjee A, Crampin AC, Dheda K, Furnham N, Glynn JR, Grandjean L, Ha DM, Hasan R, Hasan Z, Hibberd ML, Joloba M, Jones-Lopez EC, Matsumoto T, Miranda A, Moore DJ, Mocillo N, Panaiotov S, Parkhill J, Penha C, Perdigao J, Portugal I, Rchiad Z, Robledo J, Sheen P, Shesha NT, Sirgel FA, Sola C, Sousa EO, Streicher EM, Van Helden P, Viveiros M, Warren RM, McNerney R, Pain A, Clark TG. Author correction: Genome-wide analysis of multi- and extensively drug-resistant mycobacterium tuberculosis. Nature genetics 2018;50:764.

68.   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;39:045005.

69.   Kriel NL, Gallant J, van Wyk N, van Helden P, Sampson SL, Warren RM, Williams MJ. Mycobacterial nucleoid associated proteins: An added dimension in gene regulation. Tuberculosis 2018;108:169-177.

70.   Derendinger B, de Vos M, 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). Scientific reports 2018;8:3206.

71.   Davids M, Pooran AS, Pietersen E, Wainwright HC, Binder A, Warren R, Dheda K. Regulatory t cells subvert mycobacterial containment in patients failing extensively drug-resistant tuberculosis treatment. American journal of respiratory and critical care medicine 2018;198:104-116.

72.   Machado A, Rito T, Ghebremichael S, Muhate N, Maxhuza G, Macuamule C, Moiane I, Macucule B, Marranangumbe AS, Baptista J, Manguele J, Koivula T, Streicher EM, Warren RM, Kallenius G, van Helden P, Correia-Neves M. Genetic diversity and potential routes of transmission of mycobacterium bovis in mozambique. PLoS neglected tropical diseases 2018;12:e0006147.

73.   Ates LS, Dippenaar A, Ummels R, Piersma SR, van der Woude AD, van der Kuij K, Le Chevalier F, Mata-Espinosa D, Barrios-Payan J, Marquina-Castillo B, Guapillo C, Jimenez CR, Pain A, Houben ENG, Warren RM, Brosch R, Hernandez-Pando R, Bitter W. Mutations in ppe38 block pe_pgrs secretion and increase virulence of mycobacterium tuberculosis. Nature microbiology 2018;3:181-188.

74.   Theron G, Venter R, Smith L, Esmail A, Randall P, Sood V, Oelfese S, Calligaro G, Warren R, Dheda K. False-positive xpert mtb/rif results in retested patients with previous tuberculosis: Frequency, profile, and prospective clinical outcomes. Journal of clinical microbiology 2018;56.

Mouton JM, Heunis T, Dippenaar A, Gallant JL, Kleynhans L, Sampson SL. Comprehensive Characterization of the Attenuated Double Auxotroph Mycobacterium tuberculosisΔleuDΔpanCD as an Alternative to H37Rv. Front Microbiol. 2019;10:1922. doi: 10.3389/fmicb.2019.01922. eCollection 2019. PubMed PMID: 31481950; PubMed Central PMCID: PMC6710366.

75.   van der Heijden YF, Hughes J, Dowdy DW, Streicher E, Chihota V, Jacobson KR, Warren R, Theron G. Overcoming limitations of tuberculosis information systems: Researcher and clinician perspectives. Public health action 2019;9:120-127.

76.   Adesokan HK, Akinseye VO, Streicher EM, Van Helden P, Warren RM, Cadmus SI. Reverse zoonotic tuberculosis transmission from an emerging uganda i strain between pastoralists and cattle in south-eastern nigeria. BMC veterinary research 2019;15:437.

77.   Engelthaler DM, Streicher EM, Kelley EJ, Allender CJ, Wiggins K, Jimenez D, Lemmer D, Vittinghoff E, Theron G, Sirgel FA, Warren RM, Metcalfe JZ. Minority mycobacterium tuberculosis genotypic populations as an indicator of subsequent phenotypic resistance. American journal of respiratory cell and molecular biology 2019;61:789-791.

78.   Bernitz N, Kerr TJ, de Waal C, Cooper DV, Warren RM, Van Helden PD, Parsons SDC, Miller MA. Test characteristics of assays to detect mycobacterium bovis infection in high-prevalence african buffalo (syncerus caffer) herds. Journal of wildlife diseases 2019.

79.   Roos EO, Scott LA, Ndou S, Olea-Popelka F, Buss PE, de Klerk-Lorist LM, Warren RM, van Helden PD, Sylvester TT, Miller MA, Parsons SDC. Cytokine gene expression assay as a diagnostic tool for detection of mycobacterium bovis infection in warthogs (phacochoerus africanus). Scientific reports 2019;9:16525.

80.   Mogashoa T, Melamu P, Derendinger B, Ley SD, Streicher EM, Iketleng T, Mupfumi L, Mokomane M, Kgwaadira B, Rankgoane-Pono G, Tsholofelo TT, Kasvosve I, Moyo S, Warren RM, Gaseitsiwe S. Detection of second line drug resistance among drug resistant mycobacterium tuberculosis isolates in botswana. Pathogens 2019;8.

81.   Bouton TC, de Vos M, Ragan EJ, White LF, Van Zyl L, Theron D, Horsburgh CR, Warren RM, Jacobson KR. Switching to bedaquiline for treatment of rifampicin-resistant tuberculosis in south africa: A retrospective cohort analysis. PloS one 2019;14:e0223308.

82.   Georghiou SB, Schumacher SG, Rodwell TC, Colman RE, Miotto P, Gilpin C, Ismail N, Rodrigues C, Warren R, Weyer K, Zignol M, Arafah S, Cirillo DM, Denkinger CM. Guidance for studies evaluating the accuracy of rapid tuberculosis drug-susceptibility tests. The Journal of infectious diseases 2019;220:S126-S135.

83.   Chileshe J, Roos EO, Goosen WJ, Buss P, Hausler G, Rossouw L, Manemela T, van Helden P, Warren R, Parsons SD, Miller M. An interferon-gamma release assay for the diagnosis of the mycobacterium bovis infection in white rhinoceros (ceratotherium simum). Veterinary immunology and immunopathology 2019;217:109931.

84.   Dheda K, Gumbo T, Maartens G, Dooley KE, Murray M, Furin J, Nardell EA, Warren RM, Lancet Respiratory Medicine drug-resistant tuberculosis Commission g. The lancet respiratory medicine commission: 2019 update: Epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant and incurable tuberculosis. The Lancet Respiratory medicine 2019;7:820-826.

85.   Bernitz N, Kerr TJ, Goosen WJ, Higgitt RL, de Waal C, Clarke C, Cooper DV, Warren RM, van Helden PD, Parsons SDC, Miller MA. Impact of mycobacterium bovis-induced pathology on interpretation of quantiferon(r)-tb gold assay results in african buffaloes (syncerus caffer). Veterinary immunology and immunopathology 2019;217:109923.

86.   Ronacher K, Chegou NN, Kleynhans L, Djoba Siawaya JF, du Plessis N, Loxton AG, Maasdorp E, Tromp G, Kidd M, Stanley K, Kriel M, Menezes A, Gutschmidt A, van der Spuy GD, Warren RM, Dietze R, Okwera A, Thiel B, Belisle JT, Cliff JM, Boom WH, Johnson JL, van Helden PD, Dockrell HM, Walzl G. Distinct serum biosignatures are associated with different tuberculosis treatment outcomes. Tuberculosis 2019;118:101859.

87.   Wang Q, Modongo C, Allender C, Engelthaler DM, Warren RM, Zetola NM, Shin SS. Utility of targeted, amplicon-based deep sequencing to detect resistance to first-line tuberculosis drugs in botswana. Antimicrobial agents and chemotherapy 2019;63.

88.   Feliciano CS, Menon LJB, Anselmo LMP, Dippenaar A, Warren RM, Silva WA, Jr., Bollela VR. Xpert mtb/rif performance to diagnose tuberculosis and rifampicin resistance in a reference centre in southern brazil. ERJ open research 2019;5.

89.   Bernitz N, Kerr TJ, Goosen WJ, Clarke C, Higgitt R, Roos EO, Cooper DV, Warren RM, van Helden PD, Parsons SDC, Miller MA. Parallel measurement of ifn-gamma and ip-10 in quantiferon(r)-tb gold (qft) plasma improves the detection of mycobacterium bovis infection in african buffaloes (syncerus caffer). Preventive veterinary medicine 2019;169:104700.

90.   Machado KCT, Fortuin S, Tomazella GG, Fonseca AF, Warren RM, Wiker HG, de Souza SJ, de Souza GA. On the impact of the pangenome and annotation discrepancies while building protein sequence databases for bacteria proteogenomics. Frontiers in microbiology 2019;10:1410.

91.   Dippenaar A, De Vos M, Marx FM, Adroub SA, van Helden PD, Pain A, Sampson SL, Warren RM. 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 2019;75:103948.

92.   Grobbelaar M, Louw GE, Sampson SL, van Helden PD, Donald PR, Warren RM. Evolution of rifampicin treatment for tuberculosis. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019;74:103937.

93.   Chirenda J, Chipinduro M, de Kock M, Spies C, Sakubani CT, Warren 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;8:185-189.

94.   Meehan CJ, Goig GA, Kohl TA, Verboven L, Dippenaar A, Ezewudo M, Farhat MR, Guthrie JL, Laukens K, Miotto P, Ofori-Anyinam B, Dreyer V, Supply P, Suresh A, Utpatel C, van Soolingen D, Zhou Y, Ashton PM, Brites D, Cabibbe AM, de Jong BC, de Vos M, Menardo F, Gagneux S, Gao Q, Heupink TH, Liu Q, Loiseau C, Rigouts L, Rodwell TC, Tagliani E, Walker TM, Warren RM, Zhao Y, Zignol M, Schito M, Gardy J, Cirillo DM, Niemann S, Comas I, Van Rie A. Whole genome sequencing of mycobacterium tuberculosis: Current standards and open issues. Nature reviews Microbiology 2019;17:533-545.

95.   van Leeuwen LM, Versteegen P, Zaharie SD, van Elsland SL, Jordaan A, Streicher EM, Warren RM, van der Kuip M, van Furth AM. Bacterial genotyping of central nervous system tuberculosis in south africa: Heterogenic mycobacterium tuberculosis infection and predominance of lineage 4. Journal of clinical microbiology 2019;57.

96.   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. Bedaquiline microheteroresistance after cessation of tuberculosis treatment. The New England journal of medicine 2019;380:2178-2180.

97.   Mogashoa T, Melamu P, Ley SD, Streicher EM, Iketleng T, Kelentse N, Mupfumi L, Mokomane M, Kgwaadira B, Novitsky V, Kasvosve I, Moyo S, Warren RM, Gaseitsiwe S. Genetic diversity of mycobacterium tuberculosis strains circulating in botswana. PloS one 2019;14:e0216306.

98.   Chileshe J, Goosen WJ, Buss PE, van Helden PD, Warren R, Parsons SDC, Miller MA. A commercial elisa for detection of interferon gamma in white rhinoceros. Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc 2019;31:531-536.

99. Ley SD, de Vos M, Van Rie A, Warren RM. Deciphering within-host microevolution of mycobacterium tuberculosis through whole-genome sequencing: The phenotypic impact and way forward. Microbiology and molecular biology reviews : MMBR 2019;83.

100. Naidoo CC, Nyawo GR, Wu BG, Walzl G, Warren RM, Segal LN, Theron G. The microbiome and tuberculosis: State of the art, potential applications, and defining the clinical research agenda. The Lancet Respiratory medicine 2019;7:892-906.

101. Miller MA, Buss P, Roos EO, Hausler G, Dippenaar A, Mitchell E, van Schalkwyk L, Robbe-Austerman S, Waters WR, Sikar-Gang A, Lyashchenko KP, Parsons SDC, Warren R, van Helden P. Fatal tuberculosis in a free-ranging african elephant and one health implications of human pathogens in wildlife. Frontiers in veterinary science 2019;6:18.

102. Adesokan HK, Streicher EM, van Helden PD, Warren RM, Cadmus SIB. Genetic diversity of mycobacterium tuberculosis complex strains isolated from livestock workers and cattle in nigeria. PloS one 2019;14:e0211637.

103. Bulabula ANH, Nelson JA, Musafiri EM, Machekano R, Sam-Agudu NA, Diacon AH, Shah M, Creswell J, Theron G, Warren RM, Jacobson KR, Chirambiza JP, Kalumuna D, Bisimwa BC, Katoto P, Kaswa MK, Birembano FM, Kitete L, Grobusch MP, Kashongwe ZM, Nachega JB. 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: A retrospective province-wide cohort study. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019;69:1278-1287.

104. Dheda K, Lenders L, Srivastava S, Magombedze G, Wainwright H, Raj P, Bush SJ, Pollara G, Steyn R, Davids M, Pooran A, Pennel T, Linegar A, McNerney R, Moodley L, Pasipanodya JG, Turner CT, Noursadeghi M, Warren RM, Wakeland E, Gumbo T. Spatial network mapping of pulmonary multidrug-resistant tuberculosis cavities using rna sequencing. American journal of respiratory and critical care medicine 2019;200:370-380.

105. Wasserman S, Denti P, Brust JCM, Abdelwahab M, Hlungulu S, Wiesner L, Norman J, Sirgel FA, Warren RM, Esmail A, Dheda K, Gandhi NR, Meintjes G, Maartens G. Linezolid pharmacokinetics in south african patients with drug-resistant tuberculosis and a high prevalence of hiv coinfection. Antimicrobial agents and chemotherapy 2019;63.

106. Khan PY, Yates TA, Osman M, Warren RM, van der Heijden Y, Padayatchi N, Nardell EA, Moore D, Mathema B, Gandhi N, Eldholm V, Dheda K, Hesseling AC, Mizrahi V, Rustomjee R, Pym A. Transmission of drug-resistant tuberculosis in hiv-endemic settings. The Lancet Infectious diseases 2019;19:e77-e88.

107. Warren R, Ismail N, Chegou NN, et al. Tuberculosis research in South Africa over the past 30 years: From bench to bedside. South African Medical Journal; SOUTH AFRICAN MEDICAL RESEARCH COUNCIL50 YEARS OF GROUND BREAKING HEALTH RESEARCH AND INNOVATION. 2019.

108. Shanley CA, Henao-Tamayo MI, Bipin C, Mugasimangalam R, Verma D, Ordway DJ, Streicher EM, Orme IM. Biology of clinical strains of Mycobacterium tuberculosis with varying levels of transmission. Tuberculosis (Edinb). 2018 Mar;109:123-133. doi: 10.1016/j.tube.2018.02.003. Epub 2018 Feb 9.

PMID: 29559116

109. Kapp E, Visser H, Sampson SL, Malan SF, Streicher EM, Foka GB, Warner DF, Omoruyi SI, Enogieru AB, Ekpo OE, Zindo FT, Joubert J. Versatility of 7-Substituted Coumarin Molecules as Antimycobacterial Agents, Neuronal Enzyme Inhibitors and Neuroprotective Agents. Molecules. 2017 Sep 30;22(10):1644. doi: 10.3390/molecules22101644.

PMID: 28973990

110. Hoal EG, Dippenaar A, Kinnear C, van Helden PD, Möller M. The arms race between man and Mycobacterium tuberculosis: Time to regroup.Infect Genet Evol. 2018 Dec;66:361-375. doi: 10.1016/j.meegid.2017.08.021. Epub 2017 Aug 23. Review. PubMed PMID: 28843547.

111. 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. Front Microbiol. 2019;10:1922. doi: 10.3389/fmicb.2019.01922. eCollection 2019. PubMed PMID: 31481950; PubMed Central PMCID: PMC6710366.​​

​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