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Rapid Pyrazinamide Drug Susceptibility Testing using a Closed-Tube PCR Assay of the Entire pncA gene.

Whitfield MG, Marras SAE, Warren RM, Van Rie A, Rice J, Wangh LJ, Kreiswirth BN.

Sci Rep. 2020 Mar 6;10(1):4234. doi: 10.1038/s41598-020-61286-7.


Author Correction: Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase.

Ezewudo M, Borens A, Chiner-Oms Á, 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.

Sci Rep. 2020 Feb 21;10(1):3531. doi: 10.1038/s41598-020-58955-y.


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.

Mishra H, Reeve BWP, Palmer Z, Caldwell J, Dolby T, Naidoo CC, Jackson JG, Schumacher SG, Denkinger CM, Diacon AH, van Helden PD, Marx FM, Warren RM, Theron G.

Lancet Respir Med. 2020 Apr;8(4):368-382. doi: 10.1016/S2213-2600(19)30370-4. Epub 2020 Feb 14.


Phylogenomic assessment of drug-resistant Mycobacterium tuberculosis strains from Beira, Mozambique.

Namburete EI, Dippenaar A, Conceição EC, Feliciano C, Nascimento MMPD, Peronni KC, Silva WA Jr, Ferro JJ, Harrison LH, Warren RM, Bollela VR.

Tuberculosis (Edinb). 2020 Jan 29;121:101905. doi: 10.1016/ [Epub ahead of print]


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.

Venter R, Minnies S, Derendinger B, Tshivhula H, de Vos M, Dolby T, Ruiters A, Warren RM, Theron G.

Sci Rep. 2020 Feb 14;10(1):2633. doi: 10.1038/s41598-020-59164-3.


Rifampicin Resistant Tuberculosis in Lesotho: Diagnosis, Treatment Initiation and Outcomes.

Katende B, Esterhuizen TM, Dippenaar A, Warren RM.

Sci Rep. 2020 Feb 5;10(1):1917. doi: 10.1038/s41598-020-58690-4.


Discordances between molecular assays for rifampicin resistance in Mycobacterium tuberculosis: frequency, mechanisms and clinical impact.

Van Rie A, Whitfield MG, De Vos E, Scott L, Da Silva P, Hayes C, Heupink TH, Sirgel FA, Stevens W, Warren RM.

J Antimicrob Chemother. 2020 Feb 4. pii: dkz564. doi: 10.1093/jac/dkz564. [Epub ahead of print]


A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic.

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.

BMC Med. 2020 Feb 4;18(1):24. doi: 10.1186/s12916-019-1487-2.


Reverse zoonotic tuberculosis transmission from an emerging Uganda I strain between pastoralists and cattle in South-Eastern Nigeria.

Adesokan HK, Akinseye VO, Streicher EM, Van Helden P, Warren RM, Cadmus SI.

BMC Vet Res. 2019 Dec 4;15(1):437. doi: 10.1186/s12917-019-2185-1.


Minority Mycobacterium tuberculosis Genotypic Populations as an Indicator of Subsequent Phenotypic Resistance.

Engelthaler DM, Streicher EM, Kelley EJ, Allender CJ, Wiggins K, Jimenez D, Lemmer D, Vittinghoff E, Theron G, Sirgel FA, Warren RM, Metcalfe JZ.

Am J Respir Cell Mol Biol. 2019 Dec;61(6):789-791. doi: 10.1165/rcmb.2019-0178LE. No abstract available.


Test Characteristics of Assays to Detect Mycobacterium bovis Infection in High-Prevalence African Buffalo (Syncerus caffer) Herds.

Bernitz N, Kerr TJ, de Waal C, Cooper DV, Warren RM, Van Helden PD, Parsons SDC, Miller MA.

J Wildl Dis. 2020 Apr;56(2):462-465. Epub 2019 Nov 21.


Cytokine gene expression assay as a diagnostic tool for detection of Mycobacterium bovis infection in warthogs (Phacochoerus africanus).

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.

Sci Rep. 2019 Nov 11;9(1):16525. doi: 10.1038/s41598-019-53045-0.


Detection of Second Line Drug Resistance among Drug Resistant Mycobacterium Tuberculosis Isolates in Botswana.

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.

Pathogens. 2019 Oct 28;8(4). pii: E208. doi: 10.3390/pathogens8040208.


Switching to bedaquiline for treatment of rifampicin-resistant tuberculosis in South Africa: A retrospective cohort analysis.

Bouton TC, de Vos M, Ragan EJ, White LF, Van Zyl L, Theron D, Horsburgh CR, Warren RM, Jacobson KR.

PLoS One. 2019 Oct 17;14(10):e0223308. doi: 10.1371/journal.pone.0223308. eCollection 2019.


The Lancet Respiratory Medicine Commission: 2019 update: epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant and incurable tuberculosis.

Dheda K, Gumbo T, Maartens G, Dooley KE, Murray M, Furin J, Nardell EA, Warren RM; Lancet Respiratory Medicine drug-resistant tuberculosis Commission group.

Lancet Respir Med. 2019 Sep;7(9):820-826. doi: 10.1016/S2213-2600(19)30263-2. Review.


Impact of Mycobacterium bovis-induced pathology on interpretation of QuantiFERON®-TB Gold assay results in African buffaloes (Syncerus caffer).

Bernitz N, Kerr TJ, Goosen WJ, Higgitt RL, de Waal C, Clarke C, Cooper DV, Warren RM, van Helden PD, Parsons SDC, Miller MA.

Vet Immunol Immunopathol. 2019 Nov;217:109923. doi: 10.1016/j.vetimm.2019.109923. Epub 2019 Aug 8.


Distinct serum biosignatures are associated with different tuberculosis treatment outcomes.

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.

Tuberculosis (Edinb). 2019 Sep;118:101859. doi: 10.1016/ Epub 2019 Aug 12.


Utility of Targeted, Amplicon-Based Deep Sequencing To Detect Resistance to First-Line Tuberculosis Drugs in Botswana.

Wang Q, Modongo C, Allender C, Engelthaler DM, Warren RM, Zetola NM, Shin SS.

Antimicrob Agents Chemother. 2019 Oct 22;63(11). pii: e00982-19. doi: 10.1128/AAC.00982-19. Print 2019 Nov.


Xpert MTB/RIF performance to diagnose tuberculosis and rifampicin resistance in a reference centre in southern Brazil.

Feliciano CS, Menon LJB, Anselmo LMP, Dippenaar A, Warren RM, Silva WA Jr, Bollela VR.

ERJ Open Res. 2019 Aug 5;5(3). pii: 00043-2019. doi: 10.1183/23120541.00043-2019. eCollection 2019 Jul.


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).

Bernitz N, Kerr TJ, Goosen WJ, Clarke C, Higgitt R, Roos EO, Cooper DV, Warren RM, van Helden PD, Parsons SDC, Miller MA.

Prev Vet Med. 2019 Aug 1;169:104700. doi: 10.1016/j.prevetmed.2019.104700. Epub 2019 May 23.


On the Impact of the Pangenome and Annotation Discrepancies While Building Protein Sequence Databases for Bacteria Proteogenomics.

Machado KCT, Fortuin S, Tomazella GG, Fonseca AF, Warren RM, Wiker HG, de Souza SJ, de Souza GA.

Front Microbiol. 2019 Jun 20;10:1410. doi: 10.3389/fmicb.2019.01410. eCollection 2019.


Whole genome sequencing provides additional insights into recurrent tuberculosis classified as endogenous reactivation by IS6110 DNA fingerprinting.

Dippenaar A, De Vos M, Marx FM, Adroub SA, van Helden PD, Pain A, Sampson SL, Warren RM.

Infect Genet Evol. 2019 Nov;75:103948. doi: 10.1016/j.meegid.2019.103948. Epub 2019 Jul 2.


Evolution of rifampicin treatment for tuberculosis.

Grobbelaar M, Louw GE, Sampson SL, van Helden PD, Donald PR, Warren RM.

Infect Genet Evol. 2019 Oct;74:103937. doi: 10.1016/j.meegid.2019.103937. Epub 2019 Jun 24.


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.

Chirenda J, Chipinduro M, de Kock M, Spies C, Sakubani CT, Warren RM, Sampson SL, Streicher EM.

Int J Mycobacteriol. 2019 Apr-Jun;8(2):185-189. doi: 10.4103/ijmy.ijmy_46_19.


Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues.

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.

Nat Rev Microbiol. 2019 Sep;17(9):533-545. doi: 10.1038/s41579-019-0214-5. Review.


Bacterial Genotyping of Central Nervous System Tuberculosis in South Africa: Heterogenic Mycobacterium tuberculosis Infection and Predominance of Lineage 4.

van Leeuwen LM, Versteegen P, Zaharie SD, van Elsland SL, Jordaan A, Streicher EM, Warren RM, van der Kuip M, van Furth AM.

J Clin Microbiol. 2019 Jul 26;57(8). pii: e00415-19. doi: 10.1128/JCM.00415-19. Print 2019 Aug.


Genetic diversity of Mycobacterium tuberculosis strains circulating in Botswana.

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.

PLoS One. 2019 May 7;14(5):e0216306. doi: 10.1371/journal.pone.0216306. eCollection 2019.


Deciphering Within-Host Microevolution of Mycobacterium tuberculosis through Whole-Genome Sequencing: the Phenotypic Impact and Way Forward.

Ley SD, de Vos M, Van Rie A, Warren RM.

Microbiol Mol Biol Rev. 2019 Mar 27;83(2). pii: e00062-18. doi: 10.1128/MMBR.00062-18. Print 2019 May 15. Review.


The microbiome and tuberculosis: state of the art, potential applications, and defining the clinical research agenda.

Naidoo CC, Nyawo GR, Wu BG, Walzl G, Warren RM, Segal LN, Theron G.

Lancet Respir Med. 2019 Oct;7(10):892-906. doi: 10.1016/S2213-2600(18)30501-0. Epub 2019 Mar 22. Review.


Genetic diversity of Mycobacterium tuberculosis complex strains isolated from livestock workers and cattle in Nigeria.

Adesokan HK, Streicher EM, van Helden PD, Warren RM, Cadmus SIB.

PLoS One. 2019 Feb 20;14(2):e0211637. doi: 10.1371/journal.pone.0211637. eCollection 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: A Retrospective Province-Wide Cohort Study.

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 PDMC, Kaswa MK, Birembano FM, Kitete L, Grobusch MP, Kashongwe ZM, Nachega JB.

Clin Infect Dis. 2019 Sep 27;69(8):1278-1287. doi: 10.1093/cid/ciy1105.


Spatial Network Mapping of Pulmonary Multidrug-Resistant Tuberculosis Cavities Using RNA Sequencing.

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.

Am J Respir Crit Care Med. 2019 Aug 1;200(3):370-380. doi: 10.1164/rccm.201807-1361OC.


Linezolid Pharmacokinetics in South African Patients with Drug-Resistant Tuberculosis and a High Prevalence of HIV Coinfection.

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.

Antimicrob Agents Chemother. 2019 Feb 26;63(3). pii: e02164-18. doi: 10.1128/AAC.02164-18. Print 2019 Mar.


Parallel testing increases detection of Mycobacterium bovis-infected African buffaloes (Syncerus caffer).

Bernitz N, Goosen WJ, Clarke C, Kerr TJ, Higgitt R, Roos EO, Cooper DV, Warren RM, van Helden PD, Parsons SDC, Miller MA.

Vet Immunol Immunopathol. 2018 Oct;204:40-43. doi: 10.1016/j.vetimm.2018.09.004. Epub 2018 Sep 18.


Transmission of drug-resistant tuberculosis in HIV-endemic settings.

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.

Lancet Infect Dis. 2019 Mar;19(3):e77-e88. doi: 10.1016/S1473-3099(18)30537-1. Epub 2018 Dec 13. Review. Erratum in: Lancet Infect Dis. 2019 Mar 6;:.


Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase.

Ezewudo M, Borens A, Chiner-Oms Á, 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.

Sci Rep. 2018 Oct 18;8(1):15382. doi: 10.1038/s41598-018-33731-1. Erratum in: Sci Rep. 2020 Feb 21;10(1):3531.


Impact of alcohol consumption on tuberculosis treatment outcomes: a prospective longitudinal cohort study protocol.

Myers B, Bouton TC, Ragan EJ, White LF, McIlleron H, Theron D, Parry CDH, Horsburgh CR, Warren RM, Jacobson KR.

BMC Infect Dis. 2018 Sep 29;18(1):488. doi: 10.1186/s12879-018-3396-y.


Using routinely collected laboratory data to identify high rifampicin-resistant tuberculosis burden communities in the Western Cape Province, South Africa: A retrospective spatiotemporal analysis.

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.

PLoS Med. 2018 Aug 21;15(8):e1002638. doi: 10.1371/journal.pmed.1002638. eCollection 2018 Aug.


Mixed Mycobacterium tuberculosis-Strain Infections Are Associated With Poor Treatment Outcomes Among Patients With Newly Diagnosed Tuberculosis, Independent of Pretreatment Heteroresistance.

Shin SS, Modongo C, Baik Y, Allender C, Lemmer D, Colman RE, Engelthaler DM, Warren RM, Zetola NM.

J Infect Dis. 2018 Nov 5;218(12):1974-1982. doi: 10.1093/infdis/jiy480.


Geospatial distribution of Mycobacterium tuberculosis genotypes in Africa.

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.

PLoS One. 2018 Aug 1;13(8):e0200632. doi: 10.1371/journal.pone.0200632. eCollection 2018.


Unexpected Genomic and Phenotypic Diversity of Mycobacterium africanum Lineage 5 Affects Drug Resistance, Protein Secretion, and Immunogenicity.

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.

Genome Biol Evol. 2018 Aug 1;10(8):1858-1874. doi: 10.1093/gbe/evy145.


The potential use of rifabutin for treatment of patients diagnosed with rifampicin-resistant tuberculosis.

Whitfield MG, Warren RM, Mathys V, Scott L, De Vos E, Stevens W, Streicher EM, Groenen G, Sirgel FA, Van Rie A.

J Antimicrob Chemother. 2018 Oct 1;73(10):2667-2674. doi: 10.1093/jac/dky248.


Rv1460, a SufR homologue, is a repressor of the suf operon in Mycobacterium tuberculosis.

Willemse D, Weber B, Masino L, Warren RM, Adinolfi S, Pastore A, Williams MJ.

PLoS One. 2018 Jul 6;13(7):e0200145. doi: 10.1371/journal.pone.0200145. eCollection 2018. Erratum in: PLoS One. 2018 Nov 29;13(11):e0208568.


Diagnostic Accuracy and Utility of FluoroType MTBDR, a New Molecular Assay for Multidrug-Resistant Tuberculosis.

de Vos M, Derendinger B, Dolby T, Simpson J, van Helden PD, Rice JE, Wangh LJ, Theron G, Warren RM.

J Clin Microbiol. 2018 Aug 27;56(9). pii: e00531-18. doi: 10.1128/JCM.00531-18. Print 2018 Sep.


IP-10: A potential biomarker for detection of Mycobacterium bovis infection in warthogs (Phacochoerus africanus).

Roos EO, Olea-Popelka F, Buss P, de Klerk-Lorist LM, Cooper D, Warren RM, van Helden PD, Parsons SDC, Miller MA.

Vet Immunol Immunopathol. 2018 Jul;201:43-48. doi: 10.1016/j.vetimm.2018.05.007. Epub 2018 May 21.


Antigen-specific interferon-gamma release is decreased following the single intradermal comparative cervical skin test in African buffaloes (Syncerus caffer).

Clarke C, Cooper D, Goosen WJ, McFadyen R, Warren RM, van Helden PD, Parsons SDC, Miller MA.

Vet Immunol Immunopathol. 2018 Jul;201:12-15. doi: 10.1016/j.vetimm.2018.05.002. Epub 2018 May 15.


Drug-Penetration Gradients Associated with Acquired Drug Resistance in Patients with Tuberculosis.

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.

Am J Respir Crit Care Med. 2018 Nov 1;198(9):1208-1219. doi: 10.1164/rccm.201711-2333OC.


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.

Feliciano CS, Namburete EI, Rodrigues Plaça J, Peronni K, Dippenaar A, Warren RM, Silva WA Jr, Bollela VR.

Tuberculosis (Edinb). 2018 May;110:59-67. doi: 10.1016/ Epub 2018 Apr 5.


Papanicolaou induced fluorescence, Ziehl-Neelsen and Auramine O stains on lymph node fine needle aspiration biopsy specimens from children: A comparative study.

Selepe MM, van Wyk AC, Hoek KGP, Prince Y, van Helden PD, Warren RM, Wright CA.

Diagn Cytopathol. 2018 Jul;46(7):589-592. doi: 10.1002/dc.23956. Epub 2018 May 3.


Arrays of rectangular subcritical speech bands: Intelligibility improved by noise-vocoding and expanding to critical bandwidths.

Warren RM, Bashford JA Jr, Lenz PW.

J Acoust Soc Am. 2018 Apr;143(4):EL305. doi: 10.1121/1.5034170.

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