Publications | Division of Medical Microbiology

2023

Abotsi RE, Dube FS, Rehman AM, Claassen-Weitz S, Xia Y, Simms V, Mwaikono KS, Gardner-Lubbe S, McHugh G, Ngwira LG, Kwambana-Adams B, Heyderman RS, Odland JØ, Ferrand RA, Nicol MP; BREATHE study team. Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease. Microbiome. 2023;11(1):29.

Apolisi I, Cox H, Tyeku N, Daniels J, Mathee S, Cariem R, Douglas-Jones B, Ngambu N, Mudaly V, Mohr-Holland E, Isaakidis P, Pfaff C, Furin J, Reuter A. Tuberculosis Diagnosis and Preventive Monotherapy Among Children and Adolescents Exposed to Rifampicin-Resistant Tuberculosis in the Household. Open Forum Infect Dis. 2023;10(3):ofad087.

Arakkal A, Centner CM, Hilton T, Nortje M, Held M, Roche S, Brink AJ, Mendelson M, Laubscher M. Developing an antibiogram for empiric antibiotic prescribing for adult non-spinal orthopaedic infections in a developing world setting. Eur J Orthop Surg Traumatol. 2023 Sep 15.

Bamford C, Blumberg LH, Bosman M, Frean J, Hoek KGP, Miles J, Sriruttan C, Vorster I, Oosthuizen MC. Neoehrlichiosis in Symptomatic Immunocompetent Child, South Africa. Emerging Infectious Disease. 2023; 29(2):407-410

Bobak CA, Botha M, Workman L, Hill JE, Nicol MP, Holloway JW, Stein DJ, Martinez L, Zar HJ. Gene Expression in Cord Blood and Tuberculosis in Early Childhood: A Nested Case-Control Study in a South African Birth Cohort. Clin Infect Dis. 2023 14;77(3):438-449.

Boshoff HIM, Warner DF, Gold B. Editorial: Drug-resistant Mycobacterium tuberculosis. Front Cell Infect Microbiol. 2023;13:1215294.

Campaniço A, Harjivan SG, Freitas E, Serafini M, Gaspar MM, Capela R, Gomes P, Jordaan A, Madureira AM, André V, Silva AB, Duarte MT, Portugal I, Perdigão J, Moreira R, Warner DF, Lopes F. Structural Optimization of Antimycobacterial Azaaurones Towards Improved Solubility and Metabolic Stability. ChemMedChem. 2023;18(24):e202300410.

Chengalroyen M. Current Perspectives and Challenges of MAIT Cell-Directed Therapy for Tuberculosis Infection. Pathogens. 2023; 12(11): 11-12

Chengalroyen MD, Mehaffy C, Lucas M, Bauer N, Raphela ML, Oketade N, Warner DF, Lewinsohn DA, Lewinsohn DM, Dobos KM, Mizrahi V. Modulation of riboflavin biosynthesis and utilization in mycobacteria. bioRxiv [Preprint]. 2023;2023.08.30.555301

Claassen-Weitz S, Gardner-Lubbe S, Xia Y, Mwaikono KS, Mounaud SH, Nierman WC, Workman L, Zar HJ, Nicol MP. Succession and determinants of the early life nasopharyngeal microbiota in a South African birth cohort. Microbiome. 2023;11(1):127.

Derendinger B, Dippenaar A, de Vos M, Huo S, Alberts R, Tadokera R, Limberis J, Sirgel F, Dolby T, Spies C, Reuter A, Folkerts M, Allender C, Lemmer D, Van Rie A, Gagneux S, Rigouts L, Te Riele J, Dheda K, Engelthaler DM, Warren R, Metcalfe J, Cox H, Theron G. Bedaquiline resistance in patients with drug-resistant tuberculosis in Cape Town, South Africa: a retrospective longitudinal cohort study. Lancet Microbe. 2023;4(12):e972-e982

Dheda K, Centner CM, Wilson L, Pooran A, Grimwood S, Ghebrekristos YT, Oelofse S, Joubert IA, Esmail A, Tomasicchio M. Intensive Care Unit Sluice Room Sinks as Reservoirs and Sources of Potential Transmission of Carbapenem-Resistant Bacteria in a South African Tertiary Care Hospital. Infection and Drug Resistance. 2023; 16: 5427-5432
Dickson L, Le Roux SR, Mitrani L, Hill J, Jassat W, Cox H, Mlisana K, Black J, Loveday M, Grant A, Kielmann K, Ndjeka N, Moshabela M, Nicol M. Organisation of care for people receiving drug-resistant tuberculosis treatment in South Africa: a mixed methods study. BMJ Open. 2023;13(11):e067121.

du Preez C, Legoabe LJ, Jordaan A, Jesumoroti OJ, Warner DF, Beteck RM. Arylnitro monocarbonyl curcumin analogues: synthesis and in vitro antitubercular evaluation. Chem Biol Drug Des. 2023; 101(3):717-726.

Dube PS, Angula KT, Legoabe LJ, Jordaan A, Boitz Zarella JM, Warner DF, Doggett JS, Beteck RM. Quinolone-3-amidoalkanol: A New Class of Potent and Broad-Spectrum Antimicrobial Agent. ACS Omega. 2023;8(19):17086-1710

Dube PS, Legoabe LJ, Jordaan A, Sigauke L, Warner DF, Beteck RM. Quinolone analogues of benzothiazinone: Synthesis, antitubercular structure-activity relationship and ADME profiling. Eur J Med Chem. 2023;258:115539.

Gebremicael MN, Nuttall JJC, Tootla HD, Khumalo A, Tooke L, Salie S, Muloiwa R, Rhoda N, Basera W, Eley BS. Candida bloodstream infection among children hospitalised in three public-sector hospitals in the Metro West region of Cape Town, South Africa. BMC Infect Dis. 2023;23(1):67.

Ghebrekristos YT, Beylis N, Centner CM, Venter R, Derendinger B, Thsivhula H, Naidoo S, Alberts R, Prins B, Tokota A, Dolby T, Marx F, Omar SV, Warren R, Grant T. Xpert MTB/ RIF ultra on contaminated liquid cultures for tuberculosis and rifamicin-resistance detection: a diagnostic accuracy evaluation. The Lancet Microbe. 2023; 4(10):e822-829

Gigi RMS, Mdingi MM, Jung H, Claassen-Weitz S, Bütikofer L, Klausner JD, Muzny CA, Taylor CM, van de Wijgert JHHM, Peters RPH, Low N. Genital tract infections, the vaginal microbiome and gestational age at birth among pregnant women in South Africa: A cohort study protocol. BMJ Open. 2023; 13(12): 1-8

Gizamba JM, Paul L, Dlamini SK, Odayar J. Incidence and distribution of human leptospirosis in the Western Cape Province, South Africa (2010-2019): a retrospective study. Pan African Medical Journal. 2023; 44:121

Goig GA, Menardo F, Salaam-Dreyer Z, Dippenaar A, Streicher L, Daniels J, Reuter A, Borell S, Reinhard M, Doetsch A, Beisel C, Warren RM, Gagneux S, Cox H. Effect of compensatory evolution facilitates the emergence and transmission of rifampicin-resistant Mycobacterium tuberculosis in a high-endemic setting. Lancet Microbe. 2023; 4:e506-e515

Hall MB, Rabodoarivelo MS, Koch A, Dippenaar A, George S, Grobbelaar M, Warren R, Walker TM, Cox H, Gagneux S, Crook D, Peto T, Rakotosamimanana N, Grandjean Lapierre S, Iqbal Z. Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis. Lancet Microbe. 2023;4(2):e84-e92.

Jesumoroti OJ, Beteck RM, Jordaan AE, Warner DF, Legoabe LJ. Exploration of 4-aminopyrrolo[2,3-d]pyrimidine as antitubercular agents. Molecular Diversity. 2023; 27: 753-765

Kapp E, Calitz H, Streicher EM, Dippenaar A, Egieyeh S, Jordaan A, Warner DF, Joubert J, Malan SF, Sampson SL. Discovery and biological evaluation of an adamantyl-amide derivative with likely MmpL3 inhibitory activity. Tuberculosis (Edinb). 2023;141:102350.

Kekana D, Naicker SD, Shuping L, Velaphi S, Nakwa FL, Wadula J, Govender NP. Candida auris Clinical Isolates Associated with Outbreak in Neonatal Unit of Tertiary Academic Hospital, South Africa. Emerging Infectious Disease. 2023; 29(10): 2044-2053

Koller TO, Scheid U, Kösel T, Herrmann J, Krug D, Boshoff HI, Beckert B, Evans JC, Schlemmer J, Sloan. B, Weiner DM, Via LE, Moosa A, Ioerger TR, Gille F, Siebke M, Seedorf T, Plettenburg O, Warnke AL, Ullrich J, Warrass R, Barry CE III, Warner DF, Mizrahi V, Kirschning A, Wilson DN, Müller R. The myxobacterial antibiotic myxovalargin: Biosynthesis, structural revision, total synthesis and molecular characterization of ribosomal inhibition. J Am Chem Soc. 2023;145(2):851-863.

Koeppel L, Denkinger CM, Wyss R, Broger T, Chegou NN, Dunty JM, Scott K, Caceres T, Du Toit E, Ugarte-Gill C, Nicol M, Gotuzzo E, Corstjens PLAM, Geluk AK, Sutherland J, sigal GB, Moreau E, Albertini A, Mantsoki A, Ongarello S, Walzl G, Suarez MF. Diagnostic performance of host protein signatures as a triage test for active pulmonary TB. Journal of Clinical Microbiology. 2023; 61(10):1-13

Lakoh S, Kamudumuli PS, Penney ROS, Haumba SM, Jarvis JN, Hassan AJ, Moudoute NLE, Ocansey BK, Izco S, Kipkerich S, Sacarlal J, Awopeju AT, Govender NP, Munyanji CIM, Guyguy K, Orefuwa E, Denning DW. Diagnostic capacity for invasive fungal infections in advanced HIV disease in Africa: a continent-wide survey. Lancet Infectious Diseases. 2023; 23:598-608

Magobo RE, Ismail H, Lowe M, Strasheim W, Mogokotleng R, Perovic O, Kwenda S, Ismail A, Makua M, Bore A, Phayane R, Naidoo H, Dennis T, Ngobese M, Wijnant W, Govender NP. Outbreak of NDM-1- and OXA-181- Producing Klebsiella pneumoniae Bloodstream Infections in a Neonatal Unit, South Africa. Emerging Infectious Disease. 2023; 29(8):1531-1539

Marais G, Hardie D, Brink A. A case for investment in clinical metagenomics in low-income and middle-income countries. Lancet Microbe. 2023 Mar;4(3):e192-e199

Marais G, Valley-Omar Z, Marais S, McMullen K, Bateman K, der Westhuizen DV, Maseko M, Hardie D, Brink A. Clinical metagenomics in a resource-limited setting. J Infect. 2023;87(6):604-606.

Martinez L, Gray DM, Botha M, Nel M, Chaya S, Jacobs C, Workman L, Nicol MP, Zar HJ. The Long-Term Impact of Early-Life Tuberculosis Disease on Child Health: A Prospective Birth Cohort Study. Am J Respir Crit Care Med. 2023;207(8):1080-1088.

Mbamalu O, Surenda S, Nampoothiri V, Bonaconsa C, Edathadathil F, Zhu N, Lambert H, Tarrant C, Ahmad R, Boutall A, Brink A, Steenkamp E, Holmes A, Singh S, Charani E, Mendelson M. Survey of healthcare worker perceptions of changes in infection control and antimicrobial stewardship practices in India and South Africa during the COVID-19 pandemic. IJID Regions. 2023 6: 90-98

Mbamalu O, Surendran S, Nampoothiri V, Bonaconsa C, Edathadathil F, Zhu N, Carter V, Lambert H, Tarrant C, Ahmad R, Brink A, Steenkamp E, Holmes A, Singh S, Charani E, Mendelson M. A survey of patient and public perceptions and awareness of SARS-CoV-2-related risks among participants in India and South Africa. PLOS Glob Public Health. 2023;3(7):e0001078.

Middelkoop K, Koch AS, Hoosen Z, Bryden W, Call C, Seldon R, Warner DF, Wood R, Andrews JR. Environmental air sampling for detection and quantification of Mycobacterium tuberculosis in clinical settings: Proof of concept. Infect Control Hosp Epidemiol. 2023;44(5):774-779

Moodley C, Tootla H, Amien I, Engel ME. Evaluating the utility of the Allplex STI Essential Assay to determine the occurrence of urogenital sexually transmitted infections among symptomatic and asymptomatic patients in Cape Town, South Africa. PLoS One. 2023;18(11):e0292534.

Naicker SD, Shuping L, Zulu TG, Mpembe RS, Mhlanga M, Tsotetsi EM, Maphanga TG, Govender NP; MMed, FC Path SA, for GERMS-SA. Epidemiology and susceptibility of Nakaseomyces (formerly Candida) glabrata bloodstream isolates from hospitalised adults in South Africa. Med Mycol. 2023;61(6):myad057

Nzimande SP, Govender NP, Maphanga TG. In vitro manogepix susceptibility testing of South African Emergomyces africanus, Emergomyces pasteurianus, and Blastomyces emzantsi clinical isolates. Antimicrobial Agents and Chemotherapy. 2023; 67(12):1-4

Oderinlo OO, Jordaan A, Seldon R, Isaacs M, Hoppe HC, Warner DF, Tukulula M, Khanye SD. Hydrazone-tethered 5-(Pyridin-4-yl)-4H-1,2,4-triazole-3-thiol hybrids: synthesis, characterisation, in silico ADME studies, and in vitro antimycobacterial evaluation and cytotoxicity. ChemMedChem. 2023;18(6):e202200572

Omollo C, Singh V, Kigondu E, Wasuna A, Agarwal P, Moosa A, Ioerger TR, Mizrahi V, Chibale K, Warner DF. Developing synergistic drug combinations to restore antibiotic sensitivity in drug-resistant Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2023;65(5):e02554-20

Opperman CJ, Singh S, Davids T, Cox H, Warren R, Goosen W. Identifying non- tuberculosis mycobacteria: Is it time to introduce new molecular assays? S Afr Med J. 2023 ;113(6):4-5

Opperman CJ. Withdrawing antibiotics in the terminally ill ICU patient: Should it be a road less travelled? J Intensive Care Soc. 2023;24(2):234

Overmeyer AJ, Prentice E, Brink A, Lennard K, Moodley C. The genomic characterization of carbapenem-resistant Serratia marcescens at a tertiary hospital in South Africa. JAC antimicrob Resist. 2023 25;5(4):dlad089

Paccoud O, Shuping L, Mashau R, Greene G, Quan V, Meiring S, Govender NP; for GERMS-SA. Impact of prior cryptococcal antigen screening on in-hospital mortality in cryptococcal meningitis or fungaemia among HIV-seropositive individuals in South Africa: a cross-sectional observational study. Clin Microbiol Infect. 2023;29(8):1063-1069.

Peters RPH, Jung H, Mitchev N, Mdingi MM, Gigi R, Shroufi A, Martinez FP, Bamford C. Antimicrobial Resistance and Molecular Typing of Neisseria gonorrhoeae Isolates From the Eastern Cape Province in South Africa. Sex Transm Dis. 2023;50(12):821-826

Peters RPH, McIntyre JA, Garrett N, Brink AJ, Celum CL, Bekker LG. Doxycycline post-exposure prophylaxis for sexually transmitted infections in South Africa. South Afr J HIV Med. 2023;24(1):1510

Pietersen E, Anderson K, Cox H, Dheda K, Bian A, Shepherd BE, Sterling T, Warren RM, van der Heijden YF. Variation in missed doses and reasons for discontinuation of anti-tuberculosis drugs during hospital treatment for drug-resistant tuberculosis in South Africa. PLoS One. 2023;18(2):e0281097.

Reddy DL, Nel J, Govender NP. Review: Emergomycosis. J Mycol Med. 2023;33(1):10131

Reiche MA, Jacobs CA, Aaron JS, Mizrahi V, Warner DF, Chew TL. A comprehensive strategy to strengthen bioimaging in Africa through the Africa Microscopy Initiative. Nat Cell Biol. 2023;25(10):1387-1393.

Reid M, Agbassi YJP, Arinaminpathy N, Bercasio A, Bhargava A, Bhargava M, Bloom A, attamanchi A, Chaisson R, Chin D, Churchyard G, Cox H, Denkinger CM, Ditiu L, Dowdy D, Dybul M, Fauci A, Fedaku E, Gidado M, Harrington M, Hauser J, Heitkamp P, Herbert N, Herna Sari A, Hopewell P, Kendall E, Khan A, Kim A, Koek I, Kondratyuk S, Krishnan N, Ku CC, Lessem E, McConnell EV, Nahid P, Oliver M, Pai M, Raviglione M, Ryckman T, Schäferhoff M, Silva S, Small P, Stallworthy G, Temesgen Z, van Weezenbeek K, Vassall A, Velásquez GE, Venkatesan N, Yamey G, Zimmerman A, Jamison D, Swaminathan S, Goosby E. Scientific advances and the end of tuberculosis: a report from the Lancet Commission on Tuberculosis. Lancet. 2023;402(10411):1473-1498

Santos JA, Timinskas K, Lamers MH, Venclovas Č, Warner DF, Gessner SJ. RecA-NT homology motif in ImuB is essential for mycobacterial ImuA'-ImuB protein interaction and mutasome function. bioRxiv [Preprint]. 2023:2023.03.28.534377

Shawa R, Coomans F, Cox HS, London L. A promising potential: Using the right to enjoy the benefits of the scientific progress to advance public health in Africa. African Human Rights Law Journal. 2023; 23:30-47

Shuping L, Maphanga TG, Naicker SD, Mpembe R, Ngoma N, Velaphi S, Nakwa F, Wadula J, Jaglal P, Govender NP. High Prevalence of Candida auris Colonization during Protracted Neonatal Unit Outbreak, South Africa. Emerging Infectious Disease. 2023; 29(9); 1913-1916

Van der Westhuyzen M, Samodien N, Brink AJ, Moodley C. Utility of the BioFire® FilmArray® Pneumonia Panel plus assay for syndromic testing of lower respiratory tract infections in a low/middle-income setting. JAC- Antimicrobial Resistance.2023;5(1) dlac139

Wake RM, Molloy SF, Jarvis JN, Harrison TS, Govender NP. Cryptococcal Antigenemia in Advanced Human Immunodeficiency Virus Disease: Pathophysiology, Epidemiology, and Clinical Implications. Clin Infect Dis. 2023;76(4):764-770.

Warner DF, Wood R. New tricks for an old dog: opportunities for better tuberculosis control. J Int AIDS Soc. 2023; 26(3):e26081

WARNINNG Collaborators. Ten golden rules for optimal antibiotic use in hospital settings: the WARNING call to action. 2023 18(1): 50

Winkler KR, Mizrahi V, Warner DF, De Wet TJ. High-throughput functional genomics: (myco)bacterial perspective. Mol Microbiol. 2023;120(2):141-158

Wojno J, Rebe K, van deer Plas H, Hlazo M, Poole t, Cass S, van der Merwe F, Laubscher M, Opperman C, Singh S, Abrahams R, Curle P, Hilton T, Laubscher M, Scott E, Smythe W, Brink A. Bactreriophages – an introduction to laboratory aspects: a laboratory-based study in South Africa. 2023 5: 84-89.

Yang Q, Kamat S, Mohamed N, Valdez RR, Lin S, Su M, Quintana A, Kiratisin P, Rodriguez-Zulueta AP, Brink A. Antimicrobial susceptibility amaong gram-negative isolates in pediatric patients in :atin America, Africa-Middle East and Asia from 2016-2020 compared to 2011-2015: Results from the ATLAS surveillance study. Journal of the Pediatric Infectious Diseases Society. 2023 12(8):459-470

Yoon H, Wake RM, Nakouzi AS, Wang T, Agalliu I, Tiemessen CT, Govender NP, Jarvis JN, Harrison TS, Pirofski LA. Association of Antibody Immunity With Cryptococcal Antigenemia and Mortality in a South African Cohort With Advanced Human Immunodeficiency Virus Disease. Clin Infect Dis. 2023;76(4):649-657

Young Lee S, Gill CM, Nicolau DP, Brink AJ on behalf of ERACE-PA Global study group. Activity of novel B-lactam/B-lactamase inhibitor combinations against serine carbapenemase producing carbapenem-resistant pseudomonas aeruginosa. Journal of Antimicrobial Chemotherapy. 2023 78(12): 2795-2800

Zwyer M, Rutaihwa LK, Windels E, Hella J, Menardo F, Sasamalo M, Sommer G, Schmülling L, Borrell S, Reinhard M, Dötsch A, Hiza H, Stritt C, Sikalengo G, Fenner L, De Jong BC, Kato-Maeda M, Jugheli L, Ernst JD, Niemann S, Jeljeli L, Ballif M, Egger M, Rakotosamimanana N, Yeboah-Manu D, Asare P, Malla B, Dou HY, Zetola N, Wilkinson RJ, Cox H, Carter EJ, Gnokoro J, Yotebieng M, Gotuzzo E, Abimiku A, Avihingsanon A, Xu ZM, Fellay J, Portevin D, Reither K, Stadler T, Gagneux S, Brites D. Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania. PLoS Pathog. 2023 Apr 4;19(4):e1010893.

2022

Brink AJ, Centner CM, Opperman S. Microbiology Assessments in Critically Ill Patients. Semin Respir Crit Care Med. 2022 Feb;43(1):75-96
Brink AJ, Richards GA. Antimicrobial stewardship: : Leveraging the “Butterfly effect of hand hygiene. Antibiotics. 2022; 11: 1348
Brink AJ, Richards GA, Tootla H, Prentice E. Epidemiology of gram-negative bacteria during COVID-19. What is the real pandemic? Current Opinion Infect Dis. 2022; 35: 595-604
Carrara E, Savoldi A, Piddock LJV, Franceschi F, Ellis S, Sharland M, Brink AJ, Harris PNA, Levy-Hara G, Rohit A, Tsioutis C, Zayyad H, Giske C, Chiamenti M, Bragantini D, Righi E, Gorska A, Tacconelli E. Clinical management of severe infections caused by carbapenem-resistant gram-negative bacteria: a worldwide cross-sectional survey addressing the use of antibiotic combinations. Clin Microbiol Infect. 2022 Jan;28(1):66-72
Mokwele RN, Schellack N, Bronkshorst E, Brink AJ, Schweickerdt L, Godman B. Using mystery shoppers to determine practices pertaining to antibiotic dispensing without a prescription among community pharmacies in South Africa – a pilot survey. 2022 Feb 7;4(1) 1-10
Papavarnavas NS, Brink AJ, Dlamini S, Waswrman S, Whitelaw A, Ntusi NAB, Mendelson M. Parctice update to optimise the performance and interpretation of blood cultures: 2022. SAMJ 2022; 112(6): 397-402
De Vries E, Johnson Y, Willems B, Bedeker W, Ras T, Coetzee R, Tembo Y, Brink AJ. Improving primary care antimicrobial stewardship by implementing a peer audit and feedback intervention in Cape Town community health care centres. SAMJ 2022; 112(10): 812-818
Marais G, Hsiao N, Iranzadeh A, Boolabh D, Joseph R, Enoch A, Chu CY, Williamson C, Brink A, Hardie D. Improved oral detection is a characteristic of Omicron infection and his implications for clinical sampling and tissue tropism. Journal of Clinical Virology. 2022 May; 152: 150170
Gill CM, AktabE, Alfauzan W, Bourassa L, Brink A, Burnham CD, Canton R, Carmeliu Y, Falcone M, Kiffer C, Marchese A, Martinez O, Purnaras S, Satlin MJ, Seifert H, Thabit AK, Thimson KS, Villegas MV, Nicolau DP, ERACE-PA. Multicenter prospective validation of a phenotypic algorithem to guide carbapenemase testing in carbapenem-resistant pseudomonas aeruginosa using the ERACE-PA Global surveillance program. Open Forum Infectious Diseases. 2022 Dec 13; 9(2)
Godman B, Egwuenu A, Wesangula E, Schellack N, Kalungia AC, Tiroyakgosi C, Kgatlwane J, Mwita JC, Patrick O, Niba LL, Amu AA, Oguntade RT, Alabi ME, Ncube NBQ, Sefah IA, Acolatse J, Incoom R, Guantai AN, Oluka M, Opanga S, Chikowe I, Khuluza F, Chiumia FK, Jana CE, Kalemeera F, Hango E, Fadare J, Ogunleye OO, Ebruke BE, Meyer JC, Massele A, Malande OO, Kibuule D, Kapona O, Zaranyika T, Bwakura-Dangarembizi M, Kujinga T, Saleem Z, Kurdi A, Shahwan M, Jairoun AA, Wale J, Brink AJ. Tackling antimicrobial resistance across sub-Saharan Africa: current challenges and implications for the future. Expert Opin Drug Saf. 2022 Aug;21(8):1089-1111
Greybe L, Nuttall JJC, Brink AJ, Tootla HD. Descriptive analysis of infections due to New Delhi metallo-β-lactamase-producing Enterobacterales in children at Red Cross War Memorial Children's Hospital. S Afr J Infect Dis. 2022 Jul 27;37(1):440
Peters RPH, Garrett N, Chandiwana N, Chandiwana N, Kularatne R, Brink AJ, Cohen K, Gill K, Chidarikire T, Wattrus C, Nel JS, Moosa MYS, Bekker LG. Southern African HIV Clinicians Society 2022 guideline for the management of sexually transmitted infections: Moving towards best practice. SA J HIV Med 2022;23,a1450.
Opperman CJ, Moodley C, Lennard K, Smith M, Ncayiyana J, Vulindlu M, Gafoor M, Govender N, Ismail H, Bamford C, McCarthy KM, Nicol MP, Centner CM. A citywide, clonal outbreak of Pseudomonas aeruginosa. International Journal of Infectious Diseases. 2022; 117: 74-86
Opperman CJ, Wojno JM, Brink AJ. Treating bacterial infections with bacteriophages in the 21st century. Southern African Journal of Infectious diseases. 2022; 37(1), a346
Copelyn J, Eley B, Cox H, Workman L, Dheda K, Nicol MP, Zar HJ. Treatment response in Paediatric Pulmonary tuberculosis- A prospective longitudinal study. Journal of the Pediatric Infectious Diseases Society. 2022; 11(7)329-36
Cox H, Workman L, Bateman L, Franckling-Smith Z, Prins M, Luiz J, Van Heerden J, Edries LAT, Africa S, Allen V, Baard C, Zemanay W, Nicol MP, Zar HJ. 2022. Oral swabs tested with Xpert MTB/RIF Ultra for diagnosis of pulmonary tuberculosis in children: a diagnostic accuracy study. Clin Infect Dis. 2022; 121:31-38
Cox H, Goig GA, Salaam-Dreyer Z, Dippenaar A, Reuter A, Mohr-Holland E, Daniels J, Cudahy PGT, Nicol MP, Borrell S, Reinhard M, Doetsch A, Beisel C, Gagneux S, Warren RM, Furin J. 2022. Whole-Genome Sequencing Has the Potential To Improve Treatment for Rifampicin-Resistant Tuberculosis in High-Burden Settings: a Retrospective Cohort Study. J Clin Microbiol. 2022; 60(3):e0236221
Mohr-Holland E, Daniels J, Reuter A, Rodriguez CA, Mitnick C, Kock Y, Cox V, Furin J, Cox H. 2022. Early mortality during rifampicin-resistant TB treatment. Int J Tuberc Lung Dis 26:150-157
Reuter A, Apolisi I, Daniels J, Furin J, Cox H. Household contact management for rifampicin-resistant tuberculosis. Lancet Glob Health. 2022 Oct;10(10):e1387
Merker M, Rasigade JP, Barbier M, Cox H, Feuerriegel S, Kohl TA, Shitikov E, Klaos K, Gaudin C, Antoine R, Diel R, Borrell S, Gagneux S, Nikolayevskyy V, Andres S, Crudu V, Supply P, Niemann S, Wirth T. Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis. Nat Commun. 2022 Aug 30;13(1):5105.
Furin J, Reuter A, Eyde L, Cox H. A test of infection should not be a "standard" for guiding TB preventive therapy in at-risk populations. Int J Tuberc Lung Dis. 2022 Nov 1;26(11):1092-1093
Memani B, Furin J, Cox H, Reuter A. A very sneaky bug: perspectives of front-line clinicians on whole-genome sequencing for drug-resistant TB. Int J Tuberc Lung Dis. 2022 Dec 1;26(12):1180-1182
Le Roux SR, Jassat W, Dickson L, Mitrani L, Cox H, Mlisana K, Black J, Loveday M, Grant AD, Moshabela M, Kielmann K, Nicol MP. The role of emergent champions in policy implementation for decentralised drug-resistant tuberculosis care in South Africa. BMJ Glob Health. 2022 Dec;7(12):e008907.
Le Roux SR, Jassat W, Dickson L, Mitrani L, Cox H, Mlisana K, Black J, Loveday M, Grant AD, Moshabela M, Kielmann K, Nicol MP. The role of emergent champions in policy implementation for decentralised drug-resistant tuberculosis care in South Africa. BMJ Glob Health. 2022 Dec;7(12):e008907.
Wake RM, Ismail NA, Omar SV, Ismail F, Tiemessen CT, Harrison TS, Jarvis JN, Govender NP. Prior Pulmonary Tuberculosis Is a Risk Factor for Asymptomatic Cryptococcal Antigenemia in a Cohort of Adults With Advanced Human Immunodeficiency Virus Disease. Open Forum Infect Dis. 2022 Apr 17;9(7)
Mapengo RE, Maphanga TG, Grayson W, Govender NP. Endemic mycoses in South Africa, 2010-2020: A decade-long description of laboratory-diagnosed cases and prospects for the future. PLoS Negl Trop Dis. 2022;16(9):e0010737
Finci I, Albertini A, Merker M, Andres S, Bablishvili N, Barilar I, Cáceres T, Crudu V, Gotuzzo E, Hapeela N, Hoffmann H, Hoogland C, Kohl TA, Kranzer K, Mantsoki A, Maurer FP, Nicol MP, Noroc E, Plesnik S, Rodwell T, Ruhwald M, Savidge T, Salfinger M, Streicher E, Tukvadze N, Warren R, Zemanay W, Zurek A, Niemann S, Denkinger CM. Investigating resistance in clinical Mycobacterium tuberculosis complex isolates with genomic and phenotypic antimicrobial susceptibility testing: a multicentre observational study. Lancet Microbe. 2022;3(9):e672-e682.
Wobudeya E, Bonnet M, Walters EG, Nabeta P, Song R, Murithi W, Mchembere W, Dim B, Taguebue JV, Orne-Gliemann J, Nicol MP, Marcy O. Diagnostic Advances in Childhood Tuberculosis-Improving Specimen Collection and Yield of Microbiological Diagnosis for Intrathoracic Tuberculosis. Pathogens. 2022;11(4):389.
Barr DA, Schutz C, Balfour A, Shey M, Kamariza M, Bertozzi CR, de Wet TJ, Dinkele R, Ward A, Haigh KA, Kanyik JP, Mizrahi V, Nicol MP, Wilkinson RJ, Lalloo DG, Warner DF, Meintjes G, Davies G. Serial measurement of M. tuberculosis in blood from critically-ill patients with HIV-associated tuberculosis. EBioMedicine. 2022 Apr;78:103949
Alene KA, Murray MB, van de Water BJ, Becerra MC, Atalell KA, Nicol MP, Clements ACA. Treatment Outcomes Among Pregnant Patients With Multidrug-Resistant Tuberculosis: A Systematic Review and Meta-analysis. JAMA Netw Open. 2022;5(6):e2216527.
Allali I, Abotsi RE, Ah Tow L, Thabane L, Zar HJ, Mulder NM, Nicol MP. Correction to: Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. Microbiome. 2022 Jan 19;10(1):10
Zar HJ, MacGinty R, Workman L, Botha M, Johnson M, Hunt A, Burd T, Nicol MP, Flasche S, Quilty BJ, Goldblatt D. Natural and hybrid immunity following four COVID-19 waves: A prospective cohort study of mothers in South Africa. EClinicalMedicine. 2022;53:101655.
Zar HJ, MacGinty R, Workman L, Burd T, Smith G, Myer L, Häggström J, Nicol MP. Klebsiella pneumoniae Lower Respiratory Tract Infection in a South African Birth Cohort: a Longitudinal Study. Int J Infect Dis. 2022;121:31-38
Martinez L, Ncayiyana JR, Goddard E, Botha M, Workman L, Burd T, Myer L, Nicol MP, Zar HJ. Vitamin D Concentrations in Infancy and the Risk of Tuberculosis Disease in Childhood: A Prospective Birth Cohort in Cape Town, South Africa. Clin Infect Dis. 2022;74(11):2036-2043.
Boloko L, Schutz C, Sibiya N, Balfour A, Ward A, Shey M, Nicol MP, Burton R, Wilkinson RJ, Maartens G, Meintjes G, Barr DA. Xpert Ultra testing of blood in severe HIV-associated tuberculosis to detect and measure Mycobacterium tuberculosis blood stream infection: a diagnostic and disease biomarker cohort study. Lancet Microbe. 2022 Jul;3(7):e521-e532.
Omollo C, Moosa A, Chibale K, Warner DF. Fusidic acid-based drug combinations exhibit enhanced activity against Mycobacterium tuberculosis. bioRxiv 2022
Patterson B, Dinkele R, Gessner S, Koch A, Hoosen Z, January V, Leonard B, McKerry A, Seldon R, Vazi A, Hermans S, Cobelens F, Warner DF, Wood R. Viable aerosolized Mycobacterium tuberculosis from sputum-positive and sputum-negative TB patients: Treatment effect and secular trends. MedRxiv. 2022;
Scriba TJ, Dinkele R, Warner DF, Mizrahi V. Challenges in TB research. J Exp Med. 2022;219(12):e20221334.
Hart D, Legoabe LJ, Jesumoroti OJ, Jordaan A, Warner DF, Steventon R, Beteck RM. Nitrothiazole-thiazolidinone hybrids: synthesis and in vitro antimicrobial evaluation. Chem Biodivers. 2022; 19(11):e202200729.
Middelkoop K, Koch AS, Hoosen Z, Bryden W, Call C, Seldon R, Warner DF, Wood R, Andrews JR. Environmental air sampling for detection and quantification of Mycobacterium tuberculosis in clinical settings: Proof of concept. Infect Control Hosp Epidemiol. 2022;27:1-6.
Gessner S, Martin ZAM, Reiche MA, Santos J, Dhar N, Dinkele R, de Wet TJ, Ramudzuli A, Anoosheh S, Lang DM, Aaron J, Herrmann J, Müller R, McKinney JD, Woodgate R, Mizrahi V, Lamers M, Warner DF. (2021) The mycobacterial mutasome: composition and recruitment in live cells. bioRxiv. 2022; doi:10.1101/2021.11.16.468908
Dinkele R, Gessner S, McKerry A, Leonard B, Leukes J, Seldon R, Warner DF, Wood R. Aerosolization of Mycobacterium tuberculosis by tidal breathing. Am J Respir Crit Care Med. 2022; 206(2): 206-216
Angula KT, Legoabe LJ, Jordaan A, Warner DF, Beteck RM. Investigation of quinolone-tethered aminoguanidine as novel antibacterial agents. Arch Pharm (Weinheim). 2022; 335(10):e2200172.
Moodley R, Mashaba C, Rakodi GH, Ncube NB, Maphoru MV, Balogun MO, Jordan A, Warner DF, Khan R, Tukulula M. New Quinoline-Urea-Benzothiazole Hybrids as Promising Antitubercular Agents: Synthesis, In Vitro Antitubercular Activity, Cytotoxicity Studies, and In Silico ADME Profiling. Pharmaceuticals (Basel). 2022; 15(5):576.
Jesumoroti OJ, Beteck RM, Jordaan A, Warner DF, Legoabe LJ. Exploration of 4-aminopyrrolo[2,3-d]pyrimidine as antitubercular agents. Mol Divers. 2022; 27(2): 753-765
Raidron C, Jordaan A, Seldon R, Warner DF, de Kock C, Taylor D, Louw S, Sunassee S, Hans RH. Antiplasmodial and antimycobacterial activities of crude and lead-like enhanced extracts from Namibian medicinal plants. J Ethnopharmacol. 2022;295:115389.
Acquah KS, Beukes DR, Seldon R, Jordaan A, Sunassee SN, Warner DF, Gammon DW. Identification of Antimycobacterial Natural Products from a Library of Marine Invertebrate Extracts. Medicines (Basel). 9(2):9.
Chen D, Bryden NA, Bryden WA, McLoughlin M, Smith D, Devin AP, Caton ER, Haddaway CR, Tameris M, Scriba TJ, Hatherill M, Gessner S, Warner DF, Wood R. Non-volatile organic compounds in exhaled breath particles correspond to active tuberculosis. Sci Rep. 2022 12(1):7919.
Chengalroyen M, Mason MK, Borsellini A, Tassoni R, Abrahams GL, Lynch S, Ahn YM, Ambler J, Young K, Crowley BM, Olsen DB, Warner DF, Barry CE III, Boshoff HIM, Lamers MH, Mizrahi V. (2021). DNA-dependent binding of nargenicin to DnaE1 inhibits replication in M. tuberculosis. ACS Infect Dis. 8(3):612-625.
Barr DA, Schutz C, Balfour A, Shey M, Kamariza M, Bertozzi CR, de Wet TJ, Dinkele R, Ward A, Haigh KA, Kanyik JP, Mizrahi V, Nicol MP, Wilkinson RJ, Lalloo DG, Warner DF, Meintjes G, Davies G. (2022) Serial measurement of M. tuberculosis in blood from critically-ill patients with HIV-associated tuberculosis. EBioMedicine. 78:103949
Zürcher K, Riou J, Morrow C, Ballif M, Koch A, Bertschinger S, Warner DF, Middelkoop K, Wood R, Egger M, Fenner L. (2022) Estimating Tuberculosis Transmission Risks in a Primary Care Clinic in South Africa: Modeling of Environmental and Clinical Data. J Infect Dis. 225(9):1642-1652

2021

Maphanga TG, Naicker SD, Gomez BL, Mhlanga M, Mpembe RS, Schwartz IS, Bamford C, Nel J, Govender NP. Cross-reactivity of a histoplasma capsulatum antigen enzyme immunoassay in urine specimens persons with emergomycosis in South Afica. Medical Mycology 2021; 59(7):672-682
Annear D, Gaida R, Myburg K, Black John, Truter I, Bamford C, Govender S. Spectrum of bacterial Colonization in patients hospitalized for treatment of multidrug-resistant tuberculosis. Microbial Drug Resistance 2021; 27(5): 691-697.
Taku O, Brink AJ, Meiring T, et al. Detection of sexually transmitted pathogens and co-infection with Human papillomavirus in women residing in rural Eastern Cape, South Africa. Peer J 2020; 9(6):10793
Booley C, Chanda R, Daries P, Misland C, Brink AJ, Linde L, Opperman CJ. Exogenous fungal endophthalmitis in a potato farm worker. S Afr J Infect Dis 2021; 36(1): 329
Vosloo MN, Opperman CJ, Geyer HDW, Setshedi GM, Allam M, Kwenda S, Ismail A, Khumalo ZTH, Brink AJ, Frean JA, Rossouw J. A South African case of infant botulism with a dual toxin producing Clostridium botulism strain. International Journal of Infectious Diseases. 2021; 103:164-166
Mokoena TW, Schellack N, Brink AJ. Driving antimicrobial stewardship and awareness through the taxi community across the Tshwane District, South Africa- a baseline evaluation. J Antimicrob Agents-AMR 2021;3(3):1-6 dlab106
Du Toit JM, Wojno T, Deffur A, Brink A. Statement on analysis and interpretation of clinical human gastrointestinal microbiome testing using next-generation sequencing in South Africa. S Afr Med J. 2021 Mar 2;111(3):203-205
Van den Bergh D, Brink A. A commitment and call to strengthen and expand qualitative research efforts to improve the impact of antimicrobial stewardship. JAC- Antimicrobial Resistance 2020; 3(4): 1-4
Opperman CJ, Enslin JMN, Nuttall J, Brink AJ, Da Fonseca SP, Tootla HD. Hyditid brain cyst: A delayed diagnosis in a rural setting during COVID-19. S Afr Med J 2020; 111(11): 1050-1054
Chu CY, Marais G, Opperman C, Doolabh D, Iranzadeh A, Marais C, Cox H, Williamson C, Hardie D, Brink A. Performance of saliva and mid-turbinate swabs for detection of the beta variant in South Africa. Lancet Infect Dis 2020; 21 (10):1354
Opperman, C., Khan, F., Piercy, J. and Samodien, N., 2021. Barriers to disinfection of mobile touch screen devices amongst a multidisciplinary team in intensive care units at a tertiary hospital. GERMS, 11(2), pp.329-336
Samodien, N. Nana T,Black M, Chomba R, Khumalo A, Mothibi L, Reddy K, Chibabahi V. Prevalence and aetiologies of microbial prevalence and aetiologies of microbial co-infections in South African hospitalized with Severe Acute Respiratory Syndrome Coronavirus 2 associated pneumonia. In: Pathred Conference 2021. [online] Cape Town
Saqib U, Khan MA, Alagumuthu M, Parihar SP, and Baig MS. Na Nural. compounds as antiatherogenic agents. Cell Mol Biol (Noisy-le-grand). 2021;67(1):177-88.
Allali I, Abotsi RE, Tow LA, Thabane L, Zar HJ, Mulder NM, Nicol MP. Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. Microbiome. 2021 Dec 15;9(1):241
Mulenga H, Musvosvi M, Mendelsohn SC, Penn-Nicholson A, Kimbung Mbandi S, Fiore-Gartland A, Tameris M, Mabwe S, Africa H, Bilek N, Kafaar F, Khader SA, Carstens B, Hadley K, Hikuam C, Erasmus M, Jaxa L, Raphela R, Nombida O, Kaskar M, Nicol MP, Mbhele S, Van Heerden J, Innes C, Brumskine W, Hiemstra A, Malherbe ST, Hassan-Moosa R, Walzl G, Naidoo K, Churchyard G, Hatherill M, Scriba TJ; CORTIS Study Team. Longitudinal Dynamics of a Blood Transcriptomic Signature of Tuberculosis. Am J Respir Crit Care Med. 2021 Dec 15;204(12):1463-1472.
Claassen-Weitz S, Lim KYL, Mullally C, Zar HJ, Nicol MP. The association between bacteria colonizing the upper respiratory tract and lower respiratory tract infection in young children: a systematic review and meta-analysis. Clin Microbiol Infect. 2021 Sep;27(9):1262-1270.
Bobak CA, Kang L, Workman L, Bateman L, Khan MS, Prins M, May L, Franchina FA, Baard C, Nicol MP, Zar HJ, Hill JE. Breath can discriminate tuberculosis from other lower respiratory illness in children. Sci Rep. 2021 Feb 1;11(1):2704.
Zar HJ, Nicol MP, MacGinty R, Workman L, Petersen W, Johnson M, Goldblatt D. Antibodies to Seasonal Coronaviruses Rarely Cross-React With SARS-CoV-2: Findings From an African Birth Cohort. Pediatr Infect Dis J. 2021 Dec 1;40(12):e516-e519.
DeAtley T, Workman L, Theron G, Bélard S, Prins M, Bateman L, Grobusch MP, Dheda K, Nicol MP, Sorsdahl K, Kuo C, Stein DJ, Zar HJ. The child ecosystem and childhood pulmonary tuberculosis: A South African perspective. Pediatr Pulmonol. 2021 Jul;56(7):2212-2222.
Nicol MP, MacGinty R, Workman L, Stadler JAM, Myer L, Allen V, Ah Tow Edries L, Zar HJ. A Longitudinal Study of the Epidemiology of Seasonal Coronaviruses in an African Birth Cohort. J Pediatric Infect Dis Soc. 2021 May 28;10(5):607-614.
Salaam-Dreyer Z, Streicher EM, Sirgel FA, Menardo F, Borrell S, Reinhard M, Doetsch A, Cudahy PGT, Mohr-Holland E, Daniels J, Dippenaar A, Nicol MP, Gagneux S, Warren RM, Cox H. Rifampicin-Monoresistant Tuberculosis Is Not the Same as Multidrug-Resistant Tuberculosis: a Descriptive Study from Khayelitsha, South Africa. Antimicrob Agents Chemother. 2021 Oct 18;65(11):e0036421.
Mitrani L, Dickson-Hall L, Le Roux S, Hill J, Loveday M, Grant AD, Kielmann K, Mlisana K, Moshabela M, Nicol MP, Black J, Cox H. Diverse clinical and social circumstances: developing patient-centred care for DR-TB patients in South Africa. Public Health Action. 2021 Sep 21;11(3):120-125.
Gill CM, Aktaş E, Alfouzan W, Bourassa L, Brink A, Burnham CD, Canton R, Carmeli Y, Falcone M, Kiffer C, Marchese A, Martinez O, Pournaras S, Seifert H, Thabit AK, Villegas MV, Westblade LF, Nicolau DP; ERACE-PA Global Study Group. Elevated MICs of Susceptible Antipseudomonal Cephalosporins in Non- Carbapenemase-Producing, Carbapenem-Resistant Pseudomonas aeruginosa: Implications for Dose Optimization. Antimicrob Agents Chemother. 2021; 18;65(11):e0120421.
Mokoena TTW, Schellack N, Brink AJ. Driving antibiotic stewardship awareness through the minibus-taxi community across the Tshwane District, South Africa-a baseline evaluation. JAC Antimicrob Resist. 2021 Aug 7;3(3):dlab106.
Gill CM, Aktaþ E, Alfouzan W, Bourassa L, Brink A, Burnham CD, Canton R, Carmeli Y, Falcone M, Kiffer C, Marchese A, Martinez O, Pournaras S, Satlin M, Seifert H, Thabit AK, Thomson KS, Villegas MV, Nicolau DP; ERACE-PA Global Study Group. The ERACE-PA Global Surveillance Program: Ceftolozane/tazobactam and Ceftazidime/avibactam in vitro Activity against a Global Collection of Carbapenem-resistant Pseudomonas aeruginosa. Eur J Clin Microbiol Infect Dis. 2021 Dec;40(12):2533-2541.
Wojno JM, Du Toit E, Deffur A, Brink A. Statement on analysis and interpretation of clinical human gastrointestinal microbiome testing using next-generation sequencing in South Africa. S Afr Med J. 2021 Mar 2;111(3):203-205.
Carrara E, Savoldi A, Piddock LJV, Franceschi F, Ellis S, Sharland M, Brink AJ, Harris PNA, Levy-Hara G, Rohit A, Tsioutis C, Zayyad H, Giske C, Chiamenti M, Bragantini D, Righi E, Gorska A, Tacconelli E. Clinical management of severe infections caused by carbapenem-resistant gram-negative bacteria: a worldwide cross-sectional survey addressing the use of antibiotic combinations. Clin Microbiol Infect. 2022 Jan;28(1):66-72.
Gill CM, Brink A, Chu CY, Coetzee J, Dimopoulos G, Moodley C, Opperman CJ, Pournaras S, Tenover FC, Tickler IA, Tootla HD, Vourli S, Nicolau DP. Phenotypic/Genotypic Profile of OXA-10-Like-Harboring, Carbapenem-Resistant Pseudomonas aeruginosa: Using Validated harmacokinetic/Pharmacodynamic Models To Further Evaluate Enzyme Functionality and Clinical Implications. Antimicrob Agents Chemother. 2021 Sep 17;65(10):e0127421.

2020

Brink AJ, Richards GA. The role of multi-drug and extensive-drug resistant Gam-negative bacteria in skin and soft tissue infections. Curr Opin Infect Dis 2020;33:93-100.
Brink AJ, Richards GA. Best practice - Antibiotic decision making in intensive care units (antibiotic stewardship). Current Opinion in Critical Care 2020; 26(5):478-488
Brink AJ, Messina AP, Maslo C, Swart K, Chunnilall D, van den Bergh D, NASIPSA. Implementing a multi-faceted framework for proprietorship of hand hygiene compliance in a network of South African hospitals – Leveraging the Ubunthu philosophy. J Hospital Infection 2020;104:404-413.
Goff DA, Bauer KA, Brink AJ,Kolman S, Mendelson M, Messina AP, van den Bergh D. International Train the Trainer antibiotic stewardship program for pharmacists: Implementation, sustainability, and outcomes. J Am Coll Clin Pharm 2020;3(5):869-876
Van den Bergh D, Messina A, Goff DA, et al. A cross-sector, pharmacist-led prospective antibiotic stewardship intervention improves compliance to national community-acquired pneumonia guidelines in 39 public and private hospitals across South Africa. Int J Antimicrob Agents 2020 ; 56: 106189
Mokwele NR, Schellack N, Brink AJ. Determinants of practices pertaining to antibiotic dispensing without a prescription in community pharmacies and prescribing in General Practitioners in Gauteng Province. J Antimicrob Agents-AMR 2020 (In print).
Lowman W, Nana T, Moore C, Boyles T, Brink AJ, Cleghorn J, Devenish LM, duToit B, Fredericks ES, Lekalakala-Mokaba MR, Maluleka C, Rajabally MN, Reubenson G, Shuping L, Swart K, Swe Swe Han K, Wadula J, Wojno J, Lowman W. Clostridiodes difficile Infection Diagnosis, Management and Infection Prevention and Control Guideline. S Afr J Infect Dis 2020; 35(1): a219
Labuschaigne M, Slabbert M, Hoosien E, Budree S, Blockman M, Brink AJ. A human faecal microbiota transplant in South Africa: a legal vacuum (Part 1). S Afr Med J 2020; 110(8): 812-815
Labuschaigne M, Slabbert M, Hoosien E, Budree S, Blockman M, Brink AJ.The ethico-legal framework relevant to human faecal microbiota transplants in South Africa: human stool as tissue? (Part 2). S Afr Med J 2020; 110(8): 816-818
Labuschaigne M, Slabbert M, Hoosien E, Budree S, Blockman M, Brink A.J The ethico-legal framework relevant to faecal microbialta transplants in South Africa: human stool as a ‘drug’ or medicine (Part 3). S Afr Med J 2020 ; 110(8): 819-821
Nana T, Moore C, Brink AJ, Cleghorn J, Devenish LM, du Toit B, Fredericks ES, Lekalakala-Mokaba MR, Maluleka C, Rajabally MN, Reubenson G, Shuping L, Swart K, Swe Han KS, Wadula J, Wojno J, Lowman J. South African Society of clinical microbiology clostridioides difficile infection diagnosis, management and infection prevention and control guideline. Southern African Journal of Infectious Diseases 2020; 35(1):219
Budree S, Hoosien E, Osman M, et al. Operationalising Universal Donor Stool Banks in Low-middle Income Countries (LMIC). S Afr Med J 2020 (In print)
Perovic O, Ismail H, Quan V, Bamford C, Nana T, ChibabhaiV, Bhola P, Ramjathan P, ;Swe Swe-Han K, Wadula J, Whitelaw A, Smith M, Mbelle N, Sigh-Moodley A for GERMS-SA. Carbapenem-resistant enterobacteriacease in patients with bacteraemia at tertiary hospitals in South Africa, 2015 to 2018. Eur J Clin Microbiol Infect Dis. 2020; 39(7)1287-1294
Ogunbosi BO, Moodley C, Naicker P, Nuttall J, Bamford C, Eley B. Colonisation with extended spectrum beta-lactamase-producing and carbapenem-restant enterobacterales in children admitted to a paediatric referral hospital in South Africa. PLoS ONE 2020; 15(11)e0241776
Opperman CJ, Kruger EJ, Wright J. Bacillus species cultured relatedly from the breastmilk of a donor milk mother. S Afr J Child Health 2020; 14(1): 55-57
Opperman, C., Baloyi, B., Dlamini, S. and Samodien, N. Blood culture contamination rates at different level healthcare institutions in the Western Cape, South Africa. Southern African Journal of Infectious Diseases 2020;35(1):a222.
Opperman, C., Marais, G., Naidoo, M., Hsiao, M. and Samodien, N. Response to a cluster of Severe Acute Respiratory Syndrome Coronavirus 2 cases at a diagnostic laboratory. African Journal of Laboratory Medicine 2020; 9(1).
Swart C, Meldau S, Centner CM, Marais AD, Omar F. Validation of PHASE for deriving N-acetyltransferase 2 haplotypes in the Western Cape mixed ancestry population. African Journal of Laboratory Medicine. 2020;9(1):988.
Siaway ACM, Kamgaing EK, Rogombe M, Obiang T, Massala EM, Mbadinga MJVM, Leboueny M, Ndjindji OM, Mveang-Nzoghe A, Ondo JP, Ndong AM, Essone PN, Agnandji ST, Kaba M, Ategbo S, Siawaya JFD. HIV-exposed uninfected compared with unexposed infants show the presence of leucocytes, lower lactoferrin levels and antimicrobial-resistant micro-organisms in the stools. Paediatrics and International Child Health 2020; 1-10
Maartens G, Griesel R, Dube F, Nicol M, Mendelson M. Etiology of pulmonary infections in Human immunodeficiency virus-infected inpatients using sputum multiplex real-time polymerase chain reaction. Clinical Infectious Diseases 2020; 70(6): 1147-1152
Manenzhe RI, Dube FS, Wright M, Lennard K, Zar HJ, Mounaud S, Nierman WC, Nicol MP, Moodley C. Longitudinal changes in the nasopharyngeal resistone of South African infants using shogun metagenomic sequencing. PLoS ONE 2020; 15(4) e0231887.
Nicol MP, Zar HJ. Advances in the diagnosis of pulmonary tuberculosis in children. Paediatr Respir Rev. 2020 Nov;36:52-56.
Ojo-Okunola A, Cacciatore S, Nicol MP, du Toit E. The Determinants of the Human Milk Metabolome and Its Role in Infant Health. Metabolites. 2020 Feb20;10(2):77.
Marais BJ, Nicol M, Zar HJ. Key advances and remaining challenges in childhood and adolescent tuberculosis. Paediatr Respir Rev. 2020 ;36:25-26.
Allali I, Abotsi RE, Tow LA, Thabane L, Zar HJ, Mulder NM, Nicol MP. Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. Microbiome. 2021;9(1):241.
Muloiwa R, Dube FS, Nicol MP, Hussey GD, Zar HJ. Risk factors for Bordetella pertussis disease in hospitalized children. PLoS One. 2020;15(10):e0240717.
Claassen-Weitz S, Lim KYL, Mullally C, Zar HJ, Nicol MP. The association between bacteria colonizing the upper respiratory tract and lower respiratory tract infection in young children: a systematic review and meta-analysis. Clin Microbiol Infect. 2021;27(9):1262-1270.
Broger T, Nicol MP, Sigal GB, Gotuzzo E, Zimmer AJ, Surtie S, Caceres-Nakiche T, Mantsoki A, Reipold EI, Székely R, Tsionsky M, van Heerden J, Plisova T, Chikamatsu K, Lowary TL, Pinter A, Mitarai S, Moreau E, Schumacher SG, Denkinger CM. Diagnostic accuracy of 3 urine lipoarabinomannan tuberculosis assays in HIV-negative outpatients. J Clin Invest. 20202;130(11):5756-5764.
Hill J, Dickson-Hall L, Grant AD, Grundy C, Black J, Kielmann K, Mlisana K, Mitrani L, Loveday M, Moshabela M, Le Roux S, Jassat W, Nicol M, Cox H. Drug-resistant tuberculosis patient care journeys in South Africa: a pilot study using routine laboratory data. Int J Tuberc Lung Dis. 2020;24(1):83-91.
McHugh G, Rehman AM, Simms V, Gonzalez-Martinez C, Bandason T, Dauya E, Moyo B, Mujuru H, Rylance J, Sovershaeva E, Weiss HA, Kranzer K, Odland J, Ferrand RA; BREATHE Clinical Trial Team. Chronic lung disease in children and adolescents with HIV: a case-control study. Trop Med Int Health. 2020;25(5):590-599.
Muloiwa R, Dube FS, Nicol MP, Hussey GD, Zar HJ. Co-detection of Bordetella pertussis and other respiratory organisms in children hospitalised with lower respiratory tract infection. Sci Rep. 2020;10(1):16412.
Lounnas M, Diack A, Nicol MP, Eyangoh S, Wobudeya E, Marcy O, Godreuil S, Bonnet M. Laboratory development of a simple stool sample processing method diagnosis of pediatric tuberculosis using Xpert Ultra. Tuberculosis (Edinb). 2020;125:102002.
Sossen B, Broger T, Kerkhoff AD, Schutz C, Trollip A, Moreau E, Schumacher SG, Burton R, Ward A, Wilkinson RJ, Barr DA, Nicol MP, Denkinger CM, Meintjes G. "SILVAMP TB LAM" Rapid Urine Tuberculosis Test Predicts Mortality in Patients Hospitalized With Human Immunodeficiency Virus in South Africa. Clin Infect Dis. 2020;71(8):1973-1976.
Antel K, Oosthuizen J, Malherbe F, Louw VJ, Nicol MP, Maartens G, Verburgh E. Correction to: Diagnostic accuracy of the Xpert MTB/Rif Ultra for tuberculosis adenitis. BMC Infect Dis. 2020 Mar 2;20(1):187.
Furin J, Loveday M, Hlangu S, Dickson-Hall L, le Roux S, Nicol M, Cox H. "A very humiliating illness": a qualitative study of patient-centered Care for Rifampicin-Resistant Tuberculosis in South Africa. BMC Public Health. 2020 Jan 17;20(1):76.
Naudé PJW, Claassen-Weitz S, Gardner-Lubbe S, Botha G, Kaba M, Zar HJ, Nicol MP, Stein DJ. Association of maternal prenatal psychological stressors and distress with maternal and early infant faecal bacterial profile. Acta Neuropsychiatr. 2020 Feb;32(1):32-42.
Nabeta P, Seshadri P, Havumaki J, Mbhele S, Hendricks L, Perkins MD, Nicol MP, Denkinger CM. First clinical assessment of a prototype assay to detect the enzymatic activity of β-lactamase as a marker for pulmonary tuberculosis. Diagn Microbiol Infect Dis. 2020 ;97(2):115026.
Manenzhe RI, Dube FS, Wright M, Lennard K, Mounaud S, Lo SW, Zar HJ, Nierman WC, Nicol MP, Moodley C. Characterization of Pneumococcal Colonization Dynamics and Antimicrobial Resistance Using Shotgun Metagenomic Sequencing in Intensively Sampled South African Infants. Front Public Health. 2020;8:543898.
Muloiwa R, Nicol MP, Hussey GD, Zar HJ. Diagnostic limitations of clinical case definitions of pertussis in infants and children with severe lower respiratory tract infection. PLoS One. 2020;15(7):e0235703.
Flygel TT, Sovershaeva E, Claassen-Weitz S, Hjerde E, Mwaikono KS, Odland JØ, Ferrand RA, Mchugh G, Gutteberg TJ, Nicol MP, Cavanagh JP, Flægstad T; BREATHE Study Team. Composition of Gut Microbiota of Children and Adolescents With Perinatal Human Immunodeficiency Virus Infection Taking Antiretroviral Therapy in Zimbabwe. J Infect Dis. 2020;221(3):483-492.
Shah M, Paradis S, Betz J, Beylis N, Bharadwaj R, Caceres T, Gotuzzo E, Joloba M, Mave V, Nakiyingi L, Nicol MP, Pradhan N, King B, Armstrong D, Knecht D, Maus CE, Cooper CK, Dorman SE, Manabe YC. Multicenter Study of the Accuracy of the BD MAX Multidrug-resistant Tuberculosis Assay for Detection of Mycobacterium tuberculosis Complex and Mutations Associated With Resistance to Rifampin and Isoniazid. Clin Infect Dis. 2020 ;71(5):1161-1167.
Tomasicchio M, Limberis J, van der Merwe R, Jacobson R, Meldau R, Theron G, Nicol M, Warren R, Dheda K. Differential RD-1-specific IFN-γ host responses to diverse Mycobacterium tuberculosis strains in HIV-uninfected persons may be explained by genotypic variation in the ESX-1 region. Int J Infect Dis. 2020;96:240-243.
Zar HJ, Moore DP, Andronikou S, Argent AC, Avenant T, Cohen C, Green RJ, Itzikowitz G, Jeena P, Masekela R, Nicol MP, Pillay A, Reubenson G, Madhi SA. Diagnosis and management of community-acquired pneumonia in children: South African Thoracic Society guidelines. Afr J Thorac Crit Care Med. 2020;26(3):10.
Broger T, Nicol MP, Székely R, Bjerrum S, Sossen B, Schutz C, Opintan JA, Johansen IS, Mitarai S, Chikamatsu K, Kerkhoff AD, Macé A, Ongarello S, Meintjes G, Denkinger CM, Schumacher SG. Diagnostic accuracy of a novel tuberculosis point-of-care urine lipoarabinomannan assay for people living with HIV: A meta-analysis of individual in- and outpatient data. PLoS Med. 2020;17(5): e1003113.
Zar HJ, Nduru P, Stadler JAM, Gray D, Barnett W, Lesosky M, Myer L, Nicol MP. Early-life respiratory syncytial virus lower respiratory tract infection in a South African birth cohort: epidemiology and effect on lung health. Lancet Glob Health. 2020 Oct;8(10):e1316-e1325.
Classen-Weitz S, Gardner-Lubbe S, Wwaikono KS, du Toit E, Zar HJ, Nicol MP. Optomizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimen. BMC Mcrobiology 2020; 20: 113
Loveday M, Cox H, Evans D, Furin J, Ndjeka N, Osman M, Naidoo K, for the Nathoanl TB Think Tank Optimising TB Treatment OutcomesTask Team. Opportunities from a new disease for an old threat: Extending COVID-19 efforts to address tuberculosis in South Africa. S Afr Med J 2020; 110(12):1160-1167
Koch A, Cox H. Preventing drug-resistant tuberculosis transmission. The Lancet 2020; 20:157-158
Kerschberger B, Telnov A, Yano N, Cox H, Zabsonre I, Kabore SM, Vambe D, Ngwenya S, Rusch B, Tombo ML, Cigeineckin I. Successful expansion of community-based drug-resistant TB care in rural Eswatini – a retrospective cohort study. Tropical Medicin and International Health 2020; 24(10): 1243-1258

2019

Manenzhe RI, Moodley C, Abdulgader SM, Robberts FJL, Zar HJ, Nicol MP, Dube FS. Nasopharyngeal Carriage of Antimicrobial-Resistant Pneumococci in an Intensively Sampled South African Birth Cohort. Front Microbiol. 2019 27;10:610.
Abdulgader SM, Robberts L, Ramjith J, Nduru PM, Dube F, Gardner-Lubbe S, Zar HJ, Nicol MP. Longitudinal Population Dynamics of Staphylococcus aureus in the Nasopharynx During the First Year of Life. Front Genet. 2019 15;10:198.
le Roux DM, Nicol MP, Myer L, Vanker A, Stadler JAM, von Delft E, Zar HJ. Lower Respiratory Tract Infections in Children in a Well-vaccinated South African Birth Cohort: Spectrum of Disease and Risk Factors. Clin Infect Dis. 2019 Mar 29.
Van Hoving DJ, Lahri S, Lategan HJ, Nicol MP, Maartens G, Meintjes G. Brief Report: Real-World Performance and Interobserver Agreement of Urine Lipoarabinomannan in Diagnosing HIV-Associated Tuberculosis in an Emergency Center. J Acquir Immune Defic Syndr. 2019 1;81(1):e10-e14.
Vanker A, Nduru PM, Barnett W, Dube FS, Sly PD, Gie RP, Nicol MP, Zar HJ. Indoor air pollution and tobacco smoke exposure: impact on nasopharyngeal bacterial carriage in mothers and infants in an African birth cohort study. ERJ Open Res. 2019 4;5(1).
Di Tanna GL, Khaki AR, Theron G, McCarthy K, Cox H, Mupfumi L, Trajman A, Zijenah LS, Mason P, Bandason T, Durovni B, Bara W, Hoelscher M, Clowes P, Mangu C, Chanda D, Pym A, Mwaba P, Cobelens F, Nicol MP, Dheda K, Churchyard G, Fielding K, Metcalfe JZ. Effect of Xpert MTB/RIF on clinical outcomes in routine care settings: individual patient data meta-analysis. Lancet Glob Health. 2019 ;7(2):e191-e199.
Hanifa Y, Toro Silva S, Karstaedt A, Sahid F, Charalambous S, Chihota VN,Churchyard GJ, von Gottberg A, McCarthy K, Nicol MP, Ndlovu NT, Stevens W, Fielding KL, Grant AD. What causes symptoms suggestive of tuberculosis in HIV-positive people with negative initial investigations? Int J Tuberc Lung Dis. 2019 ;23(2):157-165.
Loveday M, Reuter A, Furin J, Seddon JA, Cox H. The STREAM trial: missed opportunities and lessons for future clinical trials. Lancet Infect Dis. 2019 ;19(4):351-353.
Reid MJA, Arinaminpathy N, Bloom A, Bloom BR, Boehme C, Chaisson R, Chin DP, Churchyard G, Cox H, Ditiu L, Dybul M, Farrar J, Fauci AS, Fekadu E, Fujiwara PI, Hallett TB, Hanson CL, Harrington M, Herbert N, Hopewell PC, Ikeda C, Jamison DT, Khan AJ, Koek I, Krishnan N, Motsoaledi A, Pai M, Raviglione MC, Sharman A, Small PM, Swaminathan S, Temesgen Z, Vassall A, Venkatesan N, van Weezenbeek K, Yamey G, Agins BD, Alexandru S, Andrews JR, Beyeler N, Bivol S, Brigden G, Cattamanchi A, Cazabon D, Crudu V, Daftary A, Dewan P, Doepel LK, Eisinger RW, Fan V, Fewer S, Furin J, Goldhaber-Fiebert JD, Gomez GB, Graham SM, Gupta D, Kamene M, Khaparde S, Mailu EW, Masini EO, McHugh L, Mitchell E, Moon S, Osberg M, Pande T, Prince L, Rade K, Rao R, Remme M, Seddon JA, Selwyn C, Shete P, Sachdeva KS, Stallworthy G, Vesga JF, Vilc V, Goosby EP. Building a tuberculosis-free world: The Lancet Commission on tuberculosis. Lancet. 2019 ;393(10178):1331-1384.
Furin J, Cox H, Pai M. Tuberculosis. Lancet. 2019;393(10181):1642-1656.
Cox V, Cox H, Pai M, Stillo J, Citro B, Brigden G. Health care gaps in the global burden of drug-resistant tuberculosis. Int J Tuberc Lung Dis. 2019 ;23(2):125-135.
Radley JA, O'Sullivan RBG, Turton SE, Cox H, Vogt J, Morton J, Jones E, Smithson S, Lachlan K, Rankin J, Clayton-Smith J, Willoughby J, Elmslie FF, Sansbury FH, Cooper N; Deciphering Developmental Disorders (DDD) Study, Balasubramanian M. Deep phenotyping of 14 new patients with IQSEC2 variants, including monozygotic twins of discordant phenotype. Clin Genet. 2019 ;95(4):496-506. Not published at UCT, SA
Bamford C, Milligan P, Kaliski S. Dangers of Clostridium perfringens food poisoning in psychiatric patients. South African Journal of Psychiatry 2019; 25:a1339
Malande O, Nuttall J, Pillay V, Bamford C, Eley B. A ten year review of ESBL and non-ESBL Escherichia coli bloodstream infections among children at a tertiary referral hospital in South Africa. PLOS ONE 2019; 4(9): e0222675
Richards GA, Brink AJ, Feldman C. Rational use of the fluoroquinolones. SAMJ 2019; (4):378-381.
Meiring S. Cohen C, de Gouveia L, du Plessis M, Kularatne R, Hoosen A, Lekalakala R, Lengana S, Seetharam S, Naicker P, Quan V, Reubenson G, Tempia S, von Mollendorf C, von Gottberg A, GREMS-SA. Declining Incidence of Invasive Meningococcal Disease in South Africa: 2003–2016. Clinical Infectious Diseases 2019; 69(3):495–504.
Young AL, Nicol MP, Moodley C, Bamford C. The accuracy of extended-spectrum beta-lactamase detection in Escherichia coli and Klebsiella pneumoniae in South African laboratories using the Vitek 2 Gram-negative susceptibility card AST-N255. Southern African Journal of Infectious Diseases. 2019 ; 34(1) a114.
Brink AJ, Mendelson M. Be AWaRe: new metrics for paediatric antibiotic stewardship. Lancet Infect Dis 2019; 19(1):6-7. Research done whilst collaborating with Dept of Medicine in 2018
Fredericks E, Hoosen E, Brink AJ. The case in stool banks in South Africa. S Afr Med J 2019; 109(8):546-547
Bassetti M, Giacobbe DR, Vena A, Brink A. Challenges and research priorities to progress the impact of antimicrobial stewardship. Drugs in Context 2019; 8: 212600.
Brink A. Epidemiology of carbapenem-resistant Gram-negative infections globally. Current Opinion and Infectious Diseases 2019; 32 :609-616
Zurcher K, Ballif M, Fenner L, Borell S, Keller PM, Gnokoro J, Marcy O, Yotebieng M, Diero L, CarterEJ, Rockwood N, Willkinson RJ, Cox H, Ezati N, Abimiku A G, Collates J, Avihingsanon A, Kawkitinarong K, Reinhard M, Homke R, Huebener R, Gagneux S, Bottger EC, Egger M, IeDEA consortium. Drug susceptibility testing and mortality in patients treated for tuberculosis in high-burden countries: a multicentre cohort study. The Lancet and infection 2019; 19:298-307
September J, Geffen L, manning K, Naicker P, Faro C, Mendelson M, Wasserman S. Colonisation with pathogenic drug-resistant bacteria and clostridioides difficile among residents of residential care facilities in Cape Town, South Africa: a cross-sectional prevalence study. Journal of antimicrobial resistance and infection control 2019 : 8(108)
Barth DD, Naicker P, Engel K, Muhamed B, Basera W, Mayosi BM, Dale JB, Engel ME. Molecular epidemiology of noninvasive and invasive group A streptococcal infections in Cape Town. MSphere 2019 4(5): e00421-19.
Van Schalkwyk E, Mpembe RS, Thomas J, Shuping L, Ismail H, Lowman W, Karstaedt AS, Chibabhai V, Wadula J, Avenant T, Messina A, Govind CN, Moodley K, Dawood H, Ramjathan P, Govender NP, GERMS-SA. Epiddemiologic shift in candidemia driven by candida auris, South Africa, 2016-2017. Emerging Infectious Diseases 2019. 25(9):1698 -1707
Ismail H, Lowman W, Govind CN, Swe Swe-Han K, Maloba MRB, Bamford C, Perovic O. Survellance and comparison of antimicrobial susceptibility patterns of ESKAPE organism isolated in patients with bacteraemia in South Africa, 2016-2017. South African Medicine Journal 2019. 109(12):934-940.
Brink AJ. Epidemiology of carbapenem-resistant Gram-negative infections globally. Current Opinion in Infectious Diseases 2019. 32(6): 609-616.
Tebano G, Li G, Beovic B, Bielicki J, Brink A, Enani MA, Godman B, Hinrichsen SL, Kibuule D, Gabriel L, Oduyebo O, Sharland M, Singh S, Wertheim HFL, Nathwani D, Pulcini C, ESCMID study group for Antimcrobial Stewardship. International Journal of Antimicrobial Agents 2019. 54: 273-282.