Mark Nicol

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Lower Respiratory Tract Infections in Children in a Well-vaccinated South African Birth Cohort: Spectrum of Disease and Risk Factors.

Clin Infect Dis 2019 Oct;69(9):1588-1596

Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and Medical Research Council Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa.

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https://academic.oup.com/cid/advance-article/doi/10.1093/cid
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http://dx.doi.org/10.1093/cid/ciz017DOI Listing
October 2019

Composition of gut microbiota of children and adolescents with perinatal HIV infection taking antiretroviral therapy in Zimbabwe.

J Infect Dis 2019 Sep 24. Epub 2019 Sep 24.

Paediatric Research Group, Department of Clinical Medicine, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway.

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http://dx.doi.org/10.1093/infdis/jiz473DOI Listing
September 2019

Tuberculosis Diagnosis in Children Using Xpert Ultra on Different Respiratory Specimens.

Am J Respir Crit Care Med 2019 Aug 5. Epub 2019 Aug 5.

University of Capetown, Pediatrics & Child Health, Cape Town, South Africa.

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http://dx.doi.org/10.1164/rccm.201904-0772OCDOI Listing
August 2019

False rifampicin resistant results using Xpert MTB/RIF on urine samples in hospitalised HIV-infected patients.

South Afr J HIV Med 2019 28;20(1):978. Epub 2019 Aug 28.

Division of HIV, Infectious Diseases and Global Medicine at Zuckerberg San Francisco General Hospital and Trauma Center, Department of Medicine, University of California, San Francisco, United States.

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http://dx.doi.org/10.4102/sajhivmed.v20i1.978DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6739559PMC
August 2019

Clinical, microbiologic, and immunologic determinants of mortality in hospitalized patients with HIV-associated tuberculosis: A prospective cohort study.

PLoS Med 2019 Jul 5;16(7):e1002840. Epub 2019 Jul 5.

Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.

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http://dx.doi.org/10.1371/journal.pmed.1002840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6611568PMC
July 2019

Microbiological diagnosis of pulmonary tuberculosis in children by oral swab polymerase chain reaction.

Sci Rep 2019 Jul 25;9(1):10789. Epub 2019 Jul 25.

Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1038/s41598-019-47302-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6658562PMC
July 2019

Influence of Socio-Economic and Psychosocial Profiles on the Human Breast Milk Bacteriome of South African Women.

Nutrients 2019 Jun 20;11(6). Epub 2019 Jun 20.

Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, Observatory 7925, University of Cape Town, Cape Town, South Africa.

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http://dx.doi.org/10.3390/nu11061390DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6627120PMC
June 2019

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 May;81(1):e10-e14

Department of Medicine, Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.

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http://dx.doi.org/10.1097/QAI.0000000000002002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6522362PMC
May 2019

Etiology of Pulmonary Infections in Human Immunodeficiency Virus-infected Inpatients Using Sputum Multiplex Real-time Polymerase Chain Reaction.

Clin Infect Dis 2019 Apr 26. Epub 2019 Apr 26.

Division of Infectious Diseases and Human Immunodeficiency Virus Medicine, Department of Medicine, University of Cape Town, South Africa.

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http://dx.doi.org/10.1093/cid/ciz332DOI Listing
April 2019

Longitudinal Population Dynamics of in the Nasopharynx During the First Year of Life.

Front Genet 2019 15;10:198. Epub 2019 Mar 15.

Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.

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http://dx.doi.org/10.3389/fgene.2019.00198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6428701PMC
March 2019

Nasopharyngeal Carriage of Antimicrobial-Resistant Pneumococci in an Intensively Sampled South African Birth Cohort.

Front Microbiol 2019 27;10:610. Epub 2019 Mar 27.

Division of Medical Microbiology, Faculty of Health Science, University of Cape Town, Cape Town, South Africa.

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http://dx.doi.org/10.3389/fmicb.2019.00610DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6446970PMC
March 2019

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 Feb 4;5(1). Epub 2019 Feb 4.

Dept of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, and SAMRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa.

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http://openres.ersjournals.com/lookup/doi/10.1183/23120541.0
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http://dx.doi.org/10.1183/23120541.00052-2018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360211PMC
February 2019

Human Breast Milk Bacteriome in Health and Disease.

Nutrients 2018 Nov 3;10(11). Epub 2018 Nov 3.

Division of Medical Microbiology, Department of Pathology, University of Cape Town, Observatory, Cape Town 7925, South Africa.

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http://www.mdpi.com/2072-6643/10/11/1643
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http://dx.doi.org/10.3390/nu10111643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6266581PMC
November 2018

Accuracy of Xpert Mtb/Rif Ultra for the Diagnosis of Pulmonary Tuberculosis in Children.

Pediatr Infect Dis J 2018 10;37(10):e261-e263

Department of Paediatrics and Child Health, MRC Unit on Child and Adolescent Health, University of Cape Town and Red Cross War Memorial Children's Hospital, Cape Town, South Africa.

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http://dx.doi.org/10.1097/INF.0000000000001960DOI Listing
October 2018

Gene expression in cord blood links genetic risk for neurodevelopmental disorders with maternal psychological distress and adverse childhood outcomes.

Brain Behav Immun 2018 10 20;73:320-330. Epub 2018 May 20.

Department of Psychiatry and Mental Health, University of Cape Town, South Africa; South African Medical Research Council (SAMRC) Unit on Risk & Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa. Electronic address:

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http://dx.doi.org/10.1016/j.bbi.2018.05.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6191930PMC
October 2018

Treatment of bronchiectasis exacerbations in children: which antibiotic?

Lancet 2018 10 18;392(10154):1169-1170. Epub 2018 Sep 18.

Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service of South Africa, Cape Town, South Africa.

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http://dx.doi.org/10.1016/S0140-6736(18)32004-XDOI Listing
October 2018

Age-related waning of immune responses to BCG in healthy children supports the need for a booster dose of BCG in TB endemic countries.

Sci Rep 2018 10 17;8(1):15309. Epub 2018 Oct 17.

Academic Department of Paediatrics, St Marys Campus, Imperial College London, 2nd Floor Wright-Fleming Building, Norfolk Place, London, W2 1PG, UK.

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http://www.nature.com/articles/s41598-018-33499-4
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http://dx.doi.org/10.1038/s41598-018-33499-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6193026PMC
October 2018

Precision medicine for drug-resistant tuberculosis in high-burden countries: is individualised treatment desirable and feasible?

Lancet Infect Dis 2018 09 13;18(9):e282-e287. Epub 2018 Mar 13.

Division of Medical Microbiology and the Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, Johannesburg, South Africa.

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http://dx.doi.org/10.1016/S1473-3099(18)30104-XDOI Listing
September 2018

Characterisation of STEC and other diarrheic E. coli isolated on CHROMagar™STEC at a tertiary referral hospital, Cape Town.

BMC Microbiol 2018 06 8;18(1):55. Epub 2018 Jun 8.

Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town and National Health Laboratory Services, Cape Town, South Africa.

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http://dx.doi.org/10.1186/s12866-018-1195-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5994027PMC
June 2018

Proteomic comparison of three clinical diarrhoeagenic drug-resistant Escherichia coli isolates grown on CHROMagar™STEC media.

J Proteomics 2018 05 5;180:25-35. Epub 2017 Sep 5.

Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, South Africa. Electronic address:

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http://dx.doi.org/10.1016/j.jprot.2017.09.003DOI Listing
May 2018

Tuberculosis eradication: renewed commitment and global investment required.

Lancet Infect Dis 2018 03 7;18(3):228-229. Epub 2017 Dec 7.

Division of Medical Microbiology, University of Cape Town, Cape Town, 7925, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, Johannesburg, South Africa.

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http://dx.doi.org/10.1016/S1473-3099(17)30692-8DOI Listing
March 2018

Preventing tuberculosis-related death in children with HIV.

Lancet HIV 2018 02 23;5(2):e62-e64. Epub 2017 Nov 23.

Division of Medical Microbiology, Department of Pathology, University of Cape Town, 7925 Cape Town, South Africa; National Health Laboratory Service, Cape Town, South Africa; Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa. Electronic address:

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http://dx.doi.org/10.1016/S2352-3018(17)30208-4DOI Listing
February 2018

Xpert MTB/RIF Ultra: a gamechanger for tuberculous meningitis?

Lancet Infect Dis 2018 01 14;18(1):6-8. Epub 2017 Sep 14.

Division of Medical Microbiology, Department of Pathology, Cape Town 7925, South Africa; Institute of Infectious Diseases and Molecular Medicine, Cape Town 7925, South Africa; University of Cape Town, Cape Town 7925, South Africa; National Health Laboratory Service, Cape Town, South Africa. Electronic address:

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http://dx.doi.org/10.1016/S1473-3099(17)30536-4DOI Listing
January 2018

Tuberculin skin test conversion and primary progressive tuberculosis disease in the first 5 years of life: a birth cohort study from Cape Town, South Africa.

Lancet Child Adolesc Health 2018 01;2(1):46-55

Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and Medical Research Council Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa.

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https://linkinghub.elsevier.com/retrieve/pii/S23524642173014
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http://dx.doi.org/10.1016/S2352-4642(17)30149-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5810304PMC
January 2018

Detection of Streptococcus pneumoniae from Different Types of Nasopharyngeal Swabs in Children.

PLoS One 2013 26;8(6):e68097. Epub 2013 Jun 26.

Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068097PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694050PMC
October 2017

Impact of Point-of-Care Xpert MTB/RIF on Tuberculosis Treatment Initiation. A Cluster-randomized Trial.

Am J Respir Crit Care Med 2017 10;196(7):901-910

1 Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom.

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http://dx.doi.org/10.1164/rccm.201702-0278OCDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5649979PMC
October 2017

Global, regional, and national disease burden estimates of acute lower respiratory infections due to respiratory syncytial virus in young children in 2015: a systematic review and modelling study.

Authors:
Ting Shi David A McAllister Katherine L O'Brien Eric A F Simoes Shabir A Madhi Bradford D Gessner Fernando P Polack Evelyn Balsells Sozinho Acacio Claudia Aguayo Issifou Alassani Asad Ali Martin Antonio Shally Awasthi Juliet O Awori Eduardo Azziz-Baumgartner Henry C Baggett Vicky L Baillie Angel Balmaseda Alfredo Barahona Sudha Basnet Quique Bassat Wilma Basualdo Godfrey Bigogo Louis Bont Robert F Breiman W Abdullah Brooks Shobha Broor Nigel Bruce Dana Bruden Philippe Buchy Stuart Campbell Phyllis Carosone-Link Mandeep Chadha James Chipeta Monidarin Chou Wilfrido Clara Cheryl Cohen Elizabeth de Cuellar Duc-Anh Dang Budragchaagiin Dash-Yandag Maria Deloria-Knoll Mukesh Dherani Tekchheng Eap Bernard E Ebruke Marcela Echavarria Carla Cecília de Freitas Lázaro Emediato Rodrigo A Fasce Daniel R Feikin Luzhao Feng Angela Gentile Aubree Gordon Doli Goswami Sophie Goyet Michelle Groome Natasha Halasa Siddhivinayak Hirve Nusrat Homaira Stephen R C Howie Jorge Jara Imane Jroundi Cissy B Kartasasmita Najwa Khuri-Bulos Karen L Kotloff Anand Krishnan Romina Libster Olga Lopez Marilla G Lucero Florencia Lucion Socorro P Lupisan Debora N Marcone John P McCracken Mario Mejia Jennifer C Moisi Joel M Montgomery David P Moore Cinta Moraleda Jocelyn Moyes Patrick Munywoki Kuswandewi Mutyara Mark P Nicol D James Nokes Pagbajabyn Nymadawa Maria Tereza da Costa Oliveira Histoshi Oshitani Nitin Pandey Gláucia Paranhos-Baccalà Lia N Phillips Valentina Sanchez Picot Mustafizur Rahman Mala Rakoto-Andrianarivelo Zeba A Rasmussen Barbara A Rath Annick Robinson Candice Romero Graciela Russomando Vahid Salimi Pongpun Sawatwong Nienke Scheltema Brunhilde Schweiger J Anthony G Scott Phil Seidenberg Kunling Shen Rosalyn Singleton Viviana Sotomayor Tor A Strand Agustinus Sutanto Mariam Sylla Milagritos D Tapia Somsak Thamthitiwat Elizabeth D Thomas Rafal Tokarz Claudia Turner Marietjie Venter Sunthareeya Waicharoen Jianwei Wang Wanitda Watthanaworawit Lay-Myint Yoshida Hongjie Yu Heather J Zar Harry Campbell Harish Nair

Lancet 2017 Sep 7;390(10098):946-958. Epub 2017 Jul 7.

Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland, UK; Public Health Foundation of India, New Delhi, India. Electronic address:

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http://dx.doi.org/10.1016/S0140-6736(17)30938-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5592248PMC
September 2017

Disseminated tuberculosis among hospitalised HIV patients in South Africa: a common condition that can be rapidly diagnosed using urine-based assays.

Sci Rep 2017 09 7;7(1):10931. Epub 2017 Sep 7.

Wellcome Trust Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.

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http://dx.doi.org/10.1038/s41598-017-09895-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5589905PMC
September 2017

Genome Sequence for Shiga Toxin-Producing O26:H11, Associated with a Cluster of Hemolytic-Uremic Syndrome Cases in South Africa, 2017.

Genome Announc 2017 Sep 21;5(38). Epub 2017 Sep 21.

Centre for Enteric Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.

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http://dx.doi.org/10.1128/genomeA.00989-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5609422PMC
September 2017

Remembering the basics: interventions to improve sputum collection for tuberculosis diagnosis.

Lancet Glob Health 2017 08 15;5(8):e728-e729. Epub 2017 Jun 15.

Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town 7700, South Africa; Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7700, South Africa; National Health Laboratory Service, Johannesburg, South Africa. Electronic address:

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http://dx.doi.org/10.1016/S2214-109X(17)30227-9DOI Listing
August 2017

The Influence of HIV on the Evolution of Mycobacterium tuberculosis.

Mol Biol Evol 2017 07;34(7):1654-1668

Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, and Department of Medicine, University of Cape Town, Cape Town, South Africa.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msx107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5455964PMC
July 2017

Advances in the diagnosis of pneumonia in children.

BMJ 2017 Jul 26;358:j2739. Epub 2017 Jul 26.

Division of Medical Microbiology, Department of Pathology, University of Cape Town.

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http://dx.doi.org/10.1136/bmj.j2739DOI Listing
July 2017

Regulatory T Cells and Pro-inflammatory Responses Predominate in Children with Tuberculosis.

Front Immunol 2017 25;8:448. Epub 2017 Apr 25.

Academic Department of Paediatrics, Imperial College London, London, UK.

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http://dx.doi.org/10.3389/fimmu.2017.00448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5403917PMC
April 2017

How should tuberculosis molecular diagnostics be adapted for use in seriously ill HIV patients?

Authors:
Mark P Nicol

Expert Rev Mol Diagn 2016 12;16(12):1237-1239

a Division of Medical Microbiology, Department of Pathology and Institute for Infectious Diseases and Molecular Medicine , University of Cape Town and National Health Laboratory Service , Cape Town , South Africa.

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http://dx.doi.org/10.1080/14737159.2016.1257386DOI Listing
December 2016

Highly sensitive sequence specific qPCR detection of Mycobacterium tuberculosis complex in respiratory specimens.

Tuberculosis (Edinb) 2016 12 10;101:114-124. Epub 2016 Sep 10.

Center for Innovation in Global Health Technologies (CIGHT), Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tube.2016.09.002DOI Listing
December 2016

Tuberculosis Diagnostics: State of the Art and Future Directions.

Microbiol Spectr 2016 10;4(5)

FIND, 1202 Geneva, Switzerland.

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http://dx.doi.org/10.1128/microbiolspec.TBTB2-0019-2016DOI Listing
October 2016

Respiratory microbes present in the nasopharynx of children hospitalised with suspected pulmonary tuberculosis in Cape Town, South Africa.

BMC Infect Dis 2016 10 24;16(1):597. Epub 2016 Oct 24.

Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.

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http://dx.doi.org/10.1186/s12879-016-1934-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5075757PMC
October 2016

Human brucellosis in South Africa: Public health and diagnostic pitfalls.

S Afr Med J 2016 Aug 1;106(9):883-5. Epub 2016 Aug 1.

National Health Laboratory Service, Microbiology Laboratory, Groote Schuur Hospital, Cape Town, South Africa; Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa.

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http://dx.doi.org/10.7196/SAMJ.2016.v106i9.11020DOI Listing
August 2016

Current Knowledge and Future Research Directions on Fecal Bacterial Patterns and Their Association with Asthma.

Front Microbiol 2016 29;7:838. Epub 2016 Jun 29.

Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape TownCape Town, South Africa; Institute of Infectious Diseases and Molecular Medicine, University of Cape TownCape Town, South Africa.

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http://dx.doi.org/10.3389/fmicb.2016.00838DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4925717PMC
July 2016

Incidence and Diagnosis of Pertussis in South African Children Hospitalized With Lower Respiratory Tract Infection.

Pediatr Infect Dis J 2016 06;35(6):611-6

From the *Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa; †MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa; and ‡Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; §National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa; ¶Institute of Infectious Disease and Molecular Medicine and ||Vaccines for Africa Initiative, Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa.

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http://dx.doi.org/10.1097/INF.0000000000001132DOI Listing
June 2016

Aetiology of childhood pneumonia in a well vaccinated South African birth cohort: a nested case-control study of the Drakenstein Child Health Study.

Lancet Respir Med 2016 06 21;4(6):463-72. Epub 2016 Apr 21.

Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa; National Health Laboratory Services, Cape Town, South Africa.

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http://dx.doi.org/10.1016/S2213-2600(16)00096-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4989125PMC
June 2016

Childhood pneumonia - the Drakenstein Child Health Study.

S Afr Med J 2016 Jun 15;106(7):642-3. Epub 2016 Jun 15.

Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and Medical Research Council Unit on Child and Adolescent Health, Faculty of Health Sciences, University of Cape Town, South Africa.

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http://dx.doi.org/10.7196/SAMJ.2016.v106i7.11108DOI Listing
June 2016

Comparison of a Real-Time Multiplex PCR and Sequetyping Assay for Pneumococcal Serotyping.

PLoS One 2015 3;10(9):e0137349. Epub 2015 Sep 3.

Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0137349PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4559314PMC
May 2016

Fecal Carriage of Staphylococcus aureus in the Hospital and Community Setting: A Systematic Review.

Front Microbiol 2016 10;7:449. Epub 2016 May 10.

Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape TownCape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape TownCape Town, South Africa.

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http://dx.doi.org/10.3389/fmicb.2016.00449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4861718PMC
May 2016

HIV-Related Medical Admissions to a South African District Hospital Remain Frequent Despite Effective Antiretroviral Therapy Scale-Up.

Medicine (Baltimore) 2015 Dec;94(50):e2269

From the Clinical Infectious Diseases Research Initiative, Institute of Infectious Disease and Molecular Medicine (GM, CS, LB); Department of Medicine, Faculty of Health Sciences, University of Cape Town (GM, RB, CS, SDL); Department of Medicine, Khayelitsha District Hospital, South Africa (GM, RB); Department of Medicine, Imperial College London, London, UK (GM); The Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa (ADK, SDL); Department of Medicine, University of California San Francisco School of Medicine, San Francisco, CA, USA (ADK); Department of Global Health, Academic Medical Center, Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, The Netherlands (ADK); School of Public Health and Family Medicine, Faculty of Health Sciences, University of Cape Town (AB); Health Impact Assessment Directorate, Western Cape Department of Health (AB); Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town (AB); Department of Medicine, Mitchells Plain Hospital (GVW); Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town (MPN); National Health Laboratory Service, South Africa (MPN); and Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK (SDL).

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http://dx.doi.org/10.1097/MD.0000000000002269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5058922PMC
December 2015

Incidence of childhood pneumonia: facility-based surveillance estimate compared to measured incidence in a South African birth cohort study.

BMJ Open 2015 Dec 18;5(12):e009111. Epub 2015 Dec 18.

Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, Western Cape, South Africa.

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http://dx.doi.org/10.1136/bmjopen-2015-009111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691755PMC
December 2015

Molecular characterisation and epidemiological investigation of an outbreak of blaOXA-181 carbapenemase-producing isolates of Klebsiella pneumoniae in South Africa.

S Afr Med J 2015 Nov 8;105(12):1030-5. Epub 2015 Nov 8.

Centre for Opportunistic, Tropical and Hospital Infections, National Institute for Communicable Diseases, Groote Schuur Hospital, Cape Town, South Africa; National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa; Division of Medical Microbiology, University of Cape Town, South Africa.

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http://dx.doi.org/10.7196/SAMJ.2015.v105i12.9926DOI Listing
November 2015

A Blueprint to Address Research Gaps in the Development of Biomarkers for Pediatric Tuberculosis.

Clin Infect Dis 2015 Oct;61Suppl 3:S164-72

Department of Science and Technology and National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research/Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa.

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http://dx.doi.org/10.1093/cid/civ613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4583573PMC
October 2015

Diagnosis of Pulmonary Tuberculosis in Children: Assessment of the 2012 National Institutes of Health Expert Consensus Criteria.

Clin Infect Dis 2015 Oct;61Suppl 3:S173-8

Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, National Health Laboratory Service, Groote Schuur Hospital, South Africa.

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http://dx.doi.org/10.1093/cid/civ622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4583577PMC
October 2015

Clinical Predictors of Culture-confirmed Pulmonary Tuberculosis in Children in a High Tuberculosis and HIV Prevalence Area.

Pediatr Infect Dis J 2015 Sep;34(9):e206-10

From the *Department of Pediatrics and Child Health, University of Cape Town and Tygerberg Childrens Hospital, Cape Town, South Africa; †Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, University of the Witwatersrand, Johannesburg, South Africa; ‡Division of Clinical Pharmacology, Department of Medicine and Child Health, University of Cape Town, Cape Town, South Africa; §Red Cross War Memorial Children's Hospital, Cape Town, South Africa; ¶Department of Radiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; ‖Division of Medical Microbiology, Department of Clinical Laboratory Sciences, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service of South Africa, Cape Town, South Africa; and **Department of Paediatrics and Child Health, Red Cross Childrens Hospital, University of Cape Town, South Africa and MRC unit on Child and Adolescent Lung Health, Cape Town, South Africa.

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http://dx.doi.org/10.1097/INF.0000000000000792DOI Listing
September 2015

Underestimation of the True Specificity of the Urine Lipoarabinomannan Point-of-Care Diagnostic Assay for HIV-Associated Tuberculosis.

J Acquir Immune Defic Syndr 2015 Aug;69(4):e144-6

*Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom †The Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa ‡George Washington University School of Medicine and Health Sciences, Washington, DC §Department of Global Health, Academic Medical Center, Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, the Netherlands ‖Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa ¶National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa #Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa **Clinical Infectious Diseases Research Initiative, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa ††Department of Medicine, Imperial College, London, United Kingdom.

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http://dx.doi.org/10.1097/QAI.0000000000000672DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486367PMC
August 2015

Molecular epidemiology of Methicillin-resistant Staphylococcus aureus in Africa: a systematic review.

Front Microbiol 2015 30;6:348. Epub 2015 Apr 30.

Division of Medical Microbiology, Department of Clinical Laboratory Sciences, Faculty of Health Sciences, University of Cape Town Cape Town, South Africa ; Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town Cape Town, South Africa.

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http://journal.frontiersin.org/article/10.3389/fmicb.2015.00
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http://dx.doi.org/10.3389/fmicb.2015.00348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4415431PMC
May 2015

Editorial commentary: dead or alive: can viability staining predict response to tuberculosis treatment?

Clin Infect Dis 2015 Apr 23;60(8):1196-8. Epub 2014 Dec 23.

Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4370167PMC
April 2015

Cytotoxic mediators in paradoxical HIV-tuberculosis immune reconstitution inflammatory syndrome.

J Immunol 2015 Feb 14;194(4):1748-54. Epub 2015 Jan 14.

Clinical Infectious Diseases Research Initiative, University of Cape Town, Cape Town, 7925 South Africa; Department of Medicine, University of Cape Town, Cape Town, 7925 South Africa; Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom; Division of Medicine, Imperial College London, London W2 1PG, United Kingdom;

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http://www.jimmunol.org/lookup/doi/10.4049/jimmunol.1402105
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http://dx.doi.org/10.4049/jimmunol.1402105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4319311PMC
February 2015

Incidence and severity of childhood pneumonia in the first year of life in a South African birth cohort: the Drakenstein Child Health Study.

Lancet Glob Health 2015 Feb;3(2):e95-e103

Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and University of Cape Town, Cape Town, South Africa.

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http://dx.doi.org/10.1016/S2214-109X(14)70360-2DOI Listing
February 2015

The spread of carbapenemase-producing bacteria in Africa: a systematic review.

J Antimicrob Chemother 2015 Jan 26;70(1):23-40. Epub 2014 Sep 26.

Division of Medical Microbiology, Department of Clinical Laboratory Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa Institute for Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa

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http://dx.doi.org/10.1093/jac/dku356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5975721PMC
January 2015

Effect of empirical treatment on outcomes of clinical trials of diagnostic assays for tuberculosis.

Lancet Infect Dis 2015 Jan;15(1):17-8

Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.

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http://dx.doi.org/10.1016/S1473-3099(14)71049-7DOI Listing
January 2015

Impact of Xpert MTB/RIF for TB diagnosis in a primary care clinic with high TB and HIV prevalence in South Africa: a pragmatic randomised trial.

PLoS Med 2014 Nov 25;11(11):e1001760. Epub 2014 Nov 25.

Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa.

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http://dx.doi.org/10.1371/journal.pmed.1001760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4244039PMC
November 2014

Rapid diagnosis of pediatric mycobacterial lymphadenitis using fine needle aspiration biopsy.

Pediatr Infect Dis J 2014 Sep;33(9):893-6

From the *Division of Anatomical Pathology University Stellenbosch and National Health Laboratory Service (NHLS), Tygerberg Hospital, Port Elizabeth; †Division of Medical Microbiology, University of Cape Town and NHLS Groote Schuur Hospital; ‡Centre for Tropical Opportunistic and Hospital Infections, National Institute for Communicable Diseases and NHLS Groote Schuur Hospital; and §Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa.

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http://dx.doi.org/10.1097/INF.0000000000000312DOI Listing
September 2014

Diagnostic accuracy of a rapid urine lipoarabinomannan test for tuberculosis in HIV-infected adults.

J Acquir Immune Defic Syndr 2014 Jul;66(3):270-9

*Department of Medicine, Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda; †Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa and National Health Laboratory Service, South Africa; ‡Johns Hopkins University School of Medicine, Baltimore, MD; §Department of Medicine, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD; ‖Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda; ¶Division of Infectious Diseases, Department of Medicine, New Jersey Medical School, Newark, NJ; and #Department of Medicine, Boston Medical Center, Boston University, Boston, MA.

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http://dx.doi.org/10.1097/QAI.0000000000000151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4146703PMC
July 2014

Mixed Mycobacterium tuberculosis complex infections and false-negative results for rifampin resistance by GeneXpert MTB/RIF are associated with poor clinical outcomes.

J Clin Microbiol 2014 Jul 30;52(7):2422-9. Epub 2014 Apr 30.

Botswana-UPenn Partnership, Gaborone, Botswana Division of Infectious Diseases, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1128/JCM.02489-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4097703PMC
July 2014

Diagnostic accuracy of Xpert MTB/RIF for extrapulmonary tuberculosis specimens: establishing a laboratory testing algorithm for South Africa.

J Clin Microbiol 2014 Jun 12;52(6):1818-23. Epub 2014 Mar 12.

Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa National Health Laboratory Service, National Priority Program, Johannesburg, South Africa.

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http://dx.doi.org/10.1128/JCM.03553-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4042800PMC
June 2014

Research capacity. Enabling the genomic revolution in Africa.

Authors:
Charles Rotimi Akin Abayomi Alash'le Abimiku Victoria May Adabayeri Clement Adebamowo Ezekiel Adebiyi Adebowale D Ademola Adebowale Adeyemo Dwomoa Adu Dissou Affolabi Godfred Agongo Samuel Ajayi Sally Akarolo-Anthony Rufus Akinyemi Albert Akpalu Marianne Alberts Orlando Alonso Betancourt Ahmed Mansour Alzohairy Gobena Ameni Olukemi Amodu Gabriel Anabwani Kristian Andersen Fatiu Arogundade Oyedunni Arulogun Danny Asogun Rasheed Bakare Naby Balde Mary Lynn Baniecki Christine Beiswanger Alia Benkahla Lara Bethke Micheal Boehnke Vincent Boima James Brandful Andrew I Brooks Frank C Brosius Chester Brown Bruno Bucheton David T Burke Barrington G Burnett Stacy Carrington-Lawrence Nadia Carstens John Chisi Alan Christoffels Richard Cooper Heather Cordell Nigel Crowther Talishiea Croxton Jantina de Vries Leslie Derr Peter Donkor Seydou Doumbia Audrey Duncanson Ivy Ekem Ahmed El Sayed Mark E Engel John C K Enyaru Dean Everett Faisal M Fadlelmola Eyitayo Fakunle Kenneth H Fischbeck Anne Fischer Onikepe Folarin Junaid Gamieldien Robert F Garry Simani Gaseitsiwe Rasheed Gbadegesin Anita Ghansah Maria Giovanni Parham Goesbeck F Xavier Gomez-Olive Donald S Grant Ravnit Grewal Mark Guyer Neil A Hanchard Christian T Happi Scott Hazelhurst Branwen J Hennig Christiane Hertz- Fowler Winston Hide Friedhelm Hilderbrandt Christopher Hugo-Hamman Muntaser E Ibrahim Regina James Yasmina Jaufeerally-Fakim Carolyn Jenkins Ute Jentsch Pan-Pan Jiang Moses Joloba Victor Jongeneel Fourie Joubert Mukthar Kader Kathleen Kahn Pontiano Kaleebu Saidi H Kapiga Samar Kamal Kassim Ishmael Kasvosve Jonathan Kayondo Bernard Keavney Adeodata Kekitiinwa Sheik Humarr Khan Paul Kimmel Mary-Claire King Robert Kleta Mathurin Koffi Jeffrey Kopp Matthias Kretzler Judit Kumuthini Samuel Kyobe Catherine Kyobutungi Daniel T Lackland Karen A Lacourciere Guida Landouré Rita Lawlor Thomas Lehner Maia Lesosky Naomi Levitt Katherine Littler Zane Lombard Jeanne F Loring Sylvester Lyantagaye Annette Macleod Ebony B Madden Chengetai R Mahomva Julie Makani Manmak Mamven Marape Marape Graeme Mardon Patricia Marshall Darren P Martin Daniel Masiga Robin Mason Michael Mate-Kole Enock Matovu Mary Mayige Bongani M Mayosi Jean Claude Mbanya Sheryl A McCurdy Mark I McCarthy Helen McIlleron S O Mc'Ligeyo Corrine Merle Ana Olga Mocumbi Charles Mondo John V Moran Ayesha Motala Marva Moxey-Mims Wata Sununguko Mpoloka Chisomo L Msefula Thuli Mthiyane Nicola Mulder Gebregziab her Mulugeta Dieuodonne Mumba John Musuku Mo Nagdee Oyekanmi Nash Daouda Ndiaye Anh Quynh Nguyen Mark Nicol Oathokwa Nkomazana Shane Norris Betty Nsangi Alexander Nyarko Moffat Nyirenda Eileen Obe Reginald Obiakor Abraham Oduro Solomon F Ofori-Acquah Okechukwu Ogah Stephen Ogendo Kwaku Ohene-Frempong Akinlolu Ojo Timothy Olanrewaju John Oli Charlotte Osafo Odile Ouwe Missi Oukem-Boyer Bruce Ovbiagele Andrew Owen Mayowa Ojo Owolabi Lukman Owolabi Ellis Owusu-Dabo Guillaume Pare Rulan Parekh Hugh G Patterton Margaret B Penno Jane Peterson Rembert Pieper Jacob Plange-Rhule Martin Pollak Julia Puzak Rajkumar S Ramesar Michele Ramsay Rebekah Rasooly Shiksha Reddy Pardis C Sabeti Kwamena Sagoe Tunde Salako Oumar Samassékou Manjinder S Sandhu Osman Sankoh Fred Stephen Sarfo Marie Sarr Gasnat Shaboodien Issa Sidibe Gustave Simo Martin Simuunza Liam Smeeth Eugene Sobngwi Himla Soodyall Hermann Sorgho Oumou Sow Bah Sudha Srinivasan Dan J Stein Ezra S Susser Carmen Swanepoel Godfred Tangwa Andrew Tareila Ozlem Tastan Bishop Bamidele Tayo Nicki Tiffin Halidou Tinto Ekaete Tobin Stephen Meir Tollman Mahamadou Traoré Marsha J Treadwell Jennifer Troyer Masego Tsimako-Johnstone Vincent Tukei Ifeoma Ulasi Nzovu Ulenga Beverley van Rooyen Ablo Prudence Wachinou Salina P Waddy Alisha Wade Misaki Wayengera James Whitworth Louise Wideroff Cheryl A Winkler Sarah Winnicki Ambroise Wonkam Mengistu Yewondwos Tadase sen Nathan Yozwiak Heather Zar

Science 2014 Jun;344(6190):1346-8

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http://dx.doi.org/10.1126/science.1251546DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4138491PMC
June 2014

GeneXpert MTB/RIF version G4 for identification of rifampin-resistant tuberculosis in a programmatic setting.

J Clin Microbiol 2014 Feb 27;52(2):635-7. Epub 2013 Nov 27.

City Health Directorate, City of Cape Town, South Africa.

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http://dx.doi.org/10.1128/JCM.02517-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3911341PMC
February 2014

Determine TB-LAM lateral flow urine antigen assay for HIV-associated tuberculosis: recommendations on the design and reporting of clinical studies.

BMC Infect Dis 2013 Sep 3;13:407. Epub 2013 Sep 3.

Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.

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http://dx.doi.org/10.1186/1471-2334-13-407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3846798PMC
September 2013

Xpert MTB/RIF testing of stool samples for the diagnosis of pulmonary tuberculosis in children.

Clin Infect Dis 2013 Aug 11;57(3):e18-21. Epub 2013 Apr 11.

Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, and National Health Laboratory Service of South Africa, South Africa.

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http://dx.doi.org/10.1093/cid/cit230DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703104PMC
August 2013

A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples.

J Microbiol Methods 2013 Aug 14;94(2):103-110. Epub 2013 May 14.

Division of Medical Microbiology, Department of Clinical Laboratory Science, University of Cape Town, Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.

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http://dx.doi.org/10.1016/j.mimet.2013.05.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5809576PMC
August 2013

Xpert MTB/RIF: monitoring response to tuberculosis treatment.

Authors:
Mark P Nicol

Lancet Respir Med 2013 Aug 1;1(6):427-8. Epub 2013 Jul 1.

Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa; National Health Laboratory Service, 5.28 Falmouth, Faculty of Health Sciences, Anzio Road, Observatory, Cape Town, 7925, South Africa. Electronic address:

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http://dx.doi.org/10.1016/S2213-2600(13)70133-4DOI Listing
August 2013

Rapid diagnosis of pulmonary tuberculosis in African children in a primary care setting by use of Xpert MTB/RIF on respiratory specimens: a prospective study.

Lancet Glob Health 2013 Aug 24;1(2):e97-e104. Epub 2013 Jul 24.

Division of Medical Microbiology, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa.

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http://dx.doi.org/10.1016/S2214-109X(13)70036-6DOI Listing
August 2013

Using Xpert MTB/RIF.

Curr Respir Med Rev 2013 Jun;9:187-192

Division of Medical Microbiology, Department of Clinical Laboratory Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, South Africa ; National Health Laboratory Service, South Africa.

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http://dx.doi.org/10.2174/1573398X113099990015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785149PMC
June 2013