Networking

Networking

New networks and linkages

The Wits node is playing the leading role in a new international collaboration between Wits University, the USA National Institutes of Health (NIH), the Centers for Disease Control and Prevention (CDC), the University of Leicester, the Perinatal HIV Research Unit (PHRU) and the Aurum Institute. This new collaborative project is led by Dr. Bavesh Kana involves the detection and characterization of non-replicating bacterial populations in the sputum of patients with active TB disease.
Dr. Bavesh Kana from the Wits node collaborates with Dr. Gilla Kaplan and Dr. Dorothy Fallows from the Public Health Research Institute, USA, on a project to aimed at further understanding hetero-resistance to the first and second line antibiotics used to treat TB. This joint project, which is funded by the US National Institutes of Health, also involves participation of various members of the National TB Reference Laboratory and Siswe Clinic in Johannesburg.
The Wits node has initiated a new collaborative venture with Drs. Stoyan Stoychev and Musa Mhlanga at the Council for Scientific and Industrial Research. This collaboration involves the use mass spectroscopy and super-resolution microscopy to determine the specific changes that occur in the cell wall of mycobacteria during different stages of TB disease and under stress conditions. Members of the Wits node, together with the CSIR, are currently in the process of developing key methodologies for this project. This particular collaboration promises to strengthen the ties between the CBTBR and a key industrial partner in SA.
Dr. Bavesh Kana from the Wits node has initiated a new collaboration with Dr. Lesley Scott from the Department of Molecular Medicine and Hematology at Wits University. The ultimate aim of this partnership is to develop a robust external quality assurance system for rollout of the new GeneXpert TB diagnostic system. The Wits node is playing a critical role in this venture which will help to bolster the national TB control program further testifying to the impact of the CBTBR on TB control in South Africa.
Further collaborative links at the Department of Molecular Medicine and Hematology at Wits University, through the Wits of the CBTBR includes a new collaboration with Dr. Melinda Suchard on characterization of the immune response in humans when challenged with mutant mycobacterial strains, defective in cell wall remodeling. The Wits node is also collaborating with Dr. Pierre Durand on the phylogenetic and evolutionary analysis of cell wall remodeling enzymes in various mycobacterial species.
The Mycobacterial Referral Laboratory at the National Health Laboratory Service (Johannesburg, Central branch) has initiated a new collaboration with the Wits node which involves the characterization of discordant rifampicin resistant mutants in the Gauteng region. The strains selected for this study would comprise those samples that give inconsistent phenotypic resistance data when compared to the rifampicin resistance genotype provided by the line probe assay. The project represents an important partnership between the CBTBR and the national diagnostic platform for TB in South Africa.
The SU node group of Prof Eileen Hoal, working on host genetics of TB, collaborates with the Computational Biology Group at UCT’s IIDMM, headed by Prof Nicola Mulder. This project brings the bioinformatic power and expertise of Computational Biology to bear on the analysis of the SNP chip genetic data generated at the CBTBR.

Existing networks and linkages
The three nodes of the CBTBR are involved in wide collaborative networks that involve TB researchers and research institutions in a large number of countries. Maintaining existing collaborative networks and developing new linkages is of critical importance to the CBTBR. For this reason, members continued to devote significant time and effort to networking.

NAME	INSTITUTION	NATURE/ PURPOSE, OUTPUTS AND FUTURE DIRECTION OF COLLABORATION
Dr. William Mac Kenzie	Centers for Disease Control and Prevention, USA	Collaboration on the detection and characterization of Rpf-dependent bacterial populations in sputum. Project funded by the NIH.
Prof. Michael Barer and Dr. Galina Mukamolova	University of Leicester, UK	Collaboration on the detection and characterization of Rpf-dependent bacterial populations in sputum. Project funded by the NIH
Dr. Gavin Churchyard	The Aurum Institute	Collaboration on the detection and characterization of Rpf-dependent bacterial populations in sputum. Project funded by the NIH. The Wits node also collaborating with Dr. Churchyard on several other ventures under the auspices of the Wits-Aurum Coalition.
Prof. Gilla Kaplan and Dr. Dorothy Fallows	Public Health Research Institute, International Center for Public Health, Newark, NJ	Prof. Kaplan serves as the international member on the Board of the CBTBR. She and Dr. Kana serve on the CU-SA Fogarty AITRP Advisory Board. Furthermore, she visited the Wits node in November 2011. Dr. Kana collaborates with Dr. Kaplan and Dr. Fallows on an NIH funded project to study hetero-resistance in TB patients with active disease
Prof. Lesley Scott	University of the Witwatersrand	Ongoing collaboration on the rollout of the GeneXpert diagnostic test and establishment of an external quality assurance system.
Dr. Melinda Suchard	University of the Witwatersrand	Ongoing collaboration of immunological characterization of mutants defective for cell wall turnover/remodeling
Dr. Musa Mhlanga and Dr. Stoyan Stoychev	Council for Scientific and Industrial Research	Ongoing collaboration to develop methods for super-resolution microscopy in mycobacteria and to establish and optimize the technology for cell wall analysis in various mycobacterial strains.
Dr. Chris Edlin and Dr. Garreth Morgans	iThemba Pharmaceuticals	Ongoing collaboration on SATRII initiative for TB drug discovery
Dr. William Mac Kenzie	Centers for Disease Control and Prevention, USA	Collaboration on the detection and characterization of Rpf-dependent bacterial populations in sputum. Project funded by the NIH.
Prof. John D. McKinney	École Polytechnique Fédérale de Lausanne (EPFL), Switzerland	Collaboration on the mechanisms of propionate catabolism, funded by a grant from Swiss/ SA Joint Research Programme.
Dr. Clifton E. Barry III and Dr. Helena Boshoff	Tuberculosis Research Section, Laboratory of Host Defenses, National Institute of Allergy & Infectious Diseases, NIH, MD	Ongoing collaboration on the IMTB project, and new collaboration on the HIT-TB and SATRII projects
Prof. Česlovas Venclovas	Institute of Biotechnology, Vilnius, Lithuania	Ongoing collaboration on the structure and function of a novel mutagenic complex in mycobacteria.

Prof. Eric Rubin	Microbiology and Immunology, Harvard Medical School, USA	Collaborating member of IMTB Consortium
Prof. David Sherman	Seattle Biomed, USA	Ongoing collaboration on TB drug discovery under the auspices of the “IM TB” Consortium funded by the Bill & Melinda Gates Foundation
Prof. James Sacchettini & Dr. Tom Ioerger	Biochemistry & Biophysics, Texas A&M University, College Station, TX	Collaborating members of the “IM TB” Consortium. Also collaborating on whole-genome sequence analysis of strains of M. tuberculosis.
Prof. Sir Tom Blundell and Prof. Chris Abell	Cambridge University, UK	Collaborating members of the IMTB, HIT-TB and MM4TB Consortia
Prof. Chris Sassetti	University of Massachusetts, USA	Collaboration on carbon metabolism in M. tuberculosis. Co-authored one paper (in press). Also collaborating partner in IMTB consortium
Prof. Tanya Parish	Barts and the London, UK & Infectious Diseases Research Institute (IDRI), Seattle, USA	Collaborating member of IMTB COnsortium
Prof. Stewart Cole	EPFL, Lausanne, Switzerland	PI of the MM4TB Consortium
Prof. Vickery Arcus	AgResearch, University of Waikato, New Zealand	Collaboration on the role of VapBC toxin-antitoxin modules in the physiology of M. tuberculosis. Co-authored paper
Prof. Jonathan Blackburn	IIDMM, UCT	New collaboration on lipidomic analysis of M. tuberculosis strains
Prof. Susan Harrison	Chemical Engineering, UCT	New collaboration on TB drug discovery
Prof. Kelly Chibale	H3-D Drug Discovery Centre, UCT	Nre collaboration on SATRII and other TB drug discovery projects
A/Prof. Nicola Mulder	CBIO, IIDMM, UCT	New collaboration on bioinformatic analysis of mycobacterial genomes
Prof. Robert Wilkinson	CIDRI, IIDMM	Co-applicant on several new grant applications
Dr. S. Sampson	Imperial College, UK	The evolution and function of the PE and PPE gene families (2001-present) & the ESAT-6 secretion system interactome (2007- present).
Dr. H. Mardassi, Mr. A. Karboul and Mr. A. Namouchi	Institut Pasteur, Tunisia	Characterization of M. tuberculosis lineages through the PE/PPE gene family (2002 - present)
Dr. W. Bitter and Mr A. Abdallah	Vrije Universiteit, Amsterdam, Netherlands	The trafficking of the M. tuberculosis PE and PPE proteins (2006 – present).
Dr. John Ho	Cornell University, New York, USA	Characterization of M. tuberculosis lineages through the PE/PPE gene family (2007 –2009).

Prof. J. Ho, Dr. A. Gibson and Prof. R. Huard	Cornell University, New York, USA	The dissemination of the major RDRio sub-lineage of the LAM M. tuberculosis spoligotype family in Luso-American countries, Portugal and Africa
Dr. H. Mardassi	Institut Pasteur de Tunis, Tunisia	Characterisation of LAM evolutionary history (2007-present).
Prof. A. Steyn	K-RITH and University of Alabama, Birmingham	The ESAT-6 secretion system interactome (2007- present).
Prof. VPMG Rutten, Dr. I. van Rhijn, Dr. A.P. Koets	Utrecht University	Non-tuberculous mycobacteria in wildlife (WOTRO Integrated program proposal) (2007 - present).
Dr R. Anthony	KIT The Netherlands	MLPA assay for the detection of ofloxacin resistance and Identification of ofloxacin and amikacin heteroresistance.
Prof D. van Soolingen	RIVM The Netherlands	Evolution of the Beijing genotype Lineage
Prof D. van Soolingen	RIVM The Netherlands	Evaluation of the MIRU-VNTR typing method
Dr K Kremer	RIVM The Netherlands	Whole genome sequencing of Beijing genotype strains
Dr V Dartois	Novatis Singapore	MassArray detection of mutations conferring drug resistance
Prof E Bottger	University of Zurich	Development and evaluation of novel genetic based diagnostics for drug resistance; Evolution of ofloxacin resistance
Prof E Nardell	AIR facility, Witbank	Transmissibility of drug resistant TB
Prof. Erwin Schurr	McGill University, Montreal, Canada	Genetic epidemiology. Poster outputs; 4 papers published 2009-2010.
Prof. Laurent Abel & Alexandre Alcais	INSERM / Université Paris 5, France	Analysis of genetic epidemiology. Poster outputs; 4 papers published 2009-2010.
Dr Alkes Price	Harvard School of Public Health, Boston, USA	New collaboration. Analysis of admixture mapping.
Dr Brenna Henn	Stanford University, San Francisco, USA	Population Ancestry genetic determinations
Dr. Ingileif Jonsdottir	deCODE, Iceland	Genetic susceptibility to TB.
Dr. Lluis Quintana-Murci	Institut Pasteur, Paris, France	Genetic susceptibility to TB and population structure. Paper expected 2010.
Prof. Stefan Schreiber and Dr. Almut Nebel	Christian Albrechts University, Kiel, Germany	Investigation of candidate genes in TB. Resulted in 2 co-authored publications in 2007, and 2 co-authored publications in 2009
Prof .Megan Murray	Harvard / Broad institute	Various project including the evolution of XDR-TB strains; other mechanisms of drug resistance (in addition to genomic mutations); mechanisms of resistance to 2nd line drugs; strain fitness; certain strain families may have both increased fitness and increased potential for acquiring drug resistance. All of these projects involve whole-genome sequencing, proteomics, microarray. Prof. Murray is directly involved in project planning, paper writing, funding proposals (NIH and Wellcome trust).
Dr K Jacobson	Harvard University	GIS of drug resistant TB in the Western Cape MDR treatment outcome in Brewelskloof Hospital Treatment outcome of M(X)DR-TB in Khayelitsha

Dr. Judit Nagy	Imperial College London	Proteomics of large clusters (more transmitted) vs. small clusters (less transmitted) in the same strain family after other criteria to select isolates have been taken into consideration. The aim is to identify proteins that are differentially expressed in the same strain family which may give them an advantage to transmit better than others.
Prof. Harald Wiker and Dr G de Souza	Bergen University and Oslo University, Norway	Ongoing collaboration on the M. tuberculosis phosphorylome New collaboration on the detection of drug resistance by single run multi-locus sequencing. New collaboration on the M. tuberculosis secretome.
Dr Anita Schurch	RIVM, The Netherlands	Ongoing collaboration on M. tuberculosis genome evolution.
Dr. Hernandez Pando Rogelio	National University of Mexico	Test different drug resistant strains (MDR / XDR) in a mouse model for strain fitness/virulence. The isolates are the same as described above and will compliment the data obtained by molecular investigations. To determine whether reinfection induces reactivation.
Dr. Helen Cox	MSF	Collaboration on drug resistance in Khayelitsha, Western Cape. Impact of mixed infection on treatment outcome.
Prof. Tom Alber	Berkeley	Collaboration on the M. tuberculosis lipidome
Prof. Brigitte Gicquel	Pasteur Institute	Collaboration on mutation in M. tuberculosis DNA repair genes
Prof K Dheda	UCT	Molecular epidemiology of XDR-TB; Collaboration in diagnostic/biomarker project.
Prof R McNerney	LSTHM	Whole genome sequencing of drug resistant M. tuberculosis strains
Dr. Kim Mallard	LSTHM	Whole genome sequencing of M. tuberculosis strains
Prof Anab Pain	KAUST	Whole Genome Sequencing of Mycobacterial Species
Prof. Kathy Eisenach	Arkansas, USA	Mechanisms of strain fitness in an in vitro THP-1 cell line model. Project is in planning phase.
Prof. Stefan Kaufmann	Max Planck Institute for Infection Biology, Berlin, Germany	Collaborators on BMGF-funded project
Prof. Henry Boom	Cleveland, Ohio, US	Collaborators on BMGF-funded project
Prof. Hazel Dockrell	LondonSchool for Hygiene and Tropical Medicine, London, UK	Collaborators on BMGF-funded project, Co-applicants on grant application to BMGF
Dr. Mark Doherty	Statens Serum Institute, Kopenhagen, Denmark	Collaborator on BMGF-funded project, collaborators on NIH-sponsored study
Dr. Martin Ota	MRC, The Gambia	Collaborators on BMGF-funded project

Prof. Harriet Mayanja	Makarere University, Uganda	Collaborators on BMGF-funded project
Prof. Willem Hanekom and Dr. Hassan Mahomed	SATVI, UCT	Collaboration on TB vaccine studies and haring of technology (multicolour FACS, Luminex machine), sharing of samples (manuscript accepted for publication.
Dr. Carol Holm-Hansen	Norwegian Institute for Public Health	Collaboration on BMGF Grand Challenge Exploration grant, 2010-2011
Dr. Christoph Lange and Dr. Barbara Kalsdorf	Clinical Infectious Diseases, Center for Clinical Studies, Medical Clinic, Research Center Borstel, Germany	Collaboration on TB diagnostic study 2011
Dr. Jeff Boyle	R&D, Cellestis, Australia	Collaboration on diagnostic TB study 2010-2011
Dr. Volkmar Schoellhorn	Auto-Immune Diagnostics (AID)	Collaboration on TB diagnostic study 2010-2011
Prof N. Beyers, Dr A. Hesseling, Dr S. Tonkin, Prof B. Marais	DTTC, SU	Non-tuberculous Mycobacteria (NTM) - Prevalence and Clinical relevance in HIV-infected and HIV-uninfected children (2006 - present).
Prof. N. Beyers	DTTC, SU	Ongoing collaboration of the molecular epidemiology of M. tuberculosis in the W. Cape.
Dr. A. Michel, J. Godfroid, K. Coetzer and N. Kriek	Onderstepoort Veterinary Institute	Non-tuberculous mycobacteria in wildlife (WOTRO Integrated program proposal) (2007 - present).
Dr Mary Jackson	Colorado State University	Screen anti-TB compounds against RIF-resistant M. tuberculosis strains.
Dr Dorian Bevec	MondoBiotech, Switzerland	Screen peptides for anti-TB activity.
Dr Corli Witthuhn	Food Science, SU	Fermentation Processes to kill M. Tuberculosis
Dr Thavi Govender	Dept. Chemistry, UKZN	Test antituberculosis activity of existing antituberculosis drug derivatives. K. Onajole 2009
Prof Green	Dept Chemistry, UWC	Screen new compounds and derivatives for antituberculosis activity
Dr. S. Todorov	Univ. Sao Paulo, Brazil	Antituberculosis activity of Bacteriocins Todorov, 2008
Dr C. Kenyon	CSIR, Pretoria	Dormancy regulators of M.tb in human macrophages.
Dr. Haynes	Hong Kong University of Technology	Testing new compounds for antituberculosis activity
Prof Peter Folb	Pharmacology, UCT	Testing derivatives of Diphenyl Oxazole for antituberculosis activity
Ms. Marlein Bosman	NHLS , Green point	Collaborator on all our projects – provides routine samples.
Lily Telisinghe, Dr Salome Charalambous	Arum Health	TB in the correctional services
Dr Gerrit Coetzee	NHLS	Drug resistant TB in South Africa
Dr. Sias May	TB Control program in Suidkaap/ Lawwaaikamp	TB Control strategy.

Dr. Danie Theron	Eben donges hosp, Worcester	New project on DOTS program on farms.
Dr Else Marais	Wits/NHLS	Ongoing collaboration on the molecular epidemiology of drug resistant TB in Gauteng.
Prof C. Reinecke and Dr du Toit Loots	North West University	M.tuberculosis metabolome.
Prof C Wright	NHLS Tygerberg	The diagnostic utility of FNAB
Dr. Alistair Calver	Gold Mine in Northern province	Ongoing, outbreak of drug resistance in a setting with a good control program.
Prof. Frank Brombacher	IIDMM, UCT	Sharing of expertise (murine helminth models).
Dr A. Hesseling	SU	New collaboration to investigate genotype-immunological phenotype correlations in children.
Mrs. Lungi Kwitshana	MRC, Durban	Collaboration in project on worm-HIV co-infection.
Dr. Anna Mandalakas	Case Western Reserve University, USA	Collaboration of diagnostic studies in paediatric TB.
Dr Jurgen Seier & Ms Charon de Villiers	MRC animal unit & MRC Delft Animal Facility	The implementation of TB testing of vervet monkeys, rhesus macaques and baboons. Dr Parsons also advise the MRC on the management of TB cases and outbreaks in these units.
Dr Lize van der Merwe	Biostatistics Unit, Medical Research Council, Cape Town	Statistical analysis of genetic data and studies such as gene-gene interaction.
Mrs. Lungi Kwitshana	MRC, Durban	Collaboration in project on worm-HIV co-infection.

Networking

Enquiries: See contact us

Health Knowledge Network
for southern Africa developed by MRC