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
  1. GIS of drug resistant TB in the Western Cape
  2. 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

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