Resume of Elies Bik

Last updated: October 1, 2005

Personalia

Current work affiliation:

Current working address:

Education and Awards

• 1978-1984 High school: Gymnasium B, Christian Lyceum, Gouda, The Netherlands
• 1984-1990 University of Utrecht, M.S. degree in Chemical Biology
• 1991-1996 University of Utrecht, PhD study, conducted at the National Institute of Health and the Environment, Bilthoven, The Netherlands. Title of PhD thesis: Cholera, vaccine development and evolution of epidemic strains.
  This PhD study was awarded with the two-yearly Yamanouchi Award in May, 1996, by the Dutch Society of Medical Microbiology.

Working Experience

• 1990-1991 National Institute of Health and the Environment, Bilthoven, The Netherlands, Department of Molecular Microbiology. Research project: Cloning in Mycobacterium bovis BCG
  
  • Translocation of shuttle vectors from Escherichia coli to M. bovis and M. smegmatis
  • Development of DNA gene banks of M. tuberculosis and M. leprae using the lambda-ZAP system
  • Analysis of IS6110 hot-spot DNA region in M. tuberculosis and M. bovis BCG
  • Discovery of 36-bp direct repeat region in Mycobacteria, the start of the "spoligotyping" technique, which is now used internationally to type M. tuberculosis strains
• 1991-1996 PhD study, University of Utrecht, conducted at the National Institute of Health and the Environment, Bilthoven, The Netherlands, Department of Molecular Microbiology. Supervised by Dr. F.R. Mooi and Prof. Dr. W. Hoekstra.
  • Development of attenuated cholera vaccine strains
  • Analysis of the newly emerged epidemic Vibrio cholerae serotype O139 strain
  • Study of horizontal gene transfer of polysaccharide genes in Vibio cholerae
• 1996-1997 Post-doc position "Molecular evolution of epidemic Vibrio cholerae strains: the role of horizontal transfer of cell wall polysaccharide genes." Conducted at the National Institute of Health and the Environment, Bilthoven, The Netherlands, Laboratory of Infectious Diseases. Supervised by Dr. F.R. Mooi.
  • Investigation of role of horizontal gene transfer in development of new Vibrio cholerae serotypes
  • Development of PCR for detection of epidemic V. cholerae strains
• 1997-2001 St. Antonius Hospital in Nieuwegein, the Netherlands, Department of Medical Microbiology and Immunology.
  • Introduction of molecular techniques in the department, and setting up of a new molecular microbiology unit
  • Teaching and supervizing technicians on molecular detection and epidemiology
  • Detection of Chlamydia trachomatis, Neisseria gonorrhoeae in clinical material
  • Detection of Mycobacterium tuberculosis in clinical material
  • Detection of mecA gene for MRSA identification
  • Development of PCRs for the detection of Helicobacter pylori and enteric pathogens
  • Typing of nosocomial bacteria (e.g. Staphylococccus aureus, Stenotrophomonas)
  • HLA-B27 gene identification using a commercial PCR
  • DNA polymorphisms in interferon-gamma receptor genes of sarcoidosis patients
• 2002-2004 Post-doc position, Stanford University School of Medicine, California, USA, Department of Microbiology and Immunology.
  
  • Broad-range bacterial, archaeal, and fungal amplification of extracted DNA from clinical materials
  • Phylogenetic analysis of bacterial sequences derived from human gastric and colonic biopsies and stool samples
  • Development of DNA microarrays for detection of microbial sequences
• 2004-current Research associate, Stanford University School of Medicine, California, USA, Department of Microbiology and Immunology.
  Current research interests:
  • Study the composition of the human-associated microflora, with a focus on the gastrointestinal tract using a ribosomal clone library approach
  • Comparison of the intestinal microbial flora of healthy subjects vs. Crohns disease patients
  • Development of ribosomal rDNA microarrays
  • Isolation of microbial DNA from clinical materials

Knowledge and skills

General knowledge

• Broad knowledge of general and medical microbiology
• Experience in setting up and maintenance of a molecular microbiology unit in a peripheral hospital
• Insight into nosocomial infection problems, and infections of ICU patients
• Experience in working in a clinical setting (accuracy with clinical materials, confidentiality regarding patient data, deadlines)
• Using ribosomal rRNA genes for phylogenetic analysis
• Writing of scientific publications for international journals
• Instruction of students, technicians, and residents in molecular techniques, both in theory as in practice
• Setting up of molecular biology classes for technicians
• Development of standard operation procedures (SOPs) of molecular, microbiological and genetical engineering work, under CI level
• Managing experience

Experimental skills

• DNA isolation techniques, from clinical materials and bacteria
• DNA restriction and ligation, cloning, integrational mutagenesis, complementation
• Gel electrophoresis (agarose, acrylamide), Southern blotting, dotblots, lineblots, hybridizations (32P, ECL, Dig-dUTP)
• PCR, EIA-PCR, typing PCR (RAPD), primer development, sequencing
• Roche COBAS Amplicor (detection of Chlamydia trachomatis, Neisseria gonorrhoeae, and Mycobacterium tuberculosis)
• DNA microarray hybridizations

Computer skills

• Microsoft Office (Word, Access, Excel, PowerPoint)
• CorelDraw, MS Photo Editor, Adobe Illustrator, Adobe Photoshop
• DNA software (ARB, EstimateS, S-LIBSHUFF, GelCompar, Oligo, MegAlign, Clone)
• Internet searches (PubMed, GenBank, BLAST, ChimeraCheck)
• HTML programming

Professional Societies

• Member, American Society for Microbiology
• Member, Dutch Working Group Epidemiological Typing
• Member, Dutch Working Group Molecular Diagnostics
• Member, Dutch Society of Medical Microbiology (NVMM)
• Member, Dutch Society of Microbiology (NVvM)
• Member, European Society of Clinical Microbiology and Infectious Diseases (ESCMID)

Publications

• Hermans, P.W.M., A.R.J. Schuitema, D. van Soolingen, C.P.H.J. Verstijnen, E.M. Bik, J.E.R. Thole, A.H.J. Kolk, and J.D.A. van Embden. 1990. Specific detection of Mycobacterium tuberculosis complex strains by polymerase chain reaction. J. Clin. Microbiol. 28:1204-1213.
• Hermans, P.W.M., D. van Soolingen, E.M. Bik, P.E.W. de Haas, J.W. Dale, and J.D.A. van Embden. 1991. Insertion element IS987 from Mycobacterium bovis BCG is located in a hot-spot integration region for insertion elements in Mycobacterium tuberculosis complex strains. Infect. Immun. 59:2695-2705.
• Rijpkema, S.G.T., E.M. Bik, W.H. Jansen, H. Gielen, L.F. Versluis, A.H. Stouthamer, P.A.M. Guinée, and F.R. Mooi. 1992. Construction and analysis of a Vibrio cholerae d-aminolevulinic acid auxotroph which confers protective immunity in a rabbit model. Infect. Immun. 60:2188-2193.
• Bik, E.M., A.E. Bunschoten, R.D. Gouw, and F.R. Mooi. 1995. Genesis of the novel epidemic Vibrio cholerae O139 strain: evidence for horizontal transfer of genes involved in polysaccharide synthesis. The EMBO Journal 14:209-216.
• Mooi, F.R., A.E. Bunschoten, and E.M. Bik. 1995. The emergence of a new cholera epidemic in Asia explained at the molecular level. RIVM, Annual Scientific Report 1994, 180-181.
• Mooi, F.R. and E.M. Bik. 1995. The emergence of a novel epidemic Vibrio cholerae strain. Ned. Tijdschr. Med. Microbiol. 4:75-77.
• Bik, E.M., R.D. Gouw, and F.R. Mooi. 1996. DNA fingerprinting of Vibrio cholerae strains with a novel insertion sequence element: a tool to identify epidemic strains. J. Clin. Microbiol. 34:1453-1461.
• Bik, E.M., A.E. Bunschoten, R.J.L. Willems, A.C.Y. Chang, and F.R. Mooi. 1996. Genetic organization and functional analysis of the otn DNA essential for cell-wall polysaccharide synthesis in Vibrio cholerae O139. Mol. Microbiol. 20:799-811.
• Mooi, F.R. and E.M. Bik. 1996. Cholera vertoont zich in schaapskleren (Cholera showing in sheep's clothing). NWO Onderz. Ber. 4:6.
• Bik, E.M. and F.R. Mooi. 1996. Cholera in schaapskleren (Cholera in sheep's clothing). BIOnieuws 12:7.
• Bik, E.M. and F.R. Mooi. 1996. Het ontstaan van een cholera-epidemie verklaard op moleculair niveau (The emergence of a cholera epidemic explained at the molecular level). Infectiez. Bull. 7:139-142.
• Mooi, F.R. and E.M. Bik. 1997. The evolution of epidemic Vibrio cholerae strains. Trends in Microbiology 5:161-165.
• Visser I.J.R., P. Vellema, A.M. Weitenberg and E.M. Bik. 1997. Ernstige waterige diarree door Vibrio cholerae bij lammeren (Severe watery diarrheae in lambs, caused by Vibrio cholerae). Tijdschrift voor Diergeneeskunde 122:600-603.
• Bik, E.M. 1998. Cholera in de negentiende eeuw (Cholera in the nineteenth century). Amsterdamse Boekengids.
• Bik, E.M. 1999. De nieuwe kleren van de cholera (The cholera's new clothes). Ned. Tijdschrift voor Medische Microbiologie 7:36-37.
• v Dijk Y, Bik EM, Hochstenbach-Vernooij S, v d Vlist GJ, Savelkoul PH, Kaan JA, Diepersloot RJ. 2002. Management of an outbreak of Enterobacter cloacae in a neonatal unit using simple preventive measures. J Hosp Infect. 51:21-6.
• van Leeuwen WB, Snoeijers S, van der Werken-Libregts C, Tuip A, van der Zee A, Egberink D, de Proost M, Bik E, Lunter B, Kluytmans J, Gits E, van Duyn I, Heck M, van der Zwaluw K, Wannet W, Noordhoek GT, Mulder S, Renders N, Boers M, Zaat S, van der Riet D, Kooistra M, Talens A, Dijkshoorn L, van der Reyden T, Veenendaal D, Bakker N, Cookson B, Lynch A, Witte W, Cuny C, Blanc D, Vernez I, Hryniewicz W, Fiett J, Struelens M, Deplano A, Landegent J, Verbrugh HA, van Belkum A. Intercenter reproducibility of binary typing for Staphylococcus aureus. J Microbiol Methods 51:19-28.
• Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA. 2005. Diversity of the human intestinal microbial flora. Science 308:1635-8. Epub 2005 Apr 14.

Conferences and courses

• Workshop "Molecular pathogenesis of bacteria, basic and applied aspects". April 1992, Schierke, Germany.
• FEMS 71st Workshop "Advanced molecular biology and recombinant DNA technology in the study of bacterial pathogenesis". May 1993, Veterinary Faculty, University of Utrecht, The Netherlands.
• IRIS Symposium "Molecular mechanisms of microbial pathogenesis". October 1994, Siena, Italy
• PhD Program "Infection and Immunity". 1994-1995. Wilhelmina Children's Hospital, Utrecht, The Netherlands.
• EMBO Course "Advanced Eubacterial Genetics". May-June 1997, Umea, Sweden.
• BioMerieux Symposium "Molecular Biology and Tuberculosis", September 1998, Grimbergen, Belgium.
• Roche Symposium "Lightcycler Technology", October 1998, Utrecht, The Netherlands.
• Eijkman Centennial Conference on Infections in the 21th century. December 1998, The Hague, The Netherlands.
• Imphos Meeting "The Art of Helicobacter pylori Serology", March 1999, Baarn, The Netherlands.
• Roche COBAS Amplicor Systeem Training, October 1999, Nieuwegein, The Netherlands.
• European Meeting on Molecular Diagnostics, October 1999, Scheveningen, The Netherlands.
• International Meeting on Bacterial Epidemiological Markers (IMBEM), September 2000, Noordwijkerhout, The Netherlands.
• European Congres of Clinical Microbiology and Infectious Diseases (ECCMID), April 2001, Istanbul, Turkey.
• All Spring and Fall Meetings of the Dutch Society of Medical Microbiology (NVMM), from 1996-2001
• ASM/TIGR meeting on Microbial Genetics. January/February 2003, New Orleans, USA
• ASM Conference on Polymicrobial Diseases, October 2003, Lake Tahoe (NV), USA
• ASM General Meeting. May 2004, New Orleans, USA
• ASM Conference on Beneficial Microbes. April 2005, Lake Tahoe (NV), USA

Oral Presentations

• "Repetitive DNA elements in Mycobacteria". Fall Meeting Dutch Society of Scientific Research (NWO), Division of Microbial Pathogenesis. November 1990, Veterinary Faculty, University of Utrecht, The Netherlands.
• "Construction of a live Vibrio cholerae vaccine strain". Fall Meeting NWO, Division of Vaccines. December 1992, Central Veterinary Institute, Lelystad, The Netherlands.
• "Development of an oral live Vibrio cholerae vaccine. Fall Meeting NWO, Division of Microbial Pathogenesis. November 1993, Academic Hospital Utrecht, The Netherlands.
• "Genesis of the novel epidemic V. cholerae O139 strain: evidence for horizontal transfer of genes involved in polysaccharide synthesis". Fall Meeting NWO Division of Microbial Pathogenesis. November 1994, Veterinary Faculty, University of Utrecht, The Netherlands.
• "Characterization of an epidemic V. cholerae strain with a new serotype; implications for vaccine development". Fall Meeting NWO, Division of Vaccines. December 1994, Academic Hospital Groningen, The Netherlands.
• "Genesis of the novel epidemic V. cholerae O139 strain: evidence for horizontal transfer of genes involved in polysaccharide synthesis". Spring Meeting NWO, Division of Molecular Genetics. June 1995, TNO, Rijswijk, The Netherlands.
• "Horizontal gene transfer of LPS and capsule synthesis genes in epidemic Vibrio cholerae strains". UIFII seminar, Eijkman-Winkler Institute for Microbiology, Infectious Diseases and Inflammation. March 1997, Academic Hospital Utrecht, The Netherlands.
• "Horizontal transfer of LPS and capsule synthesis genes in epidemic Vibrio cholerae strains". Spring Meeting NWO, Division of Microbial Pathogenesis. April 1997, Lunteren, The Netherlands.
• "Transmission of Stenotrophomonas maltophilia in an intensive care unit". Fall Meeting Dutch Society of Medical Microbiology. October 1998, Bilthoven, The Netherlands.
• "Microbial typing using PCR methods". Symposium of the Dutch Working Group on Epidemiological Typing. November 2000, Bilthoven, The Netherlands.
• "The WET on the Web". Spring Meeting Dutch Society of Medical Microbiology. April 2000, Veldhoven, The Netherlands.
• "Molecular epidemiology of nosocomial Stenotrophomonas maltophilia strains in an intensive care unit". Spring Meeting Dutch Society of Medical Microbiology. March 2001, Arnhem, The Netherlands.

Abstracts and Poster Presentations

• Bik E.M., Rijpkema, S.G.T., W.H. Jansen, H. Gielen, L.F. Versluis, A.H. Stouthamer, P.A.M. Guinée, and F.R. Mooi. 1992. Construction and analysis of a Vibrio cholerae (-aminolevulinic acid auxotroph which confers protective immunity in a rabbit model. Workshop "Molecular pathogenesis of bacteria - basic and applied aspects", Schierke, Germany
• Bik E.M., Rijpkema, S.G.T., W.H. Jansen, H. Gielen, L.F. Versluis, A.H. Stouthamer, P.A.M. Guinée, and F.R. Mooi. 1992. Construction and analysis of a Vibrio cholerae (-aminolevulinic acid auxotroph which confers protective immunity in a rabbit model. FEMS 71st Workshop "Advanced molecular biology and recombinant DNA technology in the study of bacterial pathogenesis", Veterinary Faculty, University of Utrecht.
• Bik, E.M., A.E. Bunschoten, R.D. Gouw, and F.R. Mooi. 1994. Genesis of the novel epidemic V. cholerae strain: evidence for horizontal transfer of genes involved in O-antigen synthesis. IRIS Symposium "Molecular mechanisms of microbial pathogenesis", Siena, Italy.
• Bik, E.M., A.E. Bunschoten, and F.R. Mooi. 1997. Horizontal transfer of LPS and capsule synthesis genes in epidemic Vibrio cholerae strains. EMBO Course "Advanced Eubacterial Genetics", Umea, Sweden.
• Bik, E.M., M.J. Manders, Y. Kluck, M. Tersmette, B.M. de Jongh and G.P. Voorn. 1998. Transmission of Stenotrophomonas maltophilia in an intensive care unit. Eijkman Centennial Conference on Infections in the 21th century, The Hague, The Netherlands.
• Bik, E.M.,Y. Muyderman, R. Timmer and B.M. de Jongh. 1999. Detection of Helicobacter pylori in gastric samples by ureA and cagA PCR. European Meeting on Molecular Diagnostics, Scheveningen, The Netherlands.
• Bik, E.M., S. Hochstenbach, Y. van Dijk, G. van der Vlist, J. Stoof, P.H.M. Savelkoul, R.J.A. Diepersloot, and J.A. Kaan. 2000. Nosocomial transmission of Enterobacter cloacae in a neonatal unit. International Meeting on Bacterial Epidemiological Markers (IMBEM), Noordwijkerhout, The Netherlands.
• Bik, E.M., A. van Belkum, A.T. Bernards, T. Boekhout, B. Duim, P.W.M. Hermans, L.M. Schouls, W. Wannet, and L. Dijkshoorn. 2000. The WET on the Internet. International Meeting on Bacterial Epidemiological Markers (IMBEM), Noordwijkerhout, The Netherlands.
• Bik, E.M., M. Brok, P. Foppen, S. van Hamersveld, M. Tersmette, and B.M. de Jongh. 2001. Comparison of molecular and conventional detection of Campylobacter, Salmonella, Shigella, EHEC, and Clostridium difficile in feces. European Congres of Clinical Microbiology and Infectious Diseases (ECCMID), Istanbul, Turkey.
• Bik, E.M., P.B. Eckburg, S. Gill, K. Nelson, F. Francois, G. Perez-Perez, M. Blaser, and D.A. Relman. Molecular analysis of the human gastric microflora. ASM/TIGR Meeting on Microbial Genetics, January/February 2003, New Orleans, USA
• Bik, E.M., P.B. Eckburg, S. Gill, K. Nelson, F. Francois, G. Perez-Perez, M. Blaser, and D.A. Relman. Molecular analysis of the human gastric microflora. ASM General Meeting, May 2004. New Orleans, USA
• Bik, E.M., P.B. Eckburg, S. Gill, K. Nelson, E. Purdom, F. Francois, G. Perez-Perez, M. Blaser, and D.A. Relman. Molecular analysis of the human gastric microflora. ASM Meeting on Beneficial Microbes, April 2005. Lake Tahoe, USA

References