Professor Willem van Schaik

Professor Willem van Schaik

Institute of Microbiology and Infection
Professor in Microbiology and Infection

Contact details

Address
College of Medical and Dental Sciences
University of Birmingham
Edgbaston
Birmingham
B15 2TT
UK

Willem van Schaik is professor of Microbiology and Infection in the Institute of Microbiology and Infection.


Willem has published more than 60 papers in the field of molecular microbiology, the human microbiome and antibiotic resistance. He has received major grants from The Netherlands Organisation for Scientific Research, the Seventh Framework Programme of the European Commission , the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) and The Royal Society. His main research interests are the characterization of the mechanisms by which commensal bacteria evolve to become multi-drug resistant opportunistic pathogens and the metagenomic analysis of the reservoir of antibiotic resistance genes (‘the resistome’) in complex microbiomes.

Qualifications

  • PhD Microbiology (with honour); Wageningen University, the Netherlands 2005
  • MSc Food Science (with honour); Wageningen University, the Netherlands 1998 

Biography

Professor Willem van Schaik began his academic studies with a Master’s degree in Food Science at Wageningen University in the Netherlands. He then worked for two years as a junior biotechnologist in the R&D labs of the Dutch multinational food production company Numico. He then returned to Wageningen University to study for a PhD in microbiology under the supervision of Proffessor Tjakko Abee, Professor Willem de Vos and Professor Marcel Zwietering on the regulation of the stress response by the alternative sigma factor σB in Bacillus cereus.

He then did post-doctoral studies on an EMBO Long-Term Fellowship at the Pasteur Institute (Paris, France) on the regulation of virulence gene expression of Bacillus anthracis in the laboratory of Dr Agnès Fouet. He then moved to the University Medical Center Utrecht in the Netherlands, where he worked on the comparative and functional genomics of several multi-drug resistant opportunistic pathogens, including Enterococcus faecium and Klebsiella pneumoniae. His group also worked on the gut microbiome of critically ill patients that receive intensive antibiotic treatment.

In Summer 2012, he was a visiting scientist at the Broad Institute (Cambridge, USA) and Harvard Medical School (Boston, USA), where he worked with Dr. Ashlee Earl and Prof. Michael S. Gilmore. In 2017, he moved to the University of Birmingham, where he was appointed as professor in Microbiology and Infection. In the same year, he was awarded a Royal Society Wolfson Research Merit Award.

Postgraduate supervision

Willem is always interested in hearing from potential PhD students who want to apply genomic and metagenomic approaches to study the emergence of drug-resistance in opportunistic pathogens.

You can contact Willem by email

Research

The research group of Professor van Schaik combines experimental tools in molecular biology and biochemistry with the opportunities offered by the development of novel, high-throughput DNA sequencing technologies and bioinformatics to elucidate the mechanisms by which harmless commensals transition into multi-drug resistant opportunistic pathogens. The reservoir of antibiotic resistance genes (‘the resistome’) in human faeces and hospital waste water is also studied.

Functional and comparative genomics of multi-drug resistant Enterococcus faecium

Enterococcus faecium is a Gram-positive commensal of the intestinal tract of humans and animals. Interestingly, a specific sub-population of E. faecium is responsible for the vast majority of hospital-acquired infections. The Van Schaik lab uses genome sequencing, transcriptome profiling (RNA-seq), high-throughput profiling of transposon mutant libraries (Tn-seq) and novel tools for the genetic manipulation of clinical E. faecium isolates to characterize the mechanisms that contribute to the recent emergence of E. faecium as a nosocomial pathogen, including resistance to antibiotics and disinfectants, colonization of the gut, and survival in the hospital environment.

Colistin resistance in Klebsiella pneumoniae and Escherichia coli

Colistin is one of the antibiotics of last resort for the treatment of infections caused by multi-drug resistant Gram-negative bacteria. The Van Schaik lab studies how resistance to colistin emerges in the opportunistic pathogens K. pneumoniae and E. coli through in vitro evolution experiments and quantifies the trade-offs between the evolution of resistance, fitness and virulence.

Metagenomic analyses of the resistome

The Van Schaik lab has studied culture-independent methods, including metagenomic shotgun sequencing, functional metagenomics and high-throughput nanolitre-scale quantitative PCRs, to study the diversity of antibiotic resistance genes in the gut microbiota of patients and healthy individuals. The abundance and diversity of antibiotic resistance genes in hospital wastewater is another topic of study. In ongoing research, we use a variety of techniques to link resistance genes to their bacterial hosts in complex microbiota and to detect the horizontal transfer of resistance genes in situ

Other activities

  • Consultant, Janssen Research and Development (2017) 
  • Consultant, Vedanta Biosciences (2016-2017)
  • Panel member for NIH/NIAID (2015 – )
  • PhD examiner in the Netherlands, United Kingdom, Portugal, Denmark and Ireland (2013 –  )
  • Editorial Board Member, Current Opinion in Microbiology (2016 – )
  • Academic Editor PLOS One (2012 – 2016)
  • Panel member VENI Fellowship, The Netherlands Organisation for Scientific Research (2014 – 2016)
  • Scientific Advisory Board, the Health Council of the Netherlands, the Netherlands (2014 – 2016)
  • Expert Panel of European Food Safety Authority (2011)
Professor Van Schaik frequently participates in outreach activities to non-specialist audiences. These included visits to secondary schools, in which the essential role of microbes on the planet and their contribution to human health are discussed. Research in the Van Schaik lab has been covered by Dutch and British newspapers and magazines and by international news networks.

Publications

Selected recent publications

Guzmán Prieto AM, Wijngaarden J, Braat JC, Rogers MRC, Majoor E, Brouwer EC, Zhang X, Bayjanov JR, Bonten MJM, Willems RJL, van Schaik W (2017). The two-component system ChtRS contributes to chlorhexidine tolerance in Enterococcus faecium. Antimicrob Agents Chemother 61(5) e02122-16. 

van der Helm E, Imamovic L, Hashim Ellabaan MM, van Schaik W, Koza A, Sommer MOA (2017). Rapid resistome mapping using nanopore sequencing. Nucleic Acids Res 45(8):e61. 

Halaby T, Kucukkose E, Janssen AB, Rogers MR, Doorduijn DJ, van der Zanden AG, Al Naiemi N, Vandenbroucke-Grauls CM, van Schaik W (2016). Genomic characterization of colistin heteroresistance in Klebsiella pneumoniae during a nosocomial outbreak. Antimicrob Agents Chemother 60(11):6837-6843. 

Guzman Prieto AM, van Schaik W, Rogers MR, Coque TM, Baquero F, Corander J, Willems RJ (2016) Global Emergence and Dissemination of Enterococci as Nosocomial Pathogens: Attack of the Clones? Front Microbiol 2016 7:788. 

Guzmán Prieto AM, Urbanus RT, Zhang X, Bierschenk D, Koekman CA, van Luit-Asbroek M, Ouwerkerk JP, Pape M, Paganelli FL, Wobser D, Huebner J, Hendrickx AP, Bonten MJ, Willems RJ, van Schaik W (2015) The N-terminal domain of the thermo-regulated surface protein PrpA of Enterococcus faecium binds to fibrinogen, fibronectin and platelets. Sci Rep 5:18255. 

Niebel M, Quick J, Prieto AM, Hill RL, Pike R, Huber D, David M, Hornsey M, Wareham D, Oppenheim B, Woodford N, van Schaik W, Loman N (2015) Deletions in a ribosomal protein-coding gene are associated with tigecycline resistance in Enterococcus faecium. Int J Antimicrob Agents 46(5):572-5. 

van Schaik W (2015) The human gut resistome. Philos Trans R Soc Lond B Biol Sci 370(1670):20140087. 

de Been M, Lanza VF, de Toro M, Scharringa J, Dohmen W, Du Y, Hu J, Lei Y, Li N, Tooming-Klunderud A, Heederik DJ, Fluit AC, Bonten MJ, Willems RJ, de la Cruz F, van Schaik W (2014) Dissemination of cephalosporin resistance genes between Escherichia coli strains from farm animals and humans by specific plasmid lineages. PLoS Genet 10:e1004776. 

Buelow E, Gonzalez TB, Versluis D, Oostdijk EA, Ogilvie LA, van Mourik MS, Oosterink E, van Passel MW, Smidt H, D'Andrea MM, de Been M, Jones BV, Willems RJ, Bonten MJ, van Schaik W (2014) Effects of selective digestive decontamination (SDD) on the gut resistome. J Antimicrob Chemother 69:2215-23. 

Lebreton F*, van Schaik W*, McGuire AM*, Godfrey P, Griggs A, Mazumdar V, Corander J, Cheng L, Saif S, Young S, Zeng Q, Wortman J, Birren B, Willems RJ, Earl AM, Gilmore MS (2013) Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains. MBio 4:e00534-13. [* indicate equal author contributions] 

Zhang X, Rogers M, Bierschenk D, Bonten MJ, Willems RJ, van Schaik W. A LacI-family regulator activates maltodextrin metabolism of Enterococcus faecium. PLoS One 8(8):e72285. 

de Been M, van Schaik W, Cheng L, Corander J, Willems RJ (2013) Recent recombination events in the core genome are associated with adaptive evolution in Enterococcus faecium. Genome Biol Evol 5:1524-35. 

Zhang X, Top J, de Been M, Bierschenk D, Rogers M, Leendertse M, Bonten MJ, van der Poll T, Willems RJ, van Schaik W (2013) Identification of a genetic determinant in clinical Enterococcus faecium strains that contributes to intestinal colonization during antibiotic treatment. J Infect Dis 207(11):1780-6. 

Gilmore MS, Lebreton F, van Schaik W (2013) Genomic transition of enterococci from gut commensals to leading causes of multidrug-resistant hospital infection in the antibiotic era. Curr Opin Microbiol 16(1):10-6. 

Lebreton F, van Schaik W, Sanguinetti M, Posteraro B, Torelli R, Le Bras F, Verneuil N, Zhang X, Giard JC, Dhalluin A, Willems RJ, Leclercq R, Cattoir V (2012) AsrR is an oxidative stress sensing regulator modulating Enterococcus faecium opportunistic traits, antimicrobial resistance, and pathogenicity. PLoS Pathog 8:e1002834. 

Zhang X, Paganelli FL, Bierschenk D, Kuipers A, Bonten MJ, Willems RJ, van Schaik W (2012) Genome-wide identification of ampicillin resistance determinants in Enterococcus faecium. PLoS Genet 8:e1002804. 

Willems RJ, Top J, van Schaik W, Leavis H, Bonten M, Sirén J, Hanage WP, Corander J (2012) Restricted gene flow among hospital subpopulations of Enterococcus faecium. MBio.3(4):e00151-12. 

Château A, van Schaik W, Six A, Aucher W, Fouet A (2011) CodY regulation is required for full virulence and heme iron acquisition in Bacillus anthracis FASEB J 25(12):4445-56. 

Zhang X, Vrijenhoek JE, Bonten MJ, Willems RJ, van Schaik W (2011) A genetic element present on megaplasmids allows Enterococcus faecium to use raffinose as carbon source. Environ Microbiol. 2011 13(2):518-28 

van Schaik W, Top J, Riley DR, Boekhorst J, Vrijenhoek JE, Schapendonk CM, Hendrickx AP, Nijman IJ, Bonten MJ, Tettelin H, Willems RJ (2010) Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island. BMC Genomics 11:239. 

van Schaik W, Château A, Dillies MA, Coppée JY, Sonenshein AL, Fouet A. The global regulator CodY regulates toxin gene expression in Bacillus anthracis and is required for full virulence. Infect Immun. 2009 77(10):4437-45.