Research Interests

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 complex microbial ecosystems (i.e. microbiomes) 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.
• Antibiotic resistance in complex microbiomes. The Van Schaik lab is using both culture-based and culture-independent methods, including metagenomic shotgun sequencing, functional 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.

Scientific Inspiration

I am fascinated by the enormous diversity of microbial life and the adaptability of the multi-drug resistant pathogens that cause increasing numbers of infections among hospitalised patients. While it is difficult to identify a single researcher as a scientific inspiration, I am particularly inspired by researchers who perform incredibly well-designed experiments to understand the evolution and costs of antibiotic resistance (e.g. Craig Maclean, Dan Andersson) and those that implement modern genomics approaches to explore the diversity of microbial ecosystems (e.g. Jill Banfield).