Medical Microbiology Bio-IT - Group Schürch
Medical Microbiology Bio-IT - Group Schürch

Medical Microbiology - BioIT


Dissemination of physiologically important traits encoded on plasmids, integrons, transposons, and bacteriophages are highly dynamic because these mobile genetic elements (MGE) transmit with ease. The most prominent example is the spread of antimicrobial resistance genes through different hosts and environments. We develop novel computational methods to reconstruct plasmids and other MGEs and to map their dissemination.

Research program

Infection and Immunity


Anita Schürch


Related websites

Research interests

  • Population and comparative genomics of antibiotic resistance pathogens with the aim to elucidate and characterize clades and lineage in bacterial populations that are enriched in strains expressing antibiotic resistance and virulence.
  • Genome-based epidemiology of multidrug-resistant pathogens, with a special focus on reconstructing and tracking the spread of plasmids based on genome sequence data.
  • Reconstruct dissemination networks of mobile genes (including antimicrobial resistance genes) from metagenomic data to dissect dissemination of physiologically important traits between different hosts and environments. These mobile genes that flow between ecologies can create new phenotypes, shape microbial composition and strongly contribute to health and disease in humans and animals.

Group members


Malbert Rogers

PhD students

Sergio Arredondo Alonso
Jesse Kerkvliet

Key Publications

  1. S. Arredondo-Alonso, M. R. C. Rogers, J. C. Braat, T. D. Verschuuren, J. Top, J. Corander,R. J. L. Willems, and A. C. Schurch. mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species. Microbial Genomics, 4(11), 2018. View
  2. A. C. Schurch, S. Arredondo-Alonso, R. J. L. Willems, and R. V. Goering. Whole genome sequencing options for bacterial strain typing and epidemiological analysis based on single nucleotide polymorphism vs gene-by-gene-based approaches. Clinical Microbiology and Infection, 2018. View
  3. S. Arredondo-Alonso, R. J. Willems, W. van Schaik, and A. C. Schurch. On the (im) possibility of reconstructing plasmids from whole-genome short-read sequencing data. Microbial Genomics,3(10), 2017. View
  4. A. C. Schurch and W. van Schaik. Challenges and opportunities for whole-genome sequencing–based surveillance of antibiotic resistance.Annals of the New York Academy of Sciences,1388(1):108–120, 2017. View



2019 - Netherlands Center for One Health - NCOH PhD programme ‘Complex Systems’

Gene flow networks in animals, the food chain and the environment.