Research

Our research interest is to find patterns in DNA sequencing data and to apply this knowledge to the genomic epidemiology of organisms causing infectious diseases. We are interested in the genomics of plasmids and other mobile genetic elements. Our group provides bioinformatics support for a medical microbiology department of an academic hospital. We design, write and maintain pipelines and databases for genomic or metagenomic analyses, carry out or advise on analysis of high-throughput sequencing data and provide bioinformatics education and consultation.

2021

Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data

Julian A. Paganini, Nienke L. Plantinga, Sergio Arredondo-Alonso, Rob J. L. Willems, Anita C. Schürch

Microorganisms · 28 Jul 2021

Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era

Anna K. Pöntinen, Janetta Top, Sergio Arredondo-Alonso, Gerry Tonkin-Hill, Ana R. Freitas, Carla Novais, Rebecca A. Gladstone, Maiju Pesonen, Rodrigo Meneses, Henri Pesonen, John A. Lees, Dorota Jamrozy, Stephen D. Bentley, Val F. Lanza, Carmen Torres, Luisa Peixe, Teresa M. Coque, Julian Parkhill, Anita C. Schürch, Rob J. L. Willems, Jukka Corander

Nature Communications · 09 Mar 2021

Enterococcus

Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals

Sergio Arredondo-Alonso, Janetta Top, Jukka Corander, Rob J. L. Willems, Anita C. Schürch

Genome Medicine · 20 Jan 2021

Plasmid Enterococcus Antimicrobial resistance

Comparative genomics of ESBL-producing Escherichia coli (ESBL-Ec) reveals a similar distribution of the 10 most prevalent ESBL-Ec clones and ESBL genes among human community faecal and extra-intestinal infection isolates in the Netherlands (2014–17)

T D Verschuuren, D van Hout, S Arredondo-Alonso, A C Fluit, E A Reuland, J Top, A C Schürch, T Bosch, M J M Bonten, J A J W Kluytmans, R J L Willems

Journal of Antimicrobial Chemotherapy · 11 Jan 2021

WGS E.coli Antimicrobial resistance

2020

gplas: a comprehensive tool for plasmid analysis using short-read graphs

Sergio Arredondo-Alonso, Martin Bootsma, Yaïr Hein, Malbert R C Rogers, Jukka Corander, Rob J L Willems, Anita C Schürch

Bioinformatics · 01 Jun 2020

Plasmid Tool

Source

Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium

Janetta Top, Sergio Arredondo-Alonso, Anita C. Schürch, Santeri Puranen, Maiju Pesonen, Johan Pensar, Rob J. L. Willems, Jukka Corander

Microbial Genomics · 09 Mar 2020

Enterococcus

Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium

S. Arredondo-Alonso, J. Top, A. McNally, S. Puranen, M. Pesonen, J. Pensar, P. Marttinen, J. C. Braat, M. R. C. Rogers, W. van Schaik, S. Kaski, R. J. L. Willems, J. Corander, A. C. Schürch

mBio · 11 Feb 2020

Plasmid Enterococcus WGS

Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 – 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content

Denise van Hout, Tess D. Verschuuren, Patricia C. J. Bruijning-Verhagen, Thijs Bosch, Anita C. Schürch, Rob J. L. Willems, Marc J. M. Bonten, Jan A. J. W. Kluytmans

PLOS ONE · 14 Jan 2020

E.coli WGS Antimicrobial resistance

2019

Sequence-Based Epidemiology of an OXA-48 Plasmid during a Hospital Outbreak

Laura Hidalgo, Mark de Been, Malbert R. C. Rogers, Anita C. Schürch, Jelle Scharringa, Anneke van der Zee, Marc J. M. Bonten, Ad C. Fluit

Antimicrobial Agents and Chemotherapy · 21 Sep 2019

Plasmid Antimicrobial resistance

Draft Genome Sequence of Haemophilus haemolyticus Strain 16/010 O, Isolated from a Sputum Sample from a Cystic Fibrosis Patient

Ad C. Fluit, Jumamurat R. Bayjanov, Michael Tunney, J. Stuart Elborn, Malbert R. C. Rogers, Anita C. Schürch, Miquel B. Ekkelenkamp

Microbiology Resource Announcements · 06 Jul 2019

WGS

2018

mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species

Sergio Arredondo-Alonso, Malbert R. C. Rogers, Johanna C. Braat, Tess D. Verschuuren, Janetta Top, Jukka Corander, Rob J. L. Willems, Anita C. Schürch

Microbial Genomics · 01 Nov 2018

Plasmid Tool

Source App

Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene–based approaches

A.C. Schürch, S. Arredondo-Alonso, R.J.L. Willems, R.V. Goering

Clinical Microbiology and Infection · 01 Apr 2018

WGS