mr. ing. M.N. (Rob) Toonen

mr. ing. M.N. (Rob) Toonen

Full Professor
mr. ing. M.N. (Rob) Toonen
  • Department of Medical Microbiology

Research Programs

Infection & Immunity



Prof. dr. Rob Willems studied biology at the Free University in Amsterdam and acquired his PhD from the Utrecht University in 1993 on “Genetic and functional studies on Bordetella pertussis fimbriae”. After postdoc positions at the Faculty of Veterinary Medicine, Utrecht University and at the Department of Infectious Diseases of the University Hospital, Leiden he became research scientist and section head at the National Institute for Public Health and the Environment (RIVM) in 1996. In 2003 he moved from the RIVM to the University Medical Center Utrecht where he became assistant professor. In 2008 he was appointed associate professor and since December 1st 2016, he is full professor of Population Genetics of Antibiotic Resistance at the department of Medical Microbiology of the University Medical Center Utrecht. Since 1997, he has set up and been involved in various national and international studies on antibiotic resistance. From 2007-2011 he coordinated an EC FP6 project on Approaches to Control multi-resistant Enterococci (ACE) and from 2011-2015 he was principal investigator and coordinator of the EC FP7 project designated Evolution and Transmission of Antibiotic Resistance (EvoTAR). His research group aims to unravel the genetic evolution, population and functional genomics of Enterococcus faecium and Enterococcus faecalis as well as E. faecium host-pathogen interactions. His group was the first that identified structure in the E. faecium population and described that strains from hospitalized patients were genetically distinct from animal isolates and human commensal isolates. He also published the first comparative genomics paper on E. faecium using comparative genomic hybridizations as well as whole genome sequencing that revealed that E. faecium has an open genome capable for frequently incorporating new DNA in its genome. Currently, his group is also focussing on genome based epidemiology of multidrug-resistant pathogens, with a special focus reconstructing and tracking the spread of plasmids based on genome sequence data. Furthermore, his group aims to decipher the processes and molecular mechanisms that contribute to colonization resistance against high density colonization of antibiotic-resistant Enterobacteriaceae and enterococci and the consequences of intestinal outgrowth of these multidrig resistant opportunistic pathogens on pathogen-host cross-talk. Dr. Willems has authored more than 175 peer-reviewed papers and book chapters.

Side Activities

Board membership:

Chair of the Division of Microbial Genomics of the Royal Netherlands Society for Microbiology.


Contract Research:

Willems was on behalf of the UMC Utrecht principel investigator of the collaborative Research Agreement with Janssen Research & Development, LLC (63871860BAC0006) Global serotype distribution among ExPEC bacteremie isolates (2018-2020). (no personal payments).

Willems was on behalf of the UMC Utrecht principle investigator of the collaborative Research Agreement with Janssen Research & Development LLC (VAC52416BAC0008) O-serotype distribution of ExPEC isolates from urosepsis, cystitis, and asymptomatic bacteruria (2019-2021). (no personal payments)

Willems is on behalf of the UMC Utrecht principle investigator of the Janssen Research & Development LLC (VAC52416BAC0001) Genomic and Phenotypic profiling of ExPEC-associated urosepsis primary cultures (2019-2022) (no personal payments).



Willems was on behalf of the UMC Utrecht coordinator of the JPI-EC-AMR JTC 2016 project Selection and transmission of Antimicrobial Resistance (STARCS) (2017-2021) (no personal payments).

Willems was on behalf of the UMC Utrecht coordinator of the Netherlands Center of One Health Molecular mechanisms of microbiota-mediated colonization resistance against intestinal outgrowth of multidrug resistant enterobacteriaceae (2017-2021) (no personal payments)

Willems is on behalf of the UMC Utrecht collaborator on the TKI-LSH ppp allowance funded project Drivers of Selection and Spread of Mobile Genetic Elements involved in antimicrobial resistance (DISSEMINATE) (2020-2023) (no personal payments).


Courses and Conferences:

Organiser and lecturer in courses and conferences in microbiology in Utrecht, Amsterdam, Wageningen, France, Germany, United Kingdon, Norway, Denmark, and Italy (no payments).

Guest teacher refresher course Hoge school Utrecht (payments to Rob Willems)


Editorial and Review Services:

Referee for several journals and regular referee for funding organisations such as University of Tromso (Norway),Institut Pasteur (France), Irish Research Council Laureate Awards (Ireland) and German Research Foundation, DTU (Denmark), International Centre for diarrhoeal Disease Research  (Bangladesh), Marie Curie Fellowship (EU), NWO-Top (NL), ZonMW-Veni (NL) and The Welcome Trust (UK), NWO-Klein (NL) (payments to Rob Willems).

Research Output (238)

Effects of early-life antibiotics on the developing infant gut microbiome and resistome:a randomized trial

Reyman Marta, van Houten Marlies A., Watson Rebecca L., Chu Mei Ling J.N., Arp Kayleigh, de Waal Wouter J., Schiering Irene, Plötz Frans B., Willems Rob J.L., van Schaik Willem, Sanders Elisabeth A.M., Bogaert Debby 16 Feb 2022, In: Nature Communications. 13

Functional characterization of a gene cluster responsible for inositol catabolism associated with hospital-adapted isolates of Enterococcus faecium

Top Janetta, Baan Jery, Bisschop Adinda, Arredondo-Alonso Sergio, van Schaik Willem, Willems Rob J.L. 1 Sep 2021, In: Microbiology (Reading, England). 167 , p. 1-12

Recovering escherichia coli plasmids in the absence of long-read sequencing data

Paganini Julian A., Plantinga Nienke L., Arredondo-alonso Sergio, Willems Rob J.L., Schürch Anita C. 28 Jul 2021, In: Microorganisms. 9 , p. 1-20

The global dissemination of hospital clones of Enterococcus faecium

van Hal Sebastiaan J, Willems Rob J L, Gouliouris Theodore, Ballard Susan A, Coque Teresa M, Hammerum Anette M, Hegstad Kristin, Westh Hendrik T, Howden Benjamin P, Malhotra-Kumar Surbhi, Werner Guido, Yanagihara Katsunori, Earl Ashlee M, Raven Katherine E, Corander Jukka, Bowden Rory, 30 Mar 2021, In: Genome Medicine. 13 12 p.

Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era

Pöntinen Anna K, Top Janetta, Arredondo-Alonso Sergio, Tonkin-Hill Gerry, Freitas Ana R, Novais Carla, Gladstone Rebecca A, Pesonen Maiju, Meneses Rodrigo, Pesonen Henri, Lees John A, Jamrozy Dorota, Bentley Stephen D, Lanza Val F, Torres Carmen, Peixe Luisa, Coque Teresa M, Parkhill Julian, Schürch Anita C, Willems Rob J L, Corander Jukka 9 Mar 2021, In: Nature Communications. 12 13 p.

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

Arredondo-Alonso Sergio, Top Janetta, Corander Jukka, Willems Rob J L, Schürch Anita C 20 Jan 2021, In: Genome Medicine. 13 18 p.

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)

Verschuuren T D, van Hout D, Arredondo-Alonso S, Fluit A C, Reuland E A, Top J, Schürch A C, Bosch T, Bonten M J M, Kluytmans J A J W, Willems R J L 11 Jan 2021, In: The Journal of antimicrobial chemotherapy. 76 , p. 901-908 8 p.

Evolution of colistin resistance in the Klebsiella pneumoniae complex follows multiple evolutionary trajectories with variable effects on fitness and virulence characteristics

Janssen Axel B, Doorduijn Dennis J, Mills Grant, Rogers Malbert R C, Bonten Marc J M, Rooijakkers Suzan H M, Willems Rob J L, Bengoechea Jose A, van Schaik Willem 2 Nov 2020, In: Antimicrobial Agents and Chemotherapy. 65 , p. 1-15

Whole Genome Sequence Analysis of the First Vancomycin-Resistant Enterococcus faecium Isolates from a Libyan Hospital in Tripoli

Ahmed Mohamed O., Elramalli Asma K., Baptiste Keith E., Daw Mohamed A., Zorgani Abdulaziz, Brouwer Ellen, Willems Rob J.L., Top Janetta 1 Nov 2020, In: Microbial drug resistance. 26 , p. 1390-1398 9 p.

All research output

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