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In vitro and in vivo analyses and modulation of the chicken gut microbiome to combat AMR

Group and collaboration

Dr. Michael Brouwer & Dr. Kees Veldman – Wageningen Bioveterinary Research
Prof. Arjan de Visser – WUR Departement Plantwetenschappen
Prof. Muna Anjum - Animal & Plant Health Agency, United Kingdom
PhD student: Ingrid Cardenas Rey

Project description

The intestinal microbiome functions as a barrier for colonisation by ingested bacteria. As such, it is likely also a barrier for bacteria resistant to antimicrobials. The PhD project will study the chicken microbiome development of chickens on farms to determine if the reported microbial progression is reproducible between different production rounds and farms. By screening these samples for the presence of ESBL E. coli, the significance of the reduced diversity of early colonised chickens will be determined. The in vitro chicken gut model will be set up for use at WBVR to test strategies for the reduction of ESBL E. coli and compare these with published data from in vivo studies. When the model can efficiently reproduce these in vivo studies, it can be used for further study of new ESBL E. coli colonisation prevention strategies.


  • Study the relationship between the chicken gut microbiota and ESBL producing E. coli.
  • Set up an in vitro model of the caecum of chickens.
  • Study conjugation of plasmids in vitro.
  • In vitro, study the efficacy of interventions against ESBL E. coli.

The One Health European Joint Program (EJP) started on 1 January 2018. By integrating and coordinating the research programs of institutes working in the areas of public health, animal health and food safety, a sustainable European partnership is set up. A number of Dutch institutes also play a role within this program. Both RIVM, WBVR and the partners within Netherlands Centre for One Health participate in various research projects and activities aimed at knowledge integration.


PhD student interview

Interview: From Colombia via US and Australia to Lelystad to have more influence for change

After her study and internship, Ingrid Cardenas Rey started working as a heard health manager. There, most animals received the wrong antibiotics or the wrong doses. This was an eyeopener and one of her major reasons to move from veterinarian practice to research; to have more influence for change in the sector.