Final PhD Thesis Report VIMOGUT

Samenvatting

Antimicrobial resistance (AMR) tops the list of global health threats in humans and animals. Extended-spectrum beta-lactamases (ESBLs) are a relevant type of resistance mechanisms that inactivate a large group of critically important antibiotics and that have emerged globally in the livestock sector. Despite all the efforts in reducing antimicrobial consumption and banning growth promotors, a considerable proportion of ESBLs is still observed in the animal sector. AMR is a phenomenon that requires action and research using integrated strategies with a one-health approach. Based on this notion, the PhD project VIMOGUT brought together in vivo and in vitro studies to better understand the role of the chicken gut microbiota as an important ecological niche for the spread of AMR genes in the environment.

We have studied the successional dynamics of the caecal microbiota of developing broilers in relation to colonisation by ESBL- producing Escherichia coli (ESBL-Ec) in a commercial broiler farm. Our results suggested the presence of ESBL-E. coli is associated with mild but consistent reductions in broilers' caecal microbiota richness and transient microbiota compositional differences. We further documented the increasing prevalence and clonal spread of ESBL-E. coli in a single broilers' flock during a single production round and pointed at the farm environment as a likely source for ESBLs. We also advocated for additional research to more precisely understand whether the presence of ESBL-E. coli modulates the competitive landscape of the broiler microbiota or vice-versa. In vitro microbiota studies involving experimental ESBL-E. coli introduction could provide valuable answers to these questions, which can then be further confirmed under controlled animal experiments.

Another goal of the VIMOGUT PhD project was to contribute to more sustainable research by developing a cost-efficient and animal-friendly tool. We have developed an in vitro chicken caecal model capable of reproducing the physiological conditions required to culture the main members of the chicken gut microbiota. This milestone paved the road for future investigation on the effect of microbiota-targeted intervention studies and the horizontal transmission of AMR genes. In addition, the in vitro gut model also expands the possibilities of addressing other microbiota-AMR-related research questions. Our results also show that optimisation steps of such tools are a continuous process from which we learned that the choice of experimental settings impacts the in vitro cultured microbial community composition over time. Thus, pre-testing parameters and generating automated workflows are essential to reduce experimental bias, generate reliable data and draw meaningful conclusions.

The knowledge acquired during the VIMOGUT PhD project sheds light on the relationship between AMR bacteria and the broiler gut microbiota and highlights the need to consider the natural dynamics of host-microbiota development and the environment in the colonisation by resistant bacteria. Moreover, an in vitro model has been developed as a research tool to explore microbiota-based strategies to reduce the spread of AMR genes. This project supports the One Health approach to minimise the spread of AMR from animals to humans via the food chain in line with policies of the Dutch Ministry of Agriculture, Nature and Food Quality, as well as EFSA, ECDC, EMA, WOAH, WHO and FAO to tackle AMR.