12- Month PhD Report December 2021 PhD 13- VIMOGUT

12 month report of the OHEJP PhD project VIMOGUT.

The VIMOGUT project consists of in vivo analysis of the microbiome in the caecum of healthy broilers and the set-up of an in vitro model to study the transmission dynamics of antimicrobial resistance in caecal microbial communities. In the first period of 2021, the PhD student has worked on both aspects of the project.
Further data analysis was performed for the in vivo component to complete the first manuscript titled “Succession in the caecal microbiota of developing broilers colonised by Extended-spectrum β-lactamase-producing Escherichia coli”, which was submitted in September 2021. The collection of additional broiler caecal samples at farms was postponed due to COVID-19. Preparations were arranged with the hope to perform the sampling at the end of 2021. However, due to the Avian influenza outbreaks in the Netherlands, the sampling at the broiler farms had to be postponed once more until further notice, hopefully, the first quarter of 2022.
The in vitro chicken caecum model was first tested in 2020, after which further optimisation was necessary. Challenges with the oxygen sensors were under investigation and solved. The initial tests in the semi-automated in vitro chicken have been run for ~8 days. Analyses of data collected (real-time process monitoring and 16S rRNA gene analysis) have shown reproducibility and reliability of the system between experiments. Inoculation and intervention experiments have been delayed due to a hardware failure in the in vitro system secondary to a power failure at WBVR in October 2021. Applikon engineers are currently working on this issue.