In his PhD thesis, Jesse Kerkvliet (UMC Utrecht) focused on whole genome sequencing as well as metagenomics approaches, and presented several software methods that he designed that were able to recognize and reconstruct plasmid fragments that contribute to antimicrobial resistance (AMR). In addition, he investigated the effect of two different coccidiosis prevention interventions in chickens on the resistome and presented, putatively mobile, AMR genes.
Antimicrobial resistance (AMR) is a growing challenge for public health. This problem does not only focus on the clinical health of humans, but also causes issues in other aspects of public health of humans and animals. Resistant bacteria, but also genes conferring AMR, can be transferred to humans via direct animal contact, the food chain or the environment. AMR genes can arise through mutations, but can also be transferred between cells through means of horizontal gene transfer by mobile genetic elements (MGEs). An important factor in the dissemination of AMR genes is dissemination by plasmids. These extrachromosomal DNA molecules can transfer between bacterial cells, not necessarily following species barriers. This capability makes that plasmids are an important contributing factor to the spread of AMR genes. PhD candidate Jesse Kerkvliet (Department of Medical Microbiology, UMC Utrecht) used computational methods to identify and reconstruct MGEs that may contribute to AMR dissemination.
In his PhD thesis, bioinformatician Jesse Kerkvliet focused on whole genome sequencing approaches, and presented several software tools that were able to recognize and reconstruct plasmid fragments that contribute to AMR. Subsequently, he shifted to metagenomics, where the genomes of a large portion of bacteria in an environment were sequenced, and he investigated how this added complexity affected the software’s ability to recognize plasmid fragments. Finally, Jesse investigated the effect of two different prevention interventions for coccidiosis (a parasitic intestinal infection) in chickens on the resistome (all AMR genes in a particular community) and presented a large number of, putatively mobile, AMR genes.
This research project was part of the Complex Systems & Metagenomics research theme, funded by the Netherlands Centre for One Health (NCOH). Within this research theme, more than 10 PhD tracks in NCOH projects were created to foster interdisciplinary, inter-thematic, and inter-institutional research collaborations. This project is part of the overarching project DiSSeMINATE – Drivers of Selection and Spread of Mobile Genetic Elements INvolved in Antimicrobial Resistance.
Dr. Jesse Kerkvliet
Jesse Kerkvliet (1995, Lelystad) defended his PhD thesis on July 9, 2024 at Utrecht University. The title of his thesis was “Antimicrobial resistance on the move – Computational methods to identify and reconstruct mobile genetic elements contributing to AMR dissemination”. Supervisor was prof. em. Rob Willems, PhD and co-supervisor was Anita Schürch, PhD (both Department of Medical Microbiology, UMC Utrecht). Jesse Kerkvliet works as a post-doc at the National Institute for Public Health and the Environment (RIVM), investigating changes in the bacterial composition of urban waste water with the help of metagenomics data.
