Antimicrobial resistance on the move

Summary

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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. In the first half of this thesis, I focus on whole genome sequencing approaches, and present software methods that are able to recognize plasmid fragments in these experiments. In the second half of the thesis, I shift to metagenomics, where the genomes of a large portion of bacteria in an environment are sequenced, and how this added complexity affects software’s ability to recognize plasmid fragments. Finally, I investigate the effect of two different coccidiosis prevention interventions in chickens on the microbiome and present, putatively mobile, AMR genes.