Methodological aspects of investigating the resistome in pig farm environments

Antimicrobial resistance (AMR) is a major concern, particularly in the animal sector, which accounts for over 50% of global antibiotic usage. The epidemiology of AMR in farm environments remains unanswered due to methodological challenges. This project combines metagenomics and bioinformatics to optimize research on resistomes in indoor farm environments. The most cost-effective pipeline for ARG search is based on Illumina sequencing of high-depth samples. The study suggests searching against multiple ARG databases is essential for detecting the highest diversity of ARGs.