Patrick Munk, Dongsheng Yang, Timo Röder, Leonie Maier, Thomas Nordahl Petersen, Ana Sofia Ribeiro Duarte, Philip T L C Clausen, Christian Brinch, Liese Van Gompel, Roosmarijn Luiken, Jaap A Wagenaar, Heike Schmitt, Dick J J Heederik, Dik J Mevius, Lidwien A M Smit, Alex Bosser, Frank M Aarestrup
Metagenomic sequencing has proven to be a powerful tool in the monitoring of antimicrobial resistance (AMR). Here, we provide a comparative analysis of the resistome from pigs, poultry, veal calves, turkey, and rainbow trout, for a total of 538 herds across nine European countries. We calculated the effects of per-farm management practices and antimicrobial usage (AMU) on the resistome in pigs, broilers, and veal calves. We also provide an in-depth study of the associations between bacterial diversity, resistome diversity, and AMR abundances as well as co-occurrence analysis of bacterial taxa and antimicrobial resistance genes (ARGs) and the universality of the latter...
March 19, 2024: MSystems