Fig. 6

Antimicrobial resistance mobilome characterization. a Boxplot of contigs with more than 1500bp carrying antimicrobial resistance genes (ARGs). b Boxplots of chromosomal or plasmid location of ARGs containing contigs with PlasFlow. c Boxplots of integrons and lateral gene transfer events involving ARGs detected in contigs with Integron_Finder and WAAFLE, respectively. Each sample is represented by a dot with horizontal jitter for visibility. The horizontal box lines represent the first quartile, the median, and the third quartile. Whiskers include the range of points within the 1.5 interquartile range. The differences per sample type and per production system within each sample type were evaluated with the Wilcoxon signed-rank test. n = 105 metagenomes from 38 independent farms. Nineteen metagenomes per sample type per production system were used, with the exception of extensive-slurry (n = 9)