Fig. 5: Analysis of antimicrobial-resistance and virulence-associated genes.

The category “cheese-related materials” groups together milk, brine and whey culture. A Connected barplot showing the variation in the average Copies Per Million (CPM) abundance of each Antimicrobial Resistance Gene (AMRG) family between the classes of samples. B Taxonomic assignment of contigs encoding for AMRG. For each AMRG - taxon pair, each slice is proportional to the percentage of contigs reconstructed from a category of samples. The size of each pie is proportional to the number of contigs linked to an AMRG - taxon pair. C Sum of the CPM abundance of genes linked with Adherence, Biofilm formation and Motility virulence traits. Statistical differences between the groups were calculated through the Wilcoxon’s rank-sum test. Boxes represent the interquartile range (IQR) between the first and third quartiles, and the line inside represents the median (2nd quartile). Whiskers denote the lowest and the highest values within 1.5 x IQR from the first and third quartiles, respectively. The category “cheese-related materials” groups together milk, brine and whey culture. Average values are obtained from n = 308, 199, 37, 524, and 182 biologically independent samples from food contact, non food contact, operators’ swabs, final products and cheese-related materials, respectively.