Metagenomic evidence for co-occurrence of antibiotic, biocide and metal resistance genes in pigs

•A comprehensive gut microbiome metagenomic analysis of 278 pigs was conducted.•Co-selection phenomena were investigated via co-occurrence patterns as a proxy.•Twenty-seven types of co-occurrences involving 131 resistance genes were detected.•Regardless of use of antibiotics, AMR can be maintained by co-occurrence with MRGs/BRGs.•Maintenance of AMR is not a random selection process but pertains to specific phylogenetic clades.