E. coli strains sequenced in this study.

For all strains that were ESBL- and IncI1 plasmid-positive or AmpC- and IncK plasmid-positive, the Inc group of the plasmid that carried the ESBL/AmpC gene had previously been determined using a transformation-based approach [15], [18]. Identical numbers behind places of isolation indicate the exact same locations: i.e. the same retail store for chicken meat isolates, the same slaughterhouse for chicken isolates and the same farm (referred to as farms A, B, and C) for pig and pig farmer isolates.* These ESBL genes were not found in the genome assemblies: blaTEM-20 or blaTEM-1 were found instead of blaTEM-52.†This ESBL gene had previously only been typed using microarrays (no sequencing). The gene was found to belong to the CTX-M-1 group.‡These CMY genes were divided over two contigs that were connected on a scaffold. BLAST runs of the partial CMY-2 sequences against GenBank's nr database gave best hits with blaCMY-2 and mapping of raw Illumina reads against blaCMY-2 indicated that the full blaCMY-2 gene was present in the corresponding strain.n.d.: not determined.E. coli strains sequenced in this study.