In total, 150 isolates covering three species were included in the study: E. coli (n = 50) and Salmonella (n = 50) isolates from the in-house strain collection at the National Food Institute and C. jejuni (n = 50) isolates from the in-house strain collection at Statens Serum Institut. The isolates were selected on the basis of having both WGS data and phenotypes available. The Salmonella isolates included strains from 10 different serovars (Tables S1 to S3, available as Supplementary data at JAC Online). All bacterial isolates were sequenced using the Miseq platform (Illumina) to obtain paired-end sequences and assembled de novo using Velvet (reference software). Bacterial strains were screened for phenotypic resistance using MIC determinations interpreted according to EUCAST (www.eucast.org). Only the susceptibility tests relevant for antimicrobial resistance associated with chromosomal point mutations for each species were analysed (Table 2). As resistance to some of the antimicrobial agents can be caused by either acquired genes or chromosomal point mutations, ResFinder-2.1 (www.genomicepidemiology.org)31 (link) was used to detect known acquired resistance genes in the WGS data, using a threshold of 98% identity (%ID) and 60% length (minimum percentage length of the resistance gene to be covered). All isolates with disagreement between the phenotypic and predicted susceptibility were re-tested.

Antimicrobial agents used for susceptibility tests for each species

SpeciesAntimicrobial agents
E. coliciprofloxacin, nalidixic acid, colistin, sulphonamide, tetracycline, spectinomycin
Salmonellaciprofloxacin, nalidixic acid, colistin, spectinomycin
C. jejuniciprofloxacin, nalidixic acid, erythromycin, spectinomycin

Acquired resistance genes, chromosomal point mutations or both can cause resistance to antimicrobial agents.