AIMS: To determine the genetic relatedness and the presence of virulence and antibiotic resistance genes in commensal Escherichia coli from nursery pigs in Danish intensive production.

METHODS AND RESULTS: The genetic diversity of 1000 E. coli strains randomly picked (N = 50 isolates) from cultured faecal samples (N = 4 pigs) from five intensive Danish pigs farms was analysed by repetitive extragenic palindromic-PCR (REP-PCR) and 42 unique REP-profiles were detected (similarity <92%). One profile was dominant (67·2% of strains) but farms differed significantly in the diversity of commensal E. coli: between eight and 21 different profiles per farm were detected. One to three strains representing each REP-profile were characterized by multilocus typing scheme-typing, as well as for presence of antimicrobial and virulence genes and serogrouping through microarray analysis. The 42 REP-profiles were classified into 22 different sequence types (ST) with ST10 being the most common, encompassing 10 REP-profiles. Resistance and virulence genes were detected in most of the isolates. Genes encoding AmpC-β-lactamases and quinolone resistance were found in one and three isolates, respectively. Toxin-producing genes were observed in 20 isolates.

CONCLUSIONS: A low genetic diversity was found in commensal gut E. coli from nursery pigs in Denmark. No correlation was observed between REP-profiles, ST-types and resistance/virulence patterns.

SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study analysing in depth the genetic variability of commensal E. coli from pigs in Danish intensive pig production. A tendency for higher diversity was observed with in nursery pigs that were treated with zinc oxide only, in absence of other antimicrobials. Strains with potential to disseminate virulence and antibiotic resistance genes to pathogenic subgroups of E. coli were found to be wide-spread.