Prevalence and associated plasmid resistant genome of ESBL and AmpC producing commensal E. coli isolated from lactating cows and pre-weaned calves on dairy farms in Western Australia

This study aimed to determine the prevalence and associated plasmid resistant genome of extended spectrum β-lactamase (ESBL) and Ambler class C cephalosporinase (AmpC) producing commensal Escherichia coli, using a targeted pDNA approach, from lactating cows and pre-weaned calves on dairy farms in Western Australian (WA). Following culture and modified double disc diffusion, ESBL and/or AmpC producing commensal E. coli were isolated from faecal samples and phenotypic antimicrobial resistance (AMR) determined. Plasmid DNA (pDNA) was extracted, amplified, and sequenced to identify the AMR and replicon composition. Phenotypic analysis of 1117 faecal samples from 26 Western Australian dairy farms revealed a low overall prevalence (7.3 %) of ESBL and/or AmpC-producing commensal E. coli, with 3.2 % in cows (n = 633) and 12.8 % in calves (n = 484). All isolates were classified 'non-wildtype' for ampicillin and ceftiofur, with 95.1 % classified as 'non-wildtype' multidrug resistant (MDR). While bla_TEM was common in the pDNA (total: 60.6 %; cow: 76.9 %; calf: 57.7 %), a total of 13 AMR genes were identified across 126 plasmids (cow: n = 30; calf: n = 96) isolated. Multiple correspondence analysis (with chi-square-based 95 % confidence ellipses) showed variation in pDNA AMR genes and replicons by farm, with generally distinct plasmid profiles, though some clustering suggests possible farm-to-farm plasmid transmission. In conclusion, though low in prevalence, ESBL and/or AmpC producing commensal E. coli having high phenotypic AMR, MDR, and pDNA diversity were isolated from dairy cattle on 65.4 % of screened farms.