Detection of cefotaxime- and enrofloxacin-resistant and mcr-1-positive Escherichia coli at farm level in younger and older calf groups across different production systems in Germany

Abstract Objective Studies on antibiotic resistance in calves rarely differentiate between production systems or younger and older calf groups within farms and commonly rely on non-selective laboratory methods. We investigated the qualitative farm-level detection and genetic diversity of antimicrobial-resistant E. coli from calves in different production systems in Germany using selective culture. Production systems included closed dairy farms (A), farms purchasing veal calves < 10 weeks (B), farms purchasing veal calves aged ≥ 10 weeks (C), suckler cow herds (D), and traders/collection points (E). Methods Eighty-one farms were sampled. Two pooled fecal samples representing younger and older calf groups, without recording exact ages, were collected from production systems A–C, and one sample each from D and E. Samples were cultured on MacConkey agar supplemented with cefotaxime (CTX), enrofloxacin (ENR) or colistin (COL) for qualitative detection of E. coli subpopulations. Recovered isolates were characterized by PCR for mobile ESBL-/pAmpC-associated genes, plasmid-mediated colistin resistance genes, quinolone resistance-determining region substitutions, and plasmid-mediated quinolone resistance genes. Phylogenetic relatedness of selected isolates was assessed by cgMLST-based hierarchical clustering. Results In systems A–C and among traders CTX- and ENR-resistant E. coli were widespread at farm level (> 70%), whereas suckler cow herds had substantially lower detection rates (< 25%). In systems A–C, resistant E. coli were detected more frequently at farm level in younger than older calf groups. Dominant ESBL genes were bla CTX−M−1, −15 and − 14 . Common amino acid substitutions associated with quinolone resistance included S83L and D87N/Y/H in GyrA and S80I in ParC, in addition to the detection of the qnrS and aac(6’)-Ib-cr genes. Mcr-1- positive E. coli recovered from COL-supplemented agar were detected less frequently (< 20%) in all production systems examined. Analysis of two samples from production systems A–C identified highly related isolates (HC10) within individual farms but not between farms. Conclusion Differences in the qualitative farm-level detection and genetic diversity of CTX- and ENR-resistant and mcr-1 -positive E. coli subpopulations were observed between production systems and between younger and older calf groups within farms. These findings suggest that production system and sampled calf group should be considered in the surveillance of antibiotic-resistant E. coli in calves.