Lineage-aware comparison of extended-spectrum β-lactamase-producing Escherichia coli from unweaned dairy calves and human references reveals host-structured plasmidomes and co-selection

Antimicrobial resistance in Escherichia coli is shaped not only by resistance genes themselves but also by their chromosomal or plasmid localization and co-occurrence with biocide/metal resistance genes (BMRGs), virulence-associated genes and mobile genetic elements. We applied chromosome- and plasmid-resolved genomics to 109 extended-spectrum β -lactamase-producing E. coli isolates from unweaned dairy calves ( n =484) in Germany and compared them with 479 human-associated reference genomes. Calf isolates were polyclonal and dominated by phylogroups A and B1. Resistance was predominantly plasmid-borne: 41% of isolates carried antibiotic resistance genes (ARGs) exclusively on plasmids, whereas only 4.6% carried ARGs exclusively on chromosomes. The chromosomal-versus-plasmid distribution of acquired ARGs differed significantly across phylogroups ( P <0.05) and sequence types (all P <0.01). Conjugative plasmids accounted for 94.6% of plasmid-borne ARG occurrences and carried significantly more ARGs than mobilizable plasmids ( P =3.66×10 −42 ). ARG and BMRG counts were strongly correlated at the plasmid level (ρ=0.574, P =8.0×10 −41 ), and class 1 integrons marked enriched multidrug plasmids with increased ARGs ( P =6.22×10 −34 ) and BMRGs ( P =3.00×10 −29 ). At the isolate level, calf isolates carried more acquired ARGs in unadjusted comparisons, but this host-associated difference was largely explained by population structure. At the plasmid level, however, host-associated differences persisted after adjustment: human plasmids carried more ARGs (IRR 1.66, P =0.0017) and showed a strong host×mobility interaction (IRR 4.61, P =4.9×10–8), stronger ARG–BMRG coupling and a higher prevalence of integrons. These findings show that antimicrobial resistance ecology in E. coli is shaped not only by which resistance genes are present, but by where they are located, what they are linked to and how readily their genomic carriers can disseminate.