Long-term persistence of clonal resistant and multidrug resistant E. coli despite absence of antimicrobial use in weaned dairy heifer rearing systems in Switzerland.

Antimicrobial use (AMU) in Swiss bovines is widespread, and treatment incidences are high especially in calves, fattening bull and dairy cows. In contrast, AMU in heifers is very low. It is largely unknown to what extend bacteria resistant to antimicrobials are present in this population and which phenotypes, if any, are common. In the present study, on 30 farms implementing the most frequent husbandry systems, we followed heifers during a three-months period from spring to autumn 2023 and sampled 486 heifers (each one twice) by rectal swab sampling, isolating one random isolate per heifer and yielding a total of 966 Escherichia (E.) coli isolates. These were used to infer prevalence of antimicrobial resistance through phenotypic testing using disk diffusion and, if persistence with the herd was suspected, subjected to genetic testing using whole genome sequencing. The phenotypic prevalence was low at sampling timepoints (7.3-14.2 % of isolates exhibiting resistance to >1 drug). The most frequent phenotype was streptomycin-tetracycline (n = 37), and sul2 and tetB were the most frequent resistance genes. Surprisingly, on two farms without AMU, E. coli with identical phenotype, respectively, were isolated in spring an autumn, partly in the very same individual. Single nucleotide polymorphism (SNP) differences of 2 and < 10 of isolates obtained from farms, respectively, indicate harbouring of clonal resistant bacteria. Potential explanations for this finding, among others, may be that persistence of certain isolates in the cattle gut is longer than previously thought after cessation of selection pressure, or that isolates are maintained in the population through circulation via other animals or inanimate items. Therefore, also animals of livestock production categories with little AMU shall be considered when establishing One Health approaches to combat antimicrobial resistance.