Antimicrobial resistance in Escherichia coli isolates from the calf environment on Swiss dairy farms

Antimicrobial resistance (AMR) in the intestinal commensal flora of dairy calves is acquired during the first weeks of life. It has been hypothesized that one of the sources of colonization for such bacterial strains is the calf environment, whereas antimicrobial exposure of the calves plays a role in the selection and maintenance of AMR in the flora. The objectives of this cross-sectional observational study were to explore the associations between AMR and multidrug resistance (MDR; resistance to ≥ 3 drug classes) of Escherichia coli isolated from calves' pens and herd-level factors including quantitative antimicrobial use (AMU) on 60 Swiss dairy farms. Two swabs of calf pens' walls were collected on each farm, and two E. coli isolates from each swab were tested for antimicrobial susceptibility by broth microdilution. Among 240 isolates, the proportion showing no AMR was 57.9 %. The proportion of MDR isolates was 31.3 % and at least one MDR isolate was found on 50 % of the farms. Higher odds of AMR were associated with a producer-estimated incidence of calf pneumonia > 10 % (OR 17.3, 95 % CI 2.5–118.4). The introduction of cattle from ≥ 2 farms during the previous year was associated with increased odds of MDR (OR 12.3, 95 % CI 2.0–75.7). Multidrug-resistant E. coli were common in the calf environment on Swiss dairy farms. Our results suggest that in addition to antimicrobial stewardship, farm management factors including biosecurity practices should be considered in the investigation and prevention of the spread of AMR.