Occurrence of Escherichia coli non-susceptible to quinolones in faecal samples from fluoroquinolone-treated, contact and control pigs of different ages from 24 Swiss pig farms

BACKGROUND: Despite their indispensability in human medicine, fluoroquinolones (FQ) are used for the treatment of bacterial infections in farm animals which increases the risk of transferring FQ-resistant bacteria into the environment and via the food chain to humans. The objectives of this observational study were to follow-up of the presence of quinolone non-susceptible Escherichia coli (QNSE) qualitatively and quantitatively in faecal samples of pigs at four time points (2 weeks old, 4 weeks old, 2 weeks post weaning and during fattening period). Moreover differences between groups of FQ-treated pigs, pigs with contact to treated pigs and control pigs were investigated. Additionally, quinolone and FQ resistance of Escherichia coli isolates of the faecal samples were investigated by determining minimum inhibitory concentrations (MICs). RESULTS: 40.9% of 621 fecal samples contained QNSE. Proportion of samples with detectable QNSE from treated and contact pigs did not differ significantly and were highest in piglets of 2 and 4 weeks of age. However, the proportions of samples with QNSE were significantly lowest in control pigs (7/90; 7.8%; CI = 3.5–14.7%) among all groups. Also, the number of colony-forming units was lowest in both weaners and fattening pigs of the control group compared to treated and contact groups. Following CLSI human breakpoints, in total, 50.4% out of 254 isolates in faecal samples were intermediate or resistant to ciprofloxacin. CONCLUSIONS: QNSE were present in faeces of pigs independent of age or FQ background but significantly less were found in pigs from farms without FQ usage. Due to the long half-life of FQ, it is likely that only a prolonged absence of fluoroquinolone treatments in pig farming will lead to a reduced frequency of QNSE in the farm environment. Solutions need to be found to minimise the emergence and transfer of quinolone and FQ-resistant bacteria from treated pigs to contact pigs and to farms without FQ usage. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40813-021-00209-y.