Pilot longitudinal observational study of the effect of common stress events on the shedding of antimicrobial resistant E. coli during the pig and poultry production cycle

This longitudinal observational study sampled six farms (three broiler and three pig finishing farms) before and after selected routine management events with the aim of exploring the impact of stress on antimicrobial resistant E. coli shedding. A Poisson generalised linear mixed-modelling (GLMM) approach was used for each species to evaluate differences between shedding of E. coli following the events compared to the baseline, and impact of explanatory variables. Whilst shedding varied at the sampling time points, no evidence of significant difference was detected. Our results demonstrate no significant difference in the impact of stress on E. coli (for all E. coli and resistant E. coli) shedding at different time points, contrasting with trends seen in other bacteria. However, due to this being a pilot study, we only included a small number of farms and expansion to include additional farms would be beneficial. Certain temporal and farm-level factors influencing shedding were identified which warrant further investigation.