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Clostridium difficile is the leading cause of nosocomial diarrhea in humans and a major cause of enteritis in neonatal piglets, foals and calves. The aim of this longitudinal study was to determine and compare the prevalence, antimicrobial susceptibility, and toxinotype profiles of C. difficile isolated from pigs and their environment in the indoor conventional and outdoor antimicrobial free (ABF) production systems. Ten conventional and eight ABF cohorts of 35 pigs each and their environment were sampled at different stages of production at farm and slaughter. C. difficile prevalence in pigs was highest at the farrowing stage in both conventional (34%, 120/350) and ABF (23%, 56/244) systems, and decreased with age. This reduction in C. difficile prevalence in pigs at later stages of production mirrored the decreased prevalence in the farm environment. At slaughter, C. difficile was isolated at a low frequency from the carcasses and processing environment in both production systems. All but three isolates were resistant to ciprofloxacin (99%, 505/508), while 1.0% (5/508) and 6.0% (23/508) of isolates exhibited resistance to tetracycline and erythromycin, respectively. Toxinotype V (tcdA(+)tcdB(+)) was the predominant strain identified in both systems (conventional: 94%, 376/401; ABF: 82%, 88/107), while the rest were toxinotype XIII (tcdA(+)tcdB(+)). To conclude, we isolated antimicrobial resistant C. difficile regardless of antimicrobial use on the farm. Based on the phenotypic and genotypic similarity of C. difficile isolated in this study, we conclude that the unique production practices employed in conventional and ABF production systems have no impact on the pathogen population., (Published by Elsevier B.V.)