Dynamics of Extended-spectrum cephalosporin-resistant E. coli in pig farms: a longitudinal study

Point prevalence estimates of extended-spectrum cephalosporin-resistant E. coli (ESC-R-Ec) are important surveillance measures but may not uncover the ESC-R-Ec dynamics within pig farms. We therefore performed a longitudinal study by sampling individual pigs, pig farmers and the environment. On average, 30 (range 10 to 46) piglets of 31 Swiss farms were sampled during the suckling, weaned and fattening stage (n= 2437 samples). In addition, stool from pig farmers and environmental samples were obtained and metadata collected by questionnaires. ESC-R-Ec was identified by routine culture and clonal relationships and resistance genes were derived from whole genome sequencing data.ESC-R prevalence significantly decreased from 6.2% to 3.9% and 1.8% for the suckling, weaned and fattening pigs, respectively (P<0.001). Carriage of ESC-R was detected in 25 animals at two time points and in one animal at three consecutive time points (43.9% and 1.8%). Clonal spread (n=7 farms; 22.6%) and horizontal gene transfer (n=1 farm; 3%) within samples from pigs but not between humans and animals was identified. Liquid manure (n=10 samples; 16.7%), was identified as the major environmental reservoir of ESC-R Ec in the pig farm environment. Pig farming practices like all-in-all-out systems but not antimicrobial usage (AMU) were associated with reduced risk of ESC-R-Ec. The observed farming practices were not associated with an increased prevalence of ESC-R-Ec in pig farm workers. As carriage duration is normally short within the individual pigs, the risk of recolonization and clonal spread of ESC-R-Ec might be reduced by applying appropriate decontamination strategies.