Dynamics of extended-spectrum cephalosporin-resistant Escherichia coli in pig farms: A longitudinal study

Objectives: Point prevalence estimates of extended-spectrum cephalosporin-resistant Escherichia coli (ESC-R-Ec) are important surveillance measures but may not uncover the ESC-R-Ec dynamics within pig farms. A longitudinal study was therefore performed by sampling individual pigs, pig farmers and the environ-ment. Methods: On average, 30 (range 10-46) piglets of 31 Swiss farms were sampled during the suckling, weaning and fattening stages (n = 2437 samples). In addition, stool from pig farmers and environmen-tal 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. Results: Working on pig farms was not associated with an increased prevalence of ESC-R-Ec in humans. ESC-R-Ec prevalence significantly decreased from 6.2% to 3.9% and 1.8% for the suckling, weaned and fattening pigs, respectively ( P < 0.001). Within the 57 ESC-R-positive suckling piglets, persisting carriage was detected in 25 animals at two consecutive time points and one animal at three consecutive time points. Clonal spread (n = 7 farms, 22.6%) and horizontal gene transfer (n = 1 farm, 3%) within pigs but not between humans and animals was detected. Liquid manure (n = 10 samples, 16.7%) was identified as the major environmental reservoir of ESC-R-Ec in the pig farm environment. Conclusions: Pig farming practices like all-in-all-out systems, but not antimicrobial usage, were associ-ated with reduced risk of ESC-R-Ec at the farm level. As carriage duration is normally short within the individual pigs, the risk of recolonisation and clonal spread of ESC-R-Ec might be reduced by applying appropriate decontamination strategies. (c) 2021 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY license ( http://creativecommons.org/licenses/by/4.0/ )