Characterization of third-generation cephalosporin-resistant Escherichia coli from slaughter calves and fattening pigs: A pilot study for monitoring antimicrobial resistance by whole genome sequencing in Switzerland.

Whole genome sequencing (WGS) was introduced into Swiss antimicrobial resistance monitoring in 2022 as an additional method to phenotypic antimicrobial susceptibility testing by broth microdilution to characterize presumptive third-generation cephalosporin-resistant (3GC-R) Escherichia coli. Caecal samples from Swiss slaughter calves and fattening pigs, as well as beef and pork meat from Swiss retail taken in 2021, were analyzed for the presence of 3GC-R E. coli according to European harmonized protocols. In 2021, 3GC-R E. coli was detected in 23,8 % of slaughter calves, 5,9 % of fattening pigs, and 0 % of meat. Comparative analysis of the antimicrobial resistance results obtained by phenotypic measurement and those obtained by the detection of corresponding underlying molecular mechanisms by WGS showed very high agreement (99 %). Resistance to third-generation cephalosporins (3GCs) was mainly associated with the presence of blaCTX-M-15 in E. coli isolates from calves and blaCTX-M-1 in E. coli isolates from pigs and mutations in the ampC-promoter (g.-42 C>T) in E. coli isolates from both animal species. Moreover, WGS data were used for phylogenetic analysis based on multi locus sequence types (MLST) and core genome MLST(cgMLST) revealing that 3GC-R E. coli isolated from Swiss slaughter calves and fattening pigs were genetically diverse. In this study, it was shown that using WGS alone to monitor antimicrobial resistance could detect trends in known molecular antimicrobial resistance mechanisms while also providing other valuable information about the isolates, such as genetic relatedness. However, only by combining phenotypic susceptibility testing and WGS early detection of previously unknown resistance mechanisms will be possible.