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

摘要

Whole genome sequencing (WGS) was introduced into Swiss antimicrobial resistance monitoring in 2022 as an additional method to phenotypic antimicrobial susceptibil-ity testing by broth microdilution to characterize presump-tive 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. Compara-tive analysis of the antimicrobial resistance results obtained by phenotypic measurement and those obtained by the de-tection of corresponding underlying molecular mechanisms by WGS showed very high agreement (99 %). Resistance to third-generation cephalosporins (3GCs) was mainly asso-ciated with the presence of blaCTX-M-15in E. coli isolates from calves and blaCTX-M-1 in E. coli isolates from pigs and muta-tions 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 re-sistance could detect trends in known molecular antimicro-bial resistance mechanisms while also providing other valu-able information about the isolates, such as genetic relatedness. However, only by combining phenotypic sus-ceptibility testing and WGS early detection of previously unknown resistance mechanisms will be possible.