Prevalence and molecular characteristics of colistin-resistant Escherichia coli in livestock and fresh meat detected by a selective enrichment method

Considering the increase of infections with carbapenemase-producing Enterobacterales in human medicine, colistin is nowadays listed as highest priority critically important antimicrobial for human medicine by the World Health Organization, leading to drastic restrictions on its previous widespread use in veterinary medicine. Because of the reduced but continued use of colistin in veterinary medicine, livestock and fresh meat might represent a source of colistin-resistant bacteria. Here, we performed a culture-based study followed by whole genome sequencing (WGS) to detect and characterise colistin-resistant Escherichia coli in caecal samples of Swiss livestock and fresh meat using the random sample plan of the European programme on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food. A low prevalence of colistin-resistant E. coli in Swiss livestock was detected (2.7% in calves (n = 298), 2.9% in pigs (n = 350), 0.6% in broilers (n = 805)). In fresh meat, the prevalence of colistin-resistant E. coli was comparable for beef (3.1%, n = 164) and pork (3.7%, n = 163), while chicken meat had a higher prevalence of 5.4% (n = 295). WGS highlighted that colistin resistance was mostly associated with chromosomal mutations (56%), while a lower occurrence of mcr genes (22%) was found. WGS analysis revealed a high diversity in the detected colistin-resistant E. coli as they belonged to 32 sequence types (ST) and 48 core genome STs. Fresh meat might be contaminated with colistin-resistant E. coli, but its detection is not currently implemented in the European programme on antimicrobial resistance. By an approach using selective bacterial culturing all phenotypically colistin-resistant E. coli can be detected independently from their molecular resistance mechanisms, with the disadvantage of eventually also inducing chromosomal mutations during selective overnight incubation.