mcr-1-like detection in commensal Escherichia coli and Salmonella spp. from food-producing animals at slaughter in Europe

We evaluate here the presence of the mcr-1-like and mcr-2 genes in Escherichia coil and Salmonella spp. isolated from healthy food-producing animals at slaughter between 2002 and 2014 in Europe. Isolates were retrieved from cattle, pig and chicken from 11 European countries of production. The susceptibility to colistin and antibiotics used in human medicine was determined by agar dilution. Colistin-resistant isolates were PCR-screened for mcr genes. mcr-positive isolates were typed by Pulsed-Field Gel Electrophoresis (PFGE) and Multi-Locus Sequence Typing. Among the 10,206 E. coil and 1774 Salmonella spp. isolated from cattle, pigs and chickens, 148 E. coil and 92 Salmonella spp. isolates were resistant to colistin. We found mcr-1-like gene in 68 (0.7%) E. coil and 2 (0.1%) Salmonella isolates whereas none of the isolates tested positive for mcr-2. MCR-1-like-positive E. coil were isolated from 2008 to 2014 in chicken (n = 44, 1.2%) and pigs (n = 24, 0.7%). The presence of mcr-1-like varied from 0 to 4.0% depending on the year and the animal species. mcr-1-like-positive isolates came from animals originating from Germany (n = 38), Spain (n = 23), The Netherlands (n = 5), and France (n = 4). They were distributed in 63 different PFGE types and 37 different STs, with ST10 being the most prevalent. The two mcr-1-like-positive Salmonella spp. were isolated from France and Germany from a pig and a chicken, respectively. mcr-1-like gene is present in food-producing animals at slaughter in European countries with the highest occurrence in chickens. The high clonal diversity of E. coli underlines the evidence for horizontal transfer of mcr-1-like genes.