BioProject

Colistin resistance by mobilisable mcr genes has been described in bacteria of food-animal origin worldwide, which has raised public health concerns about its potential foodborne transmission to human pathogenic bacteria.Here we provide baseline information on the molecular epidemiology of colistin-resistant, mcr-positive E. coli and Salmonella isolates in food-producing animals in Italy in 2014-2015. A total 678, 861 and 236 indicator E. coli, Extended Spectrum Beta-Lactamase (ESBL)/AmpC-producing E. coli, and Salmonella isolates, respectively, were tested for colistin susceptibility. These isolates were collected according to the EU harmonised antimicrobial resistance monitoring programme and are representative of at least 90% and 80% of the Italian poultry (broiler chickens and turkeys) and livestock (pigs and bovines <12 months) production, respectively. Whole genome sequencing by Illumina technology and bioinformatics (Center for Genomic Epidemiology pipeline) were used to type 42 mcr-positive isolates by PCR. The Extended Spectrum Beta-Lactamases (ESBL)/AmpC-producing E. coli population, co-resistant to colistin was 25.9%, 5.3%, 6.5%, and 3.9% in turkeys, broilers, pigs and bovines, respectively. Most of colistin-resistant isolates (143/161, 88.8%) harboured genes of the mcr-1 group, with the exception of four mcr-3-positive ESBL-producing E. coli from bovines, and two mcr-4-positive E. coli from pigs and bovines. In turkeys, a small proportion of colistin-resistant, mcr-1-positive Salmonella was detected (3/146, 2.0%).Irrespective of host or colistin resistance prevalence, we describe a diversity of mcr variants, including a new variant, named mcr-1.13, integrated in the chromosome in turkey and pig isolates. However, most of isolates presented mcr-1.1 and mcr-1.2 in a transferable, conjugative IncX4 plasmid detected in E. coli and in Salmonella serovars Typhimurium, Newport, Blockley from turkey. Additionally, we describe the mcr-3.2 variant in E. coli from bovines, the mcr-4.2 from pigs and the mcr-4.3 from bovines. These findings help to understand the context and epidemiology of colistin resistance in food-producing animals in Italy along with its genetic background, and highlight the likelihood of mcr horizontal transfer between commensal bacteria and major food-borne pathogens (Salmonella) within the same type of productions. Thorough action and strategies are needed in order to mitigate the risk of mcr transfer to humans, in a “One Health” perspective