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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  Escherichia 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 harmonized antimicrobial resistance monitoring program 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. Colistin resistance was mainly observed in the ESBL/AmpC  E. coli  population, and was present in 25.9, 5.3, 6.5, and 3.9% of such isolates in turkeys, broilers, pigs, and bovines, respectively. Most colistin-resistant isolates (141/161, 87.5%) harbored genes of the  mcr -1 group.  mcr- 1 was also detected in a small proportion of  Salmonella  isolates (3/146, 2.0%) in turkeys. Additional  mcr  types were  mcr -3 in four ESBL-producing  E. coli  from bovines, and two  mcr -4 in ESBL ( n  = 1) and indicator  E. coli  ( n  = 1) from pigs and bovines. We describe notable diversity of  mcr  variants with predominance of  mcr- 1.1 and  mcr- 1.2 on conjugative IncX4 plasmids in  E. coli  and in  Salmonella  serovars Typhimurium, Newport, Blockley from turkey. A new variant,  mcr -1.13 was detected in the chromosome in  E. coli  in turkey and pig isolates. Additionally, we describe  mcr -3.2 and  mcr -4.3 in  E. coli  from bovines, and  mcr -4.2 in  E. coli  from pigs. These findings elucidate the 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.

frontiers in microbiology

Molecular Epidemiology of mcr-Encoded Colistin Resistance in Enterobacteriaceae From Food-Producing Animals in Italy Revealed Through the EU Harmonized Antimicrobial Resistance Monitoring