Detection by real-time PCR of colistin resistance genes (mcr-1 to mcr-3) in animal manure and agricultural soil in Northern Italy

Introduction: The presence of antimicrobials, such as colistin, in animal manure may promote the dissemination of plasmid-mediated colistin resistance (mcr genes) into the environment. Objectives: To assess resistance to colistin mediated by mcr genes in soil fertilized with manure from intensive animal farms. Aim: To provide qualitative data for mcr-1 to mcr-3 genes in manure and soil using a real-time PCR approach. Methods: A total of 84 samples (1 sample of manure/slurry; 1 sample of soil before fertilization, T0; and 1 sample of soil about 30 days after fertilization, T30 per farm) collected from dairy (n = 11), swine (n = 10) and chicken (n = 7) farms were analysed by real-time PCR. Results: Mcr-1, mcr-2 and mcr-3 genes were detected in all three farms and samples. In swine farms, all 3 mcr genes (i.e. 5 slurry, 2 T0 and 3 T30 for mcr-1; 3 slurry for mcr-2; 3 slurry, 2 T0 and 2 T30 for mcr-3) were detected. In chicken and dairy farms, only mcr-1 (i.e. 3 manure in dairy, and 3 T0 and 1 T30 in chicken) and mcr-3 genes (i.e. 2 manure in dairy, and 1 manure and 1 T0 in chicken) were found. Mcr-1 was the most prevalent gene (20%), followed by mcr-3 (13%) and mcr-2 (3.5%). Conclusions: The presence of mcr genes into the environment, following fertilization with animal manure, may be of concern for public health since colistin is considered as last therapeutic option for treating severe human infections.