A method to detect Escherichia coli carrying the colistin-resistance genes mcr-1 and mcr-2 using a single real-time polymerase chain reaction and its application to chicken cecal and porcine fecal samples

Colistin is one of the last-resort antibiotics for the treatment of multidrug-resistant infections in humans, but transmissible colistin-resistance genes have emerged in bacteria from animals. The rapid and sensitive detection among animals of colonization with bacteria carrying these genes is critical in helping to control further spread. Here we describe a method for broth enrichment of colistin-resistant Escherichia coli from animal fecal and cecal samples followed by real-time polymerase chain reaction (PCR) for the simultaneous detection of two of the main colistin-resistance genes, mcr-1 and mcr-2. The PCR uses a single set of nondegenerative primers, and mcr variants can be differentiated by melt-curve analysis. Overnight culture enrichment was effective for amplifying colistin-resistant E. coli, even when initially present in numbers as low as 10 bacteria per gram of sample. The mcr-1 and mcr-2 genes were not found in any of the Ontario swine and poultry samples investigated