Emergence of IncX4 plasmids encoding mcr-1 in a clinical isolate of Klebsiella pneumoniae in Japan

•A colistin-resistant sequence type 1296 Klebsiella pneumoniae isolate harboring mcr-1 was isolated in a hospital in Japan.•Pulsed-field gel electrophoresis and Southern hybridization revealed that mcr-1 was located on a 33-kb plasmid.•The complete genome of the mcr-1 harboring plasmid with the size of 33kb was determined; the plasmid incompatibility was IncX4.•This is the first report of a K. pneumoniae clinical isolate harboring mcr-1 in Japan. The mcr-1 gene encodes a phosphoethanolamine transferase that confers resistance to colistin by transferring phosphoethanolamine to lipid A. A 33-kb IncX4 plasmid harboring mcr-1 was detected in a Klebsiella pneumoniae isolate and two Escherichia coli isolates, and a 66-kb IncI2 plasmid was detected in three E. coli isolates in hospitals in Okinawa, Japan.