Genomic characterisation of a blaKPC-2- and mcr-10-co-harbouring Enterobacter kobei isolate with high-level resistance to colistin and carbapenems

Abstract

The emergence and spread of colistin resistance in carbapenem-resistant Enterobacteriaceae pose a serious threat to human and animal health. This work aimed to characterize the genetic features of antimicrobial resistance of a carbapenem and colistin resistant Enterobacter kobei SCLZS19 from hospital sewage by using whole genome sequencing. Antimicrobial susceptibility tests were performed by using the disk diffusion method. Whole genome sequencing of SCLZS19 was carried out on the HiSeq 2000 combined with PacBio RSII platforms. Sequence type, plasmid incompatibility types, resistance genes, and insertion elements were identified using the MLST, PlasmidFinder, ResFinder, and ISfinder, respectively. Conjugation assays were performed using both broth- and filter-based methods with the azide-resistant Escherichia coli J53 as the recipient. The function of the mcr-9-like variant was determined by gene cloning. E. kobei SCLZS19 has a 4,862,177-bp circular chromosome, and nine circular plasmids ranging in size from 4,120 bp to 282,472 bp. It carries 11 antibiotic resistance genes (ARGs), and 10 of them are located on plasmids. The colistin resistance gene mcr-10 is located on a 118,766-bp non-transferable IncF (Y3:A-:B-) plasmid. The carbapenemase gene blaKPC-2 is carried by a self-transmissible IncP6 plasmid which is epidemic in China. In addition, SCLZS19 also carries a mcr-9-like variant on a IncHI2 (ST1) plasmid. Cloning assay shows that the mcr-9-like variant does not mediate colistin resistance in E. coli DH5α. The findings highlight that carbapenem- and colistin-resistant Enterobacterales from water environment may serve as a reservoir for clinically significant ARGs, and continuous surveillance is required.