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

Abstract

ABSTRACT: Objectives: The emergence and spread of colistin resistance in carbapenem-resistant Enterobacteriaceae pose a serious threat to human and animal health. This work aimed to characterise the genetic features of antimicrobial resistance of the carbapenem- and colistin-resistant Enterobacter kobei strain SCLZS19, isolated from hospital sewage, by using whole genome sequencing. Methods: Antimicrobial susceptibility tests were performed 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 multilocus sequence typing, 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. Results: E. kobei SCLZS19 had a 4 862 177-bp circular chromosome and nine circular plasmids ranging in size from 4120 bp to 282 472 bp. It carried 11 antibiotic resistance genes, and 10 of them were located on plasmids. The colistin resistance gene mcr-10 was located on a 118 766-bp non-transferable IncF (Y3:A-:B-) plasmid. The carbapenemase gene blaKPC-2 was carried by a self-transmissible IncP6 plasmid, which is epidemic in China. In addition, SCLZS19 also carried an mcr-9-like variant on a IncHI2 (ST1) plasmid. The cloning assay showed that the mcr-9-like variant did not mediate colistin resistance in E. coli DH5α. Conclusion: The findings highlight that carbapenem- and colistin-resistant Enterobacterales from water environments may serve as a reservoir for clinically significant antibiotic resistance genes, and continuous surveillance is required.

Keywords

• mcr-10
• blaKPC-2
• Enterobacter kobei
• XerC
• IncP6