Genome sequence of the hypervirulent ST65 Klebsiella pneumoniae isolate carrying mcr-8 from China

Abstract

Objective

In this study we report the complete genome sequence of a hypervirulent ST65 Klebsiella pneumoniae isolate harbouring mcr-8 from China. The aim was to investigate its molecular characteristics and resistance mechanisms.

Methods

Colistin-resistant hypervirulent K. pneumonia was isolated from an in-patient in China. The entire genome was sequenced on the Illumina NovaSeq 6000 System and long-read ONT Platform. De novo assembly was conducted using SPAdes and Unicycler. S1 nuclease pulsed-field gel electrophoresis, Southern blot, and antimicrobial susceptibility testing were performed. Sequence type, antimicrobial resistance, and virulence-related genes were predicted from the sequence. Circular maps of multiple plasmid comparisons were drawn by the BLAST Ring Image.

Results

The complete genome sequence of K. pneumoniae ACESH00926 consists of one chromosome and two plasmids. ACESH00926 belongs to K2 ST65 according to multilocus sequence typing. ACESH00926 also showed high resistance to colistin (MIC >8 µg/mL). Several ARGs were identified, including the mobile colistin-resistant gene, mcr-8, which was located in an IncFIl(K)/IncFIA(HI1)-type plasmid. The larger plasmid was a pK244-like virulence plasmid that carries a series of virulence genes, such as regulators of the mucoid phenotype (rmpA and rmpA2), salmochelin siderophore biosynthesis (iroB), ABC transporter (iroC), ferric aerobactin receptor (iutA), aerobactin siderophore biosynthesis protein (iucC), and aerobactin synthetase (iucA)-encoded genes, in addition to another plasmid carrying mcr-8 with a conserved genetic context (dgkA-sasA-copR-mcr-8-ccdA-ccdB-xerD-repE-parM-umuC-lexA-klcA).

Conclusions

The necessity of monitoring a combination of colistin-resistant and hypervirulent K. pneumoniae strains in the future is emphasised in this article.