Co-occurrence of three different plasmids in an extensively drug-resistant hypervirulent Klebsiella pneumoniae isolate causing urinary tract infection

•Strain XJ-K1 was an extensively drug-resistant hypervirulent Klebsiella pneumoniae.•Strain XJ-K1 co-harboured one pLVPK-like virulence plasmid and two MDR plasmids.•ST11 strain XJ-K1 harboured aadA2, sul1, mph(A), dfrA12, rmtB, blaKPC-2, blaTEM-1, blaCTX-M-65, blaSHV-12, fosA and fosA3. A single carbapenem-resistant, hypervirulent Klebsiella pneumoniae strain has attracted major public concern. The aim of the present study was to better understand the antimicrobial resistance and genetic characteristics of Klebsiella pneumoniae strain XJ-K1. Klebsiella pneumoniae strain XJ-K1 was isolated from a urine specimen of a 69-year-old male patient in a teaching hospital in Shanghai, China, in January 2018. Antimicrobial susceptibility testing, string test, whole-genome sequencing, bioinformatics analysis and phylogenetic analysis were performed in this study. Klebsiella pneumoniae XJ-K1 was an extensively drug-resistant (XDR) hypervirulent strain that showed high-level resistance to antibacterial agents. Three novel plasmids were discovered in strain XJ-K1, including a 207,409-bp IncHI1B-type rmpA2-bearing pLVPK-like virulence plasmid, a 130,628-bp Col156/IncFIB/IncFII-type aadA2-, sul1-, mph(A)- and dfrA12-bearing MDR plasmid, and a 99,408-bp IncFII/IncR-type blaKPC-2-, blaTEM-1-, blaCTX-M-65-, blaSHV-12-, rmtB- and fosA3-bearing MDR plasmid. Sequence analysis of the chromosome revealed that the aadA2, fosA and sul1 genes were harboured by XJ-K1. Multilocus sequence typing (MSLT) showed that XJ-K1 was ST11. A large number of resistance genes and a pLVPK-like virulence plasmid carried by Klebsiella pneumoniae strain XJ-K1 might be the main reasons leading to the XDR and hypervirulent phenotype. To the best of our knowledge, this is the first report in China on the co-occurrence of a pLVPK-like virulence plasmid and two MDR plasmids in a single ST11 XDR and hypervirulent Klebsiella pneumoniae isolated from patient urine, which is a serious concern for its further spread.