Epidemiology and Genomics Features of Klebsiella spp especially ST11-K64 CR-hvKP Outbreaks

We report an outbreak of carbapenemase-producing hypervirulent Klebsiella pneumoniae in two hospitals which had frequent patients transfers. Nanopore coupled illumina sequencing completed the genome of these strains. There are 12 single nucleotide polymorphisms, indicating that they are of the same cluster, and the inter-hospital transmission of infection. Molecular typing of the isolates showed that they belonged to ST11-K64 strains. Five plasmids were assembled in each of those strains. One plasmid carried a few virulence genes, including capsular polysaccharide regulator rmpA and rmpA2. Another two carried antimicrobial resistance genes including carbapenem resistant blaKPC2. Comparative genomics analysis indicated that there are frequent and rapid genomic content gain and loss along transmissions and co-exist of those progeny strains at the same ward. A 10 kb fragment carrying antimicrobial resistance genes flanked by insert sequences was found lost in plasmid of strain KP20194c in patient 3, which most possibly infected patient 4 later. However, the 10 kb fragment-store strains could also be isolated from the ward environment at the same time, which harbor different chromosome indels. Tn1721 and multiple other insert sequence mediated transpositions were also seen. These results indicated that there is a fast reshaping and diversified genomic pool of Klebsiella pneumoniae facilitated by mobile genetic elements even in short time outbreaks. The ST11-K64 CR-hvKP strains may become new significant superbugs threating public health.