Genomic characteristics of clinical important ST11 Klebsiella pneumoniae worldwide.

BACKGROUND: ST11 Klebsiella pneumoniae is among the most important clinical pathogen in China, and KL47 and KL64 are the dominant K-types of these strains. Understanding the genomic characteristics of these strains would be critical to their anti-infection treatment. METHODS: 364 genome sequences of ST11 K. pneumoniae strains isolated from 13 countries from 2003 to 2018 were collected. These genome sequences included 338 downloaded from NCBI database and 26 newly sequenced. Phylogenic analysis, pan-genome and unique genes, resistance and virulence genes analysis were conducted to elucidate the molecular characteristics of these strains. RESULTS: A total of 19,732 genes were identified from the 364 ST11 strains, and the pan-genome was open, indicating the genetic diversity of ST11 K. pneumoniae. These strains were clustered into 3 clades. Clade 1 contained the most various K-types (14/15, 93.3%) and unique genes. KL47 and KL64 were the dominant K-types of clade 2 and clade 3, accounting for 100% and 99.4% of strains in each clade. KL64 strains contained the most virulence genes, including iucA and rmpA, and the two genes tend to coexist. In addition, strains in clade 1 were isolated from all 13 countries, and the strains in clade 2 and 3 mainly from China. CONCLUSION: ST11 K. pneumoniae strains of KL64 was becoming a newly emerged superbug with more resistance and virulence genes in China, which was significant different from other countries, and we should be alert the dissemination of this subclone.