Klebsiella pneumoniae is an opportunistic pathogen, which belongs to the Enterobacteriaceae. It is also one of the ESKAPE pathogens that exhibits antimicrobial resistance and nosocomial infections worldwide. More and more carbapenem-resistant Klebsiella pneumoniae (CRKP) and extended-spectrum β-lactamases (ESBLs) have been reported. The co-occurrence of hypervirulent and antibiotic-resistant strains has driven some of the recent studies. Some of the
Klebsiella pneumoniae clonal groups commonly cause outbreaks in hospital settings. The resistance mechanism of Klebsiella pneumoniae still needs to be further explored. In this thesis, I firstly provide a phenotypic epidemiology view of Klebsiella pneumoniae in a large tertiary hospital, China, covering a large longitudinal study. Secondly, in order to examine the population structure and drug resistance characteristics of Klebsiella pneumoniae in a larger sample size, whole genome sequencing (WGS) was performed on 3061 clinical isolates. A WGS
pairwise SNPs method was also established and used to define within-ward transmissions by low-endemic-risk clones. Further, particular attention has been paid to the mechanism of polymyxin (last line) resistance in our data. Last, but not least, genome-wide association analysis are used to find new resistance sites and mechanisms in big data of Klebsiella pneumoniae. In summary, in this thesis, I conducted a systematic study from phenotype to genotype and the association between the two.