Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis.
Nosocomial infections caused by antibiotic-resistant Klebsiella pneumoniae are emerging as a major health problem worldwide, while community-acquired K. pneumoniae infections present with a range of diverse clinical pictures in different geographic areas. In particular, an invasive form of K. pneumoniae that causes liver abscesses was first observed in Asia and then was found worldwide. We are interested in how differences in gene content of the same species result in different diseases. Thus, we sequenced the whole genome of K. pneumoniae NTUH-K2044, which was isolated from a patient with liver abscess and meningitis, and analyzed differences compared to strain MGH 78578, which was isolated from a patient with pneumonia. Six major types of differences were found in gene clusters that included an integrative and conjugative element, clusters involved in citrate fermentation, lipopolysaccharide synthesis, and capsular polysaccharide synthesis, phage-related insertions, and a cluster containing fimbria-related genes. We also conducted comparative genomic hybridization with 15 K. pneumoniae isolates obtained from community-acquired or nosocomial infections using tiling probes for the NTUH-K2044 genome. Hierarchical clustering revealed three major groups of genomic insertion-deletion patterns that correlate with the strains' clinical features, antimicrobial susceptibilities, and virulence phenotypes with mice. Here we report the whole-genome sequence of K. pneumoniae NTUH-K2044 and describe evidence showing significant genomic diversity and sequence acquisition among K. pneumoniae pathogenic strains. Our findings support the hypothesis that these factors are responsible for the changes that have occurred in the disease profile over time.
Wu
Keh-Ming
KM
Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan.
Li
Ling-Hui
LH
Yan
Jing-Jou
JJ
Tsao
Nina
N
Liao
Tsai-Lien
TL
Tsai
Hui-Chi
HC
Fung
Chang-Phone
CP
Chen
Hsiang-Ju
HJ
Liu
Yen-Ming
YM
Wang
Jin-Tung
JT
Fang
Chi-Tai
CT
Chang
Shan-Chwen
SC
Shu
Hung-Yu
HY
Liu
Tze-Tze
TT
Chen
Ying-Tsong
YT
Shiau
Yih-Ru
YR
Lauderdale
Tsai-Ling
TL
Su
Ih-Jen
IJ
Kirby
Ralph
R
Tsai
Shih-Feng
SF
D001483:Base Sequence; D016000:Cluster Analysis; D017714:Community-Acquired Infections / Q000382:microbiology; D055028:Comparative Genomic Hybridization; D003428:Cross Infection; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics*; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D007710:Klebsiella Infections / Q000382:microbiology; D007711:Klebsiella pneumoniae / Q000235:genetics* / Q000302:isolation & purification; D008100:Liver Abscess / Q000382:microbiology; D008581:Meningitis / Q000382:microbiology; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA
D004269:DNA, Bacterial