Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis

Abstract

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.

FIG. 1.

Genomic maps of the K. pneumoniae NTUH-K2044 chromosome and plasmid. From the outside in, the first and second circles show the predicted protein-encoding regions on the plus and minus strands, by role, using the colors for the COG functional categories (http://www.ncbi.nlm.nih.gov/COG/grace/fiew.cgi). The third circle shows the GC skew. The fourth circle shows the transposases/transposons (blue), integrases/recombinases (green), and insertion sequences (red). The fifth and sixth circles show tRNAs and rRNAs, respectively.

FIG. 2.

Hierarchical cluster analysis of clinical isolates based on GSA with 813 genomic DNA probes. Three major groups of K. pneumoniae can be discerned based on the absence of hybridization signals for shotgun subclone probes. Group 1 strains gave signals for almost all the probes, suggesting that their sequences are nearly identical to that of the reference strain, NTUH-K2044. On the other hand, group 2 strains displayed a loss of signals for various chromosomal and plasmid probes. Three isolates (NK8, NK10, and NK5) are separated from group 1 and group 2; these isolates were classified in group 3.

FIG. 3.

Linear representation of the NTUH-K2044 genome and hybridization patterns of K. pneumoniae isolates. Deviation from the average G+C content of the sequence is shown for the chromosomal (A) and plasmid (B) sequences. The absence of a signal (deletion) for each probe is indicated by a colored vertical line. The locations of the seven INDELs in the chromosome, whose sequences are not present in the group 2 and group 3 strains, are indicated.