Genome Sequencing and Comparative Analysis ofKlebsiella pneumoniaeNTUH-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.

PecS regulates the urate-responsive expression of type 1 fimbriae in Klebsiella pneumoniae CG43

“…1 shows that the gene organization of the divergently transcribed pecS and pecM clustered with type 1 and type 3 fimbriae-coding genes could be identified in the clinical isolates K. pneumoniae CG43, NTUH-K2044 (Wu et al, 2009) and MGH 78578 (Liao et al, 2011), and the plant endophyte K. pneumoniae 342 (Fouts et al, 2008). K. pneumoniae PecS contained the characteristic N-terminal helical segment and the four residues W17, D61, W68 and R94 implicated in urate binding (Perera & Grove, 2010), and shared a sequence identity of 43, 47 and 40 %, respectively, with the PecS of S. coelicolor, A. tumefaciens and D. dadantii.…”

wzi Gene Sequencing, a Rapid Method for Determination of Capsular Type for Klebsiella Strains

“…wzi is one of the few genes present in the capsular polysaccharide cluster of all capsular types of K. pneumoniae. The alignment of previously published capsular polysaccharide cluster sequences (17,25,26,41,42) allowed us to identify within the wzi gene a region of high sequence variability flanked by conserved motifs that are suitable for primer design. The 78 K-type reference strains, including strain A1517 (17), were analyzed by PCR using the primers wzi_ for2 and wzi_rev.…”

Survival in amoeba—a major selection pressure on the presence of bacterial copper and zinc resistance determinants? Identification of a “copper pathogenicity island”

“…Transfer of such plasmids has resulted in a nosocomial outbreak of Klebsiella pneumoniae (Sandegren et al 2012). Moreover, the pco/sil cluster has been identified on pAPEC-O2-R plasmids from avian pathogenic E. coli (Johnson et al 2005), R478 from Serratia marcescens (Gilmour et al 2004), plasmids pK2044 and pLVPK from K. pneumoniae strains (Chen et al 2004;Wu et al 2009), and on the chromosome or plasmids of many pathogenic enteric bacteria such as ETEC H10407 (Crossman et al 2010) and EHEC O104:H4 (Hobman and Crossman The illustrated function of each sil and pco gene product within the operon (Gram-negative) is deduced from homology modeling. The transcription of Pco proteins PcoABCDEFG appears to be regulated by PcoRS (left).…”