Distinctive features gleaned from the comparative genomes analysis of clinical and non-clinical isolates of Klebsiella pneumoniae

Abstract

It is of interest to describe the distinctive features gleaned from the comparative genome analysis of clinical and non-clinical isolates of Klebsiella pneumoniae. The core genome of K. pneumoinae consisted of 3568 genes. Comparative genome analysis shows that mdtABCD, toxin-antitoxin systems are unique to clinical isolates and catB, benA, and transporter genes for citrate utilization are exclusive to non-clinical isolates. We further noted aromatic compound degrading genes in non-clinical isolates unlike in the later isolates. We grouped 88 core genes into 3 groups linked to infections, drug-resistance or xenobiotic metabolism using codon usage variation analysis. It is inferred using the neutrality plot analysis of GC12 with GC3 that codon usage variation is dominant over mutation pressure. Thus, we document data to distinguish clinical and non-clinical isolates of K. pneumoniae using comparative genomes analysis for understanding of genome diversity during speciation.

Keywords: Codon usage bias; Comparative genomics; Klebsiella pneumoniae.

Figure 1

Flowchart of the workflow

Figure 2

Phylogenetic tree constructed from the core genome of K. pneumoniae genomes. The scale bar, 0.01 corresponds to the substitution per amino acid within the coding regions of the core genome.

Figure 3

Core vs pan-genome development plot of K. pneumoniae genomes (EDGAR 2.2 software platform)

Figure 4

Dendogram showing the relationship between genomes based on the presence and absence of genes designated as group specific.

Figure 5

Cytoscape and GeneMANIA interaction network of known (a) clinical and (b) non-clinical unique core genes with co-expression and genetic interaction of other related genes. Nodes represent proteins and edges represent interactions between the nodes. Power law node-degree distribution of the networks in genes of clinical and non-clinical genomes (c and d). The node degree (k) is represented on the x-axis and number of nodes with a particular k is represented on the y-axis. The Pearson correlation coefficient values (r2) and the probability of degree distributions P(k) are shown. The red lines indicate the power law. The R-squared is computed on log values.

Figure 6

Visualizing common gene pools in five K. pneumoniae strains by Venn diagrams (EDGAR 2.2 software platform).

Figure 7

Neutrality plot of infection-related genes, drug resistance gene and xenobiotic metabolism genes of K. pneumoniae genome AWD5 (a-c), KP-1 (d-f), Kp342 (g-i), BA2146 (j-l), NK2044 (m-o). Individual genes are plotted based on the mean GC content in the first and second codon position (GC12) versus GC content of the third codon position (GC3).