Table 1.
Patient age, gender and source of isolates used in this study.
Figure 1.
Overview of the genome of S. pseudopneumoniae IS7493.
(a) Representation of the S. pseudopneumoniae IS7493 circular genome. The inner circles represent GC content (outer) and GC bias (innermost). (b) Full assembly revealed the presence of plasmid pDRPIS7493.
Figure 2.
Comparative genome analysis of S .pseudopneumoniae IS7493 with the selected closely related streptococci.
(s) Whole genome phylogenetic tree of selected VGS isolates (Neighbor joining) generated using CVTree [16]. The branch lengths are representative of phylogenetic distance. Color legend for asterisks: blue, Mitis group; black, Mutans group; purple, Thermophilus group; green, Pyogenic group; and red, Bovis group. (b) Summary statistics for the genome comparison of S. pseudopneumoniae IS7493 with the closely related S. pneumoniae R6 and S.mitis NCTC12261. The CDS that are not accounted for in this comparison coded for hypothetical proteins.
Table 2.
CBPs in S. pseudopneumoniae IS7493, S. mitis and S. pneumoniae.
Table 3.
Cell wall anchor proteins in S. pseudopneumoniae IS7493.
Table 4.
Structure of the neuraminidase operon in S. pseudopneumoniae IS7493.
Figure 3.
S. pseudopneumoniae cholin binding domain protein sequence of autolysin (LytA).
VGS LytA proteins have been classified into typical and atypical categories based on residue 317 and presence/absence of Thr290-Gly291. Blue: functional amidase in presence of bile; Red: non-functional amidase in presence of bile; SM: S. mitis; SPN: S. pneumoniae; SPPN: S. pseudopneumoniae. Four SPPN clinical isolates are included. LytA alleles (.1&.2) refer to loci SPPN_05425 and SPPN_09835, respectively. The multiple sequence alignment was generated with the Multiple Sequence Comparison by Log- Expectation (MUSCLE) algorithm [22], [23]. * denote sequence identity and . denote sequence similarity at the bottom of the figure. In bold: LytA protein sequences of S. pseudopneumoniae IS7493.
Table 5.
Summary of the MICs for the S. pseudopneumoniae isolates of this study with interpretation based on CLSI breakpoints for S. pneumoniae.
Figure 4.
S. pseudopneumoniae competence stimulating peptide (CSP) sequences (leader and mature peptide region sequence is shown).
According to the classification by Whatmore et al. [21], S. pseudopneumoniae encodes a type 6.1 CSP. SM: S. mitis; SPN: S. pneumoniae; SPPN: S. pseudopneumoniae; SO: S. oralis. The multiple sequence alignment was generated with the Multiple Sequence Comparison by Log- Expectation (MUSCLE) algorithm [22], [23]. In bold: CSP sequences of S. pseudopneumoniae IS7493.
Figure 5.
Summary of the genetic architecture of the competence locus that distinguish three homologous competence systems from one-another.
Blp: Bacteriocin like peptide. Cib: Competence induced bacteriocin.