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Comparative Genomic Analyses of Streptococcus pseudopneumoniae Provide Insight into Virulence and Commensalism Dynamics.

Shahinas D, Thornton CS, Tamber GS, Arya G, Wong A, Jamieson FB, Ma JH, Alexander DC, Low DE, Pillai DR - PLoS ONE (2013)

Bottom Line: Although the pathogenic potential of S. pseudopneumoniae remains uncertain, it is most commonly isolated from patients with underlying medical conditions, such as chronic obstructive pulmonary disease.Analysis of gene content reveals numerous unique features that distinguish S. pseudopneumoniae from other streptococci.Additionally, the presence of several virulence factors and antibiotic resistance mechanisms suggest the potential of this commensal species to become pathogenic or to contribute to increasing antibiotic resistance levels seen among the VGS.

View Article: PubMed Central - PubMed

Affiliation: Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.

ABSTRACT
Streptococcus pseudopneumoniae (SPPN) is a recently described species of the viridans group streptococci (VGS). Although the pathogenic potential of S. pseudopneumoniae remains uncertain, it is most commonly isolated from patients with underlying medical conditions, such as chronic obstructive pulmonary disease. S. pseudopneumoniae can be distinguished from the closely related species, S. pneumoniae and S. mitis, by phenotypic characteristics, including optochin resistance in the presence of 5% CO2, bile insolubility, and the lack of the pneumococcal capsule. Previously, we reported the draft genome sequence of S. pseudopneumoniae IS7493, a clinical isolate obtained from an immunocompromised patient with documented pneumonia. Here, we use comparative genomics approaches to identify similarities and key differences between S. pseudopneumoniae IS7493, S. pneumoniae and S. mitis. The genome structure of S. pseudopneumoniae IS7493 is most closely related to that of S. pneumoniae R6, but several recombination events are evident. Analysis of gene content reveals numerous unique features that distinguish S. pseudopneumoniae from other streptococci. The presence of loci for competence, iron transport, pneumolysin production and antimicrobial resistance reinforce the phylogenetic position of S. pseudopneumoniae as an intermediate species between S. pneumoniae and S. mitis. Additionally, the presence of several virulence factors and antibiotic resistance mechanisms suggest the potential of this commensal species to become pathogenic or to contribute to increasing antibiotic resistance levels seen among the VGS.

No MeSH data available.


Related in: MedlinePlus

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.
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pone-0065670-g004: 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.

Mentions: The divergence and genetic diversity seen in the Mitis group streptococci are thought to be primarily driven by horizontal gene transfer [54], [55]. In S. pneumoniae, induction of the competent state occurs when the extracellular concentration of the competence stimulating peptide (CSP) reaches a critical level and is sensed by the two component regulatory system ComDE, a histidine kinase receptor and a response regulator, encoded by comD and comE, respectively [56], [57]. Two allelic variants dominate amongst S. pneumoniae, comC1 and comC2, resulting in two clinically dominating pherotypes producing CSP-1 and CSP-2, respectively [21], [58]. Induction of competence by CSP is restricted by ComD receptor recognition and therefore, among pneumococci, competence is typically restricted to occur within one pherotype [59]. The comC gene, encoding CSP, is polymorphic within the pneumoniae-mitis-pseudopneumoniae cluster [2]. According to a pherotype classification scheme introduced by Whatmore et al. [21], the four S. pseudopneumoniae isolates encode a type 6.1 CSP, which has been previously observed among S. pneumoniae isolates, but not among S. mitis isolates (Figure 4). Apart from type 6.1 CSP, which is the most common pherotype observed for S. pseudopneumoniae, Leung et al. found two more pherotypes associated with S. pseudopneumoniae, CSP6.3 and SK674 [20]. A distinct signature sequence in the CSP leader peptide has been observed for each of the phylogenetic clusters [2]. The S. pseudopneumoniae IS7493 genome contains all the genes that make up the competence machinery apart from the late competence protein ComGE, the function of which remains unclear. In addition, S. pseudopneumoniae IS7493 harbors the gene that encodes the immunity factor ComM, thought to protect competent cells from their own lysins [60].


Comparative Genomic Analyses of Streptococcus pseudopneumoniae Provide Insight into Virulence and Commensalism Dynamics.

Shahinas D, Thornton CS, Tamber GS, Arya G, Wong A, Jamieson FB, Ma JH, Alexander DC, Low DE, Pillai DR - PLoS ONE (2013)

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.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3686770&req=5

pone-0065670-g004: 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.
Mentions: The divergence and genetic diversity seen in the Mitis group streptococci are thought to be primarily driven by horizontal gene transfer [54], [55]. In S. pneumoniae, induction of the competent state occurs when the extracellular concentration of the competence stimulating peptide (CSP) reaches a critical level and is sensed by the two component regulatory system ComDE, a histidine kinase receptor and a response regulator, encoded by comD and comE, respectively [56], [57]. Two allelic variants dominate amongst S. pneumoniae, comC1 and comC2, resulting in two clinically dominating pherotypes producing CSP-1 and CSP-2, respectively [21], [58]. Induction of competence by CSP is restricted by ComD receptor recognition and therefore, among pneumococci, competence is typically restricted to occur within one pherotype [59]. The comC gene, encoding CSP, is polymorphic within the pneumoniae-mitis-pseudopneumoniae cluster [2]. According to a pherotype classification scheme introduced by Whatmore et al. [21], the four S. pseudopneumoniae isolates encode a type 6.1 CSP, which has been previously observed among S. pneumoniae isolates, but not among S. mitis isolates (Figure 4). Apart from type 6.1 CSP, which is the most common pherotype observed for S. pseudopneumoniae, Leung et al. found two more pherotypes associated with S. pseudopneumoniae, CSP6.3 and SK674 [20]. A distinct signature sequence in the CSP leader peptide has been observed for each of the phylogenetic clusters [2]. The S. pseudopneumoniae IS7493 genome contains all the genes that make up the competence machinery apart from the late competence protein ComGE, the function of which remains unclear. In addition, S. pseudopneumoniae IS7493 harbors the gene that encodes the immunity factor ComM, thought to protect competent cells from their own lysins [60].

Bottom Line: Although the pathogenic potential of S. pseudopneumoniae remains uncertain, it is most commonly isolated from patients with underlying medical conditions, such as chronic obstructive pulmonary disease.Analysis of gene content reveals numerous unique features that distinguish S. pseudopneumoniae from other streptococci.Additionally, the presence of several virulence factors and antibiotic resistance mechanisms suggest the potential of this commensal species to become pathogenic or to contribute to increasing antibiotic resistance levels seen among the VGS.

View Article: PubMed Central - PubMed

Affiliation: Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.

ABSTRACT
Streptococcus pseudopneumoniae (SPPN) is a recently described species of the viridans group streptococci (VGS). Although the pathogenic potential of S. pseudopneumoniae remains uncertain, it is most commonly isolated from patients with underlying medical conditions, such as chronic obstructive pulmonary disease. S. pseudopneumoniae can be distinguished from the closely related species, S. pneumoniae and S. mitis, by phenotypic characteristics, including optochin resistance in the presence of 5% CO2, bile insolubility, and the lack of the pneumococcal capsule. Previously, we reported the draft genome sequence of S. pseudopneumoniae IS7493, a clinical isolate obtained from an immunocompromised patient with documented pneumonia. Here, we use comparative genomics approaches to identify similarities and key differences between S. pseudopneumoniae IS7493, S. pneumoniae and S. mitis. The genome structure of S. pseudopneumoniae IS7493 is most closely related to that of S. pneumoniae R6, but several recombination events are evident. Analysis of gene content reveals numerous unique features that distinguish S. pseudopneumoniae from other streptococci. The presence of loci for competence, iron transport, pneumolysin production and antimicrobial resistance reinforce the phylogenetic position of S. pseudopneumoniae as an intermediate species between S. pneumoniae and S. mitis. Additionally, the presence of several virulence factors and antibiotic resistance mechanisms suggest the potential of this commensal species to become pathogenic or to contribute to increasing antibiotic resistance levels seen among the VGS.

No MeSH data available.


Related in: MedlinePlus