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Updated: Oct 29, 2025
Genome-wide Gene Deletions in Streptococcus sanguinis by High Throughput PCR
Published on: November 23, 2012
Pangenome analysis and virulence profiling of Streptococcus intermedius
Dhiraj Sinha1,2, Xifeng Sun1,2, Mudra Khare1,2
1Aix-Marseille University, IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France.
Background:
Streptococcus intermedius, a member of the S. anginosus group, is a commensal bacterium present in the normal microbiota of human mucosal surfaces of the oral, gastrointestinal, and urogenital tracts. However, it has been associated with various infections such as liver and brain abscesses, bacteremia, osteo-articular infections, and endocarditis. Since 2005, high throughput genome sequencing methods enabled understanding the genetic landscape and diversity of bacteria as well as their pathogenic role. Here, in order to determine whether specific virulence genes could be related to specific clinical manifestations, we compared the genomes from 27 S. intermedius strains isolated from patients with various types of infections, including 13 that were sequenced in our institute and 14 available in GenBank.
Results:
We estimated the theoretical pangenome size to be of 4,020 genes, including 1,355 core genes, 1,054 strain-specific genes and 1,611 accessory genes shared by 2 or more strains. The pangenome analysis demonstrated that the genomic diversity of S. intermedius represents an "open" pangenome model. We identified a core virulome of 70 genes and 78 unique virulence markers. The phylogenetic clusters based upon core-genome sequences and SNPs were independent from disease types and sample sources. However, using Principal Component analysis based on presence/ absence of virulence genes, we identified the sda histidine kinase, adhesion protein LAP and capsular polysaccharide biosynthesis protein cps4E as being associated to brain abscess or broncho-pulmonary infection. In contrast, liver and abdominal abscess were associated to presence of the fibronectin binding protein fbp54 and capsular polysaccharide biosynthesis protein cap8D and cpsB.
Conclusions:
Based on the virulence gene content of 27 S. intermedius strains causing various diseases, we identified putative disease-specific genetic profiles discriminating those causing brain abscess or broncho-pulmonary infection from those causing liver and abdominal abscess. These results provide an insight into S. intermedius pathogenesis and highlights putative targets in a diagnostic perspective.
Insights
Specific virulence genes in Streptococcus intermedius strains correlate with distinct clinical outcomes, differentiating brain abscesses from liver abscesses. This finding aids in understanding bacterial pathogenesis and potential diagnostics.
Area of Science:
- Microbiology
- Genomics
- Infectious Diseases
Background:
- Streptococcus intermedius is a commensal bacterium with pathogenic potential.
- It is associated with serious infections like abscesses and bacteremia.
- Genomic sequencing has advanced understanding of bacterial virulence.
Purpose of the Study:
- To investigate the relationship between specific virulence genes and clinical manifestations of Streptococcus intermedius infections.
- To compare the genomes of 27 S. intermedius strains from diverse infections.
Main Methods:
- Whole-genome sequencing of 27 S. intermedius strains.
- Pangenome analysis to assess genomic diversity and identify core and accessory genes.
- Principal Component Analysis (PCA) to correlate virulence gene presence/absence with clinical data.
Main Results:
- The S. intermedius pangenome is characterized as 'open' with significant genomic diversity.
- A core virulome of 70 genes and 78 unique virulence markers were identified.
- Specific genes (sda, LAP, cps4E) were linked to brain/broncho-pulmonary infections, while others (fbp54, cap8D, cpsB) were associated with liver/abdominal abscesses.
Conclusions:
- Distinct genetic profiles of virulence genes in S. intermedius correlate with specific disease types.
- These findings offer insights into S. intermedius pathogenesis.
- Identified genetic markers may serve as targets for future diagnostic tools.
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