Pangenome analysis and virulence profiling of Streptococcus intermedius

Dhiraj Sinha,Pierre-Edouard Fournier,Mudra Khare,Michel Drancourt,Didier Raoult,Xifeng Sun

doi:10.1186/s12864-021-07829-2

Abstract

BackgroundStreptococcus 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.ResultsWe 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.ConclusionsBased 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.

Highlights

Streptococcus intermedius belongs to the S. anginosus group (SAG) that includes S. constellatus and S. anginosus [1]
Patients with invasive S. intermedius infections were described to cause significantly longer hospital stays and higher mortality than patients with other S. anginosus group infections, suggesting that identifying this species might be important for the management of patients [8]
Extraction and genome sequencing The genomic DNA of each studied S. intermedius strain was extracted in two steps: a mechanical treatment was first performed using acid-washed glass beads (G4649-500 g Sigma) and a FastPrep BIO 101 instrument (Qbiogene, Strasbourg, France) at maximum speed (6.5) for 90 s. following a 2-hour lysozyme incubation at 37 °C, DNA was extracted using an EZ1 biorobot and the EZ1 DNA Tissue kit (Qiagen, Hilden, Germany)

Summary

Introduction

Streptococcus intermedius belongs to the S. anginosus group (SAG) that includes S. constellatus and S. anginosus [1] It is part of the normal oral cavity and upper respiratory tract floras, as well as those of the gastrointestinal and female urogenital tracts [2,3,4,5]. 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. It has been associated with various infections such as liver and brain abscesses, bacteremia, osteo-articular infections, and endocarditis.

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Results

Conclusion