Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential

Niels A. Zondervan,Maria Suarez-Diez,Edoardo Saccenti,Vitor A. P. Martins dos Santos

doi:10.1186/s12864-021-07388-6

Abstract

BackgroundStaphylococcus and Streptococcus species can cause many different diseases, ranging from mild skin infections to life-threatening necrotizing fasciitis. Both genera consist of commensal species that colonize the skin and nose of humans and animals, and of which some can display a pathogenic phenotype.ResultsWe compared 235 Staphylococcus and 315 Streptococcus genomes based on their protein domain content. We show the relationships between protein persistence and essentiality by integrating essentiality predictions from two metabolic models and essentiality measurements from six large-scale transposon mutagenesis experiments. We identified clusters of strains within species based on proteins associated to similar biological processes. We built Random Forest classifiers that predicted the zoonotic potential. Furthermore, we identified shared attributes between of Staphylococcus aureus and Streptococcus pyogenes that allow them to cause necrotizing fasciitis.ConclusionsDifferences observed in clustering of strains based on functional groups of proteins correlate with phenotypes such as host tropism, capability to infect multiple hosts and drug resistance. Our method provides a solid basis towards large-scale prediction of phenotypes based on genomic information.

Highlights

Staphylococcus and Streptococcus species can cause many different diseases, ranging from mild skin infections to life-threatening necrotizing fasciitis
Few comparative genomic studies have been performed to analyse the evolution and the pathogenesis of Staphylococcus and Streptococcus species: the comparisons of the genomes of 11 Staphylococcus species determined that horizontal gene transfer of virulence factors is an important factor in adaptation of S. aureus to humans [6]; another study showed that protein domain based metabolic diversity among Streptococcus species could be used to identify differences in the metabolism of the highly pathogenic serotype 2 S. suis compared to other Streptococci [7]
We found that both S. aureus and S. pyogenes contain proteins involved in fibronectin binding, wound invasion, haemolysis, cell adhesion, Immunoglobulin A (IgA) and Immunoglobulin G (IgG) binding, multipletoxins as well as proteins involved in resisting phagocytosis and invading host cells (Table 3, Fig. 5)

Summary

Introduction

Staphylococcus and Streptococcus species can cause many different diseases, ranging from mild skin infections to life-threatening necrotizing fasciitis Both genera consist of commensal species that colonize the skin and nose of humans and animals, and of which some can display a pathogenic phenotype. Few comparative genomic studies have been performed to analyse the evolution and the pathogenesis of Staphylococcus and Streptococcus species: the comparisons of the genomes of 11 Staphylococcus species determined that horizontal gene transfer of virulence factors is an important factor in adaptation of S. aureus to humans [6]; another study showed that protein domain based metabolic diversity among Streptococcus species could be used to identify differences in the metabolism of the highly pathogenic serotype 2 S. suis compared to other Streptococci [7]. At the best of our knowledge, no work exists focusing on similarities and differences within and between Staphylococcus and Streptococcus genomes

Methods

Results

Discussion

Conclusion