Streptococcus suis: predicting pathogenicity with virulence-associated genes?

A recent publication in Porcine Health Management by April Estrada, from the Gebhart lab at the University of Minnesota, proposes new virulence-associated genes to predict the pathogenicity of US Streptococcus suis. This project continues her previous work on the classification of US S. suis strains based on pathotypes.

Streptococcus suis is the cause of neurological disease and other associated clinical signs that are well known in swine farms around the world. Some Canadian strains have been studied extensively suggesting that specific genes (epfmrp, and sly) and serotypes could lead to increased virulence. However, the variability in clinical presentations between regions has prevented researchers from finding a consensus on markers that could help predict the pathogenicity of a specific Streptococcus suis strain.

Two hundred and eight strains of Streptococcus suis were used in this project. They were divided into three categories based on their clinical presentation: pathogenic, possibly opportunistic, and commensal. A virulence-associated gene (VAG) profiling was completed for all strains and a heatmap of presence/absence of genes was created. Statistical analysis allowed the researchers to identify new VAGs. Once the proposed VAGs were identified, they validated their findings with another set of 32 Streptococcus suis strains.

When looking at the historical VAGs (epfmrp, and sly), the researchers found that the majority of isolates, even those of the pathogenic pathotype, lacked at least one of the three genes. However, all the isolates that did have the three VAGs were classified as pathogenic.

Virulence-associated gene (VAG) profiling of 208 S. suis isolates. Heatmap illustrating the presence and absence of 71 previously published VAGs in 208 isolates.

Two VAGs were identified: ofs and srtF. Over 95% (≥ 132/139) of the pathogenic isolates presented both genes and were considered as predictors of pathogenicity. Only 23% (5/22) of the commensal pathotype contained both genes. The proposed pathogenic genotype for predicting pathogenicity was further tested in a validation set consisting of 32 S. suis isolates originating from a different production company. The ofs+/srtF+ genotype was observed in 73.7% (14/19) of the isolates classified as pathogenic.

A phylogenetic tree was created by pan-genome analysis to illustrate relationships between gene clusters and production companies of origin, showing the variability between strains.

For more analysis on the genetic variability among pathogenic strains, read the full article on the journal website.


Background: There is limited information on the distribution of virulence-associated genes (VAGs) in U.S. Streptococcus suis isolates, resulting in little understanding of the pathogenic potential of these isolates. This lack also reduces our understanding of the epidemiology associated with S. suis in the United States and thus affects the efficiency of control and prevention strategies. In this study we applied whole genome sequencing (WGS)-based approaches for the characterization of S. suis and identification of VAGs.

Results: Of 208 S. suis isolates classified as pathogenic, possibly opportunistic, and commensal pathotypes, the genotype based on the classical VAGs (epfmrp, and sly encoding the extracellular protein factor, muramidase-release protein, and suilysin, respectively) was identified in 9% (epf+/mrp+/sly+) of the pathogenic pathotype. Using the chi-square test and LASSO regression model, the VAGs ofs (encoding the serum opacity factor) and srtF (encoding sortase F) were selected out of 71 published VAGs as having a significant association with pathotype, and both genes were found in 95% of the pathogenic pathotype. The ofs+/srtF+ genotype was also present in 74% of ‘pathogenic’ isolates from a separate validation set of isolates. Pan-genome clustering resulted in the differentiation of a group of isolates from five swine production companies into clusters corresponding to clonal complex (CC) and virulence-associated (VA) genotypes. The same CC-VA genotype patterns were identified in multiple production companies, suggesting a lack of association between production company, CC, or VA genotype.

Conclusions: The proposed ofs and srtF genes were stronger predictors for differentiating pathogenic and commensal S. suis isolates compared to the classical VAGs in two sets of U.S. isolates. Pan-genome analysis in combination with metadata (serotype, ST/CC, VA genotype) was illustrated to be a valuable subtyping tool to describe the genetic diversity of S. suis.

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