In vitro transcriptome analysis of two Chinese isolates of Streptococcus suis serotype 2

Abstract

The Streptococcus suis serotype 2 (S. suis 2) isolates 05ZYH33 and 98HAH33 have caused severe human infections in China. Using a strand-specific RNA-seq analysis, we compared the in vitro transcriptomes of these two Chinese isolates with that of a reference strain (P1/7). In the 89K genomic island that is specific to these Chinese isolates, a toxin-antitoxin system showed relatively high levels of transcription among the S. suis. The known virulence factors with high transcriptional activity in these two highly-pathogenic strains are mainly involved in adhesion, biofilm formation, hemolysis and the synthesis and transport of the outer membrane protein. Furthermore, our analysis of novel transcripts identified over 50 protein-coding genes with one of them encoding a toxin protein. We also predicted over 30 small RNAs (sRNAs) in each strain, and most of them are involved in riboswitches. We found that six sRNA candidates that are related to bacterial virulence, including cspA and rli38, are specific to Chinese isolates. These results provide insight into the factors responsible for the difference in virulence among the different S. suis 2 isolates.

Keywords: Novel transcripts; Streptococcus suis serotype 2; Transcriptome; Virulence factor; sRNA.

Figure 1

The pipeline for S. suis 2 transcriptome analysis Sequencing reads were first mapped to reference genome. Sequencing reads in genic region are used to calculate the expression levels of each gene, and then DEGs are identified among three isolates. Sequencing reads found in intergenic regions are used to define novel TARs, which are annotated based on homology analysis. DEG, differentially-expressed gene; TAR, transcriptionally-active region; GI, genomic island.

Figure 2

DEGs in the Chinese isolates shared a similar expression pattern In total 120 DEGs are shared by both Chinese isolates when compared with P1/7. The hierarchical heatmap (R package: pheatmap) illustrates transcriptional levels (log₂ ratios of RPKM, scale is shown at the bottom) for all the DEGs in three strains. The expression levels of DEGs in two Chinese isolates are more similar compared to P1/7.

Figure 3

COG analysis of homologous DEGs The pie chart showed the COG analysis for the classification of homologous DEGs in the 05ZYH33 and 98HAH33 isolates, compared to the P1/7 reference strain. The general categories are indicated on the outer circle and the subgroups are indicated in the inner circle with the number of genes belonging to each group listed.

Figure 4

Transcriptional activity of genes located in 89K GI of the Chinese isolates The histogram demonstrates the distribution of genes at different transcription level (RPKM values) for 98HAH33 (A) and 05ZYH33 (B). The group “RPKM <1” contains the highest number of genes, indicating the low transcriptional activity of 89K GI region during in vitro incubation of these isolates.