Whole Genome Sequencing And Comparative Genome Analysis Of Streptococcus Suis

Streptococcus suis is an important swine pathogen, causing economic loss in swine industry worldwide, and is also a threat to human health. It can lead to various syndromes such as meningitis, septicaemia, arthritis, endocarditis and abortion in pig. Human infections occur sporadically, though several outbreaks were reported. Thirty-three serotypes of S. suis have been described (types 1 to 31,33, and 1/2), and although serotype 2 is more associated with pathogenicity than others, infections of other serotypes can also occur. To date, virulence factors of S. suis are not fully identified, and the mechanism of pathogenesis and process of interaction with hosts remain unclear. In addition, the essential differences between highly virulent strains and strains of low virulence, and the genetic foundation of serotypic diversity are not characterized. Therefore, there is a great need to provide more genetic maps, in order to promote the function study of S. suis. To better understand pathogenesis, drug resistance mechanism and phylogeny among different serotypes on the genome level, we finished the following works:1. Whole genome of 8 S. suis isolated strains were sequenced, assembled and gap-filled, and 7 complete genome sequences were obtained. All 8 genomes were fully annotated and deposited in GenBank database. The 8 strains include serotypes of 1/2,1,2,3,7,9, and 14, besides, one strain with multi-drug resistance (R61) could not be assigned to any serotype. The size of the sequenced strains range from 2,034,321 bp to 2,183,059 bp, and no plasmid was identified. Pseudogenes and truncated genes were found in each strain, reflecting their role in environment adaptation.2. published S. suis genome sequences were downloaded from GenBank database, and analyzed together with the sequenced strains. Multiple sequence alignment of 13 complete genomes revealed that rearrangements and inversions occurred. According to colinearity of the 13 genomes, they can be roughly classified into 3 categories, serotype 2 strain except BM207, serotype 1/2 strain and serotype 14 strain are in one group, synteny between BM407, D12 and ST1 are in the second, and D9 and ST3 are the third.3. All CDSs for the 13 complete genomes were extracted and grouped into orthologous clusters, then gene numbers for core and pan-genome were calculated and extrapolated to a decaying function, and the result shows that final core genome size for S. suis would be 1126, and the pan-genome is open, which means that even if many genomes are added,82 new genes on average will still be introduced into the pan-genome.4. We used two methods to investigate the phylogenetic relationships among different serotypes, one of which was based on gene presence or absence among different strains and the other approach utilized the concatenated sequence of all single-copy core genes with exactly identical length from the 13 complete genomes. Except for serotype 14 strain JS14 and serotype 1/2 strain SS12, non-serotype 2 strains appeared to be phylogenetically distinct from serotype 2 strains and could be assigned into a common clade. In this clade, serotype 7 strain D9 and serotype 3 strain ST3 were more closely related than any other pairs.5. Comparative analysis between strains of high and low virulence identified several genes that are present in virulent strains but absent in less virulent strains, and they are mainly located in the previously identified 89k pathogenic island. This confirms that 89k PAI may play an important role in pathogenicity of S. suis. Integrative site of 89k PAI was also found, and may explain the transfer mechanism of this genetic area.6. In addition, comparative genome analysis between multi-drug resistance strain R61 and fully sensitive strain A7 identified some genes conferring resistance to antibiotics. Mechanisms of antibiotic resistance in this strain can be sorted into three patterns, alternation of target site, target protection and drug efflux to reduce accumulation. Moreover, the result indicated that horizontal gene transfer significantly contribute to antibiotic resistance in S. suis.