Comparative genomic analysis of Streptococcus suis reveals significant genomic diversity among different serotypes

Abstract

BackgroundStreptococcus suis (S. suis) is a major swine pathogen and an emerging zoonotic agent. Serotypes 1, 2, 3, 7, 9, 14 and 1/2 are the most prevalent serotypes of this pathogen. However, almost all studies were carried out on serotype 2 strains. Therefore, characterization of genomic features of other serotypes will be required to better understand their virulence potential and phylogenetic relationships among different serotypes.ResultsFour Chinese S. suis strains belonging to serotypes 1, 7, 9 and 1/2 were sequenced using a rapid, high-throughput approach. Based on the 13 corresponding serotype strains, including 9 previously completed genomes of this bacterium, a full comparative genomic analysis was performed. The results provide evidence that (i) the pan-genome of this species is open and the size increases with addition of new sequenced genomes, (ii) strains of serotypes 1, 3, 7 and 9 are phylogenetically distinct from serotype 2 strains, but all serotype 2 strains, plus the serotype 1/2 and 14 strains, are very closely related. (iii) all these strains, except for the serotype 1 strain, could harbor a recombinant site for a pathogenic island (89 K) mediated by conjugal transfer, and may have the ability to gain the 89 K sequence.ConclusionsThere is significant genomic diversity among different strains in S. suis, and the gain and loss of large amount of genes are involved in shaping their genomes. This is indicated by (i) pairwise gene content comparisons between every pair of these strains, (ii) the open pan-genome of this species, (iii) the observed indels, invertions and rearrangements in the collinearity analysis. Phylogenetic relationships may be associated with serotype, as serotype 2 strains are closely related and distinct from other serotypes like 1, 3, 7 and 9, but more strains need to be sequenced to confirm this.

Restoration of Bioactive Lantibiotic Suicin from a Remnant lan Locus of Pathogenic Streptococcus suis Serotype 2

“…Yet, SuiR alone was able to activate P suiA transcription, though at low efficiency, as was also observed with BovR and SpaR (24,48). Interestingly, the genome of an S. suis serotype 9 strain isolated in China was recently sequenced and shown to contain an intact sui locus (SSUD12_1302-SSUD12_1310) nearly identical to the one unveiled here (40). Although it has not been tested for lantibiotic production, the operonic association of suiK-suiR with the intact sui locus might underscore its connection to suicin production.…”

“…Following the clue of SuiK-SuiR sharing similarity with the TCS for lantibiotic regulation and comparison of its neighboring lan relics with bovicin HJ50 and salivaricin gene clusters, a primarily identical but disrupted sui locus was unveiled and reannotated in three SS2 genomes. Indeed, sui locus was potentially wide distributed in Chinese S. suis isolates because of its location on the 89K PAI (39,40). Notably, similar situations were also observed in cytolysin determinants in E. faecalis and the sal locus in S. pyogenes such that intact or disrupted versions were unveiled in different strains (31,41,42).…”

Minimum Core Genome Sequence Typing of Bacterial Pathogens: a Unified Approach for Clinical and Public Health Microbiology

“…We selected 72 isolates from 117 isolates that were previously typed using MLST. Together with 13 available completed genomes (11,12,15,(16)(17)(18), a total of 85 strains were used for this study. These 85 isolates included all 32 serotypes of reference strains.…”

Genetic Analysis of Capsular Polysaccharide Synthesis Gene Clusters from All Serotypes of Streptococcus suis: Potential Mechanisms for Generation of Capsular Variation

“…As described above and shown in Table 1, all Wzy polymerases, except for those of serotypes 1 and 14 (HG50) and serotypes 2 and 1/2 (HG54), were allocated to serotype-specific HGs. The cps gene clusters of serotypes 1 and 14 and those of serotypes 2 and 1/2 were shown to be almost identical in each pair (17,24), suggesting that the repeat unit structures of CPs are also very similar in each pair. Therefore, Wzy polymerases may differ from each other according to the repeat unit structures in the respective serotypes.…”

“…In serotypes 6,11,12,13,15,17,18,20,21,22,24,27,28,29,30, and 31, partial sequences of the cps gene clusters (orfY-cpsD genes) have been determined and deposited in the GenBank database (accession numbers JF791152 to JF791167). Furthermore, complete genome sequences of 13 S. suis nonreference strains (seven of serotype 2 and one of serotypes 1, 1/2, 3, 7, 9, and 14) have been determined to date (19)(20)(21)(22)(23)(24). A previous study analyzing 15 S. suis cps gene clusters indicated that all the cps gene clusters are located between the orfZ (conserved hypothetical protein gene) and aroA (3-phosphoshikimate 1-carboxyvinyltransferase gene) genes on the chromosome.…”