Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis

Abstract

Background: Streptococcus suis is a zoonotic pathogen that infects pigs and can occasionally cause serious infections in humans. S. suis infections occur sporadically in human Europe and North America, but a recent major outbreak has been described in China with high levels of mortality. The mechanisms of S. suis pathogenesis in humans and pigs are poorly understood.

Methodology/principal findings: The sequencing of whole genomes of S. suis isolates provides opportunities to investigate the genetic basis of infection. Here we describe whole genome sequences of three S. suis strains from the same lineage: one from European pigs, and two from human cases from China and Vietnam. Comparative genomic analysis was used to investigate the variability of these strains. S. suis is phylogenetically distinct from other Streptococcus species for which genome sequences are currently available. Accordingly, approximately 40% of the approximately 2 Mb genome is unique in comparison to other Streptococcus species. Finer genomic comparisons within the species showed a high level of sequence conservation; virtually all of the genome is common to the S. suis strains. The only exceptions are three approximately 90 kb regions, present in the two isolates from humans, composed of integrative conjugative elements and transposons. Carried in these regions are coding sequences associated with drug resistance. In addition, small-scale sequence variation has generated pseudogenes in putative virulence and colonization factors.

Conclusions/significance: The genomic inventories of genetically related S. suis strains, isolated from distinct hosts and diseases, exhibit high levels of conservation. However, the genomes provide evidence that horizontal gene transfer has contributed to the evolution of drug resistance.

Figure 1. Schematic circular diagram of the S. suis P1/7 genome.

Key for the circular diagram (outer to inner): scale (in Mb); annotated CDSs coloured according to predicted function are shown on a pair of concentric circles, representing both coding strands; Streptococcus suis orphan CDSs, purple; orthologue matches shared with the Streptococcal species, S. mutans UA159, S. gordonii Challis CH1, S. sanguinis SK36, S. pyogenes Manfredo, S. equi 4047, S. agalactiae NEM316, S. uberis 0140J, S. pneumoniae TIGR4, S. thermophilus CNRZ1066, blue; orthologue matches shared with Lactococcus lactis subsp. lactis, green; G+C% content plot; G+C deviation plot (>0% olive, <0% purple). Colour coding for P1/7 CDS functions: dark blue, pathogenicity/adaptation; black, energy metabolism; red, information transfer; dark green, surface associated; cyan, degradation of large molecules; magenta, degradation of small molecules; yellow, central/intermediary metabolism; pale green, unknown; pale blue, regulators; orange, conserved hypothetical; brown, pseudogenes; pink, phage and IS elements; grey, miscellaneous.

Figure 2. Phylogenetic relationships of S. suis to the other genome sequenced streptococci.

Unrooted majority-rule tree of Bayesian analysis of combined 16S rRNA and RNase P RNA gene datasets. The was tree built from 16S rRNA and rnpB gene sequences from the genomes of the Streptococcus species: S. suis P1/7, S. mutans UA159, S. gordonii Challis CH1, S. sanguinis SK36, S. pyogenes Manfredo, S. equi 4047, S. agalactiae NEM316, S. uberis 0140J, S. pneumoniae TIGR4, and S. thermophilus CNRZ1066. Lactococcus lactis subsp. lactis IL1403 was included as an outgroup. The numbers at the branches are posterior probabilities indicating the support for the branch. The bar indicates the number of substitutions per site (4 per 100 sites).

Figure 3. Functional distribution of Streptococcal orthologues in the S. suis P1/7 genome.

Functional groups are displayed clockwise on the web graph, in decreasing range of orthologue matches for a single category.

Figure 4. Chromosomal comparisons of S. suis strains.

Pairwise comparisons of the chromosomes of S. suis strains P1/7, SC84 and BM407 displayed using the Artemis Comparison Tool (ACT) . The sequences have been aligned from the predicted replication origins (oriC; right). The coloured bars separating sequences (red and blue) represent similarity matches identified by BLASTN analysis , with a score cut off of 100. Red lines link matches in the same orientation; blue lines link matches in the reverse orientation. The green coloured boxes on the horizontal grey lines mark up the extent of genomic islands identified on the chromosomes; pink boxes mark up the extent ICE regions.

Figure 5. Comparisons of the ICE regions from S. suis strains SC84 and S. agalactiae NEM315.

The results of a TBLASTX comparison of the ICESsu _SC84 from strain SC84 and S. agalactiae NEM315 Tn2424 is displayed using the Artemis Comparison Tool (ACT) .

Figure 6. Comparisons of the ICE regions from S. suis strains BM407 and SC84.

The results of a TBLASTX comparison of the ICESsu _BM4071 and ICESsu _BM4072 regions from strain BM407, and ICESsu _SC84 from strain SC84 is displayed using the Artemis Comparison Tool (ACT) .