Genomic comparisons of Streptococcus suis serotype 9 strains recovered from diseased pigs in Spain and Canada

Abstract

Streptococcus suis is one of the most important bacterial pathogens in the porcine industry and also a zoonotic agent. Serotype 9 is becoming one of the most prevalent serotypes within the S. suis population in certain European countries. In the present study, serotype 9 strains isolated from a country where infection due to this serotype is endemic (Spain), were compared to those recovered from Canada, where this serotype is rarely isolated from diseased pigs. For comparison purposes, strains from Brazil and the only strain isolated from a human case, in Thailand, were also incorporated. Firstly, sequence types (STs) were obtained followed by detection of putative virulence factors. Phylogenetic trees were constructed using the non-recombinant single nucleotide polymorphisms from core genomes of tested strains. Most Spanish strains were either ST123 or ST125, whereas Canadian strains were highly heterogeneous. However, the distribution of putative virulence factors was similar in both groups of strains. The fact that ST16 strains harbored more putative virulence genes and shared greater similarity with the genome of human serotype 2 strains suggests that they present a higher zoonotic and virulence potential than those from Canada and Spain. More than 80% of the strains included in this study carried genes associated with resistance to tetracycline, lincosamides and macrolides. Serotype 9 strains may be nearly 400 years old and have evolved in parallel into 2 lineages. The rapid population expansion of dominant lineage 1 occurred within the last 40 years probably due to the rapid development of the porcine industry.

Figure 1

Phylogenetic relationship of the 34 S. suis serotype 9 strains, the intermediately virulent serotype 2 strain 89-1591, and the highly virulent serotype 2 reference strain GZ1 following CGA. Absence or presence of each gene from each strain was translated to 0 or 1, respectively. Colors represent geographical origin of strains: Red: Asia; Brown: Brazil; Green: Canada; Purple: Spain; Blue: European countries (other than Spain).

Figure 2

Comparison of the gene islands or ICEs reported in this study and those found in previous studies. B and C used common ruler of size. Each arrow represents a gene. Drug resistance genes were indicated in different colors. A Comparisons of molecular characterization of the tet(W)-carrying genetic element. B Comparisons of ICEs. Integration and conjugation genes were also indicated in different colors. C Comparisons of phages. Two phages were inserted in 3 side of rum.

Figure 3

Phylogenetic relationship and evolutionary time scale of S. suis serotype 9 strains. The Bayes tree of the isolates was included on top. The inferred emerging years of each clade were marked on the branches. Colors represent geographical distribution of strains: Red: Asia; Brown: Brazil; Green: Canada; Purple: Spain; Blue: European countries (other than Spain).

Figure 4

Comparison of the cps loci among S. suis serotype 9 strains. Each colored arrow represents a gene whose predicted function is shown in the blown-up panel. The glf gene is located on the 3′ side of each locus.