Molecular characterization of Streptococcus suis isolates recovered from diseased pigs in Europe

Abstract

Streptococcus suis is a major swine pathogen and zoonotic agent, causing important economic losses to the porcine industry. Here, we used genomics approaches to characterize 251 S. suis isolates recovered from diseased pigs across Belgium, France, Germany, Hungary, the Netherlands, Spain, and the United Kingdom. We identified 13 serotypes, being serotypes 9 and 2 the most prevalent, and 34 sequence types (STs), including 16 novel STs, although ST16 and ST1 dominated the strain population. Phylogenetic analysis revealed complex genetic relationships, notable geographic clustering, and potential differential capacity for capsular switching among serotype 9 isolates. We found antimicrobial resistance (AMR) genes in 85.3% of the isolates, with high frequencies of genes conferring resistance to tetracyclines and macrolides. Specifically, 49.4% of the isolates harbored the tetO gene, and 64.9% possessed the ermB gene. Additionally, we observed a diverse array of virulence-associated genes (VAGs), including the classical VAGs mrp, epf, and sly, with variable presence across different genotypes. The high genetic diversity among European S. suis isolates highlights the importance of targeted antimicrobial use and flexible vaccine strategies. Rapid strain characterization is crucial for optimizing swine health management, enabling tailored interventions like the development of autovaccines to mitigate S. suis infections.

Keywords: Streptococcus suis; Europe; Swine infectious diseases; antimicrobial resistance; genomic epidemiology; virulence-associated genes.

Figure 1

Serotype distribution of S. suis isolates across seven European countries. Serotypes 2, 9, 1 and 7 dominated the population and there were important differences in distribution patterns across the different countries. Each country is represented by a distinct color, as indicated by the color-coded key on the chart.

Figure 2

Inferred genetic relationships between S. suis isolates recovered from diseased pigs in seven European countries based on the seven genes used in the multilocus sequence typing scheme (MLST). A maximum likelihood phylogenetic tree was constructed by concatenating the sequences of genes (aroA, cpn60, dpr, gki, mutS, recA, and thrA) used in the S. suis MLST scheme. Each sequence type (ST) is plotted with the number of isolates (N) indicated beside each ST. Colored circles represent the countries of origin for the isolates—Belgium, France, Germany, Hungary, the Netherlands, Spain, and the United Kingdom, as per the key, providing a visual representation of the geographic distribution of genetic variants. Notably, ST1 and ST16 isolates were the most prevalent, but we identified a total of 34 STs, including 16 novel STs.

Figure 3

Phylogenetic relationships based on core-genome single-nucleotide polymorphisms (SNPs), and genomic traits of the 251 S. suis isolates included in this investigation. The left panel presents a maximum-likelihood phylogenetic tree constructed using 8558 non-redundant core-genome SNP loci identified among the isolates in the study collection relative to the genome sequence of the ST1 serotype 2 reference strain P1/7. The tree, delineating several distinct clades, highlights the genetic diversity among the isolates. For reference, the serotype of each isolate, as well as the genotypes determined by MLST, are annotated along the tree, illustrating their association with specific genomic clades. The right panel depicts the presence (in purple) or absence (in light blue) of antimicrobial resistance (AMR) genes, as well as virulence-associated genes (VAGs), as determined by interrogating the whole-genome sequences of each isolate. The varying distribution of AMR and VAGs across different clades suggests patterns of acquisition and retention of these elements.

Figure 4

Inferred genetic relationships among 108 serotype 9 S. suis strains investigated in this study based on core-genome analysis. The maximum likelihood phylogenetic tree was constructed based on 15 934 non-redundant core-genome SNP loci identified relative to the genome sequence of the ST16 serotype 9 reference strain GD-0088. The tree reveals that serotype 9 isolates are distributed across several distinct genomic clades, including four newly discovered genotypes, highlighting complex evolutionary dynamics. These patterns suggest that the cps9 Cps9 capsule may confer adaptive capabilities, although further research is needed to confirm such speculation. The tree is color-coded to indicate the country of origin for each strain, showcasing the geographical distribution across Belgium, France, Germany, the Netherlands, and the United Kingdom. The clade comprising ST16 organisms along with closely related STs 1520, 2772, and 2773 has been collapsed for simplicity, focusing the analysis on broader genomic diversity within serotype 9.