Population Genomics, Virulence Traits, and Antimicrobial Resistance of Streptococcus suis Isolated in China

Abstract

Streptococcus suis is a significant zoonotic pathogen of public health importance. In this study, whole-genome sequencing of 177 isolates of Streptococcus suis, isolated from diseased swine across 15 provinces in China between 2017 and 2019, was performed. A total of 23 serotypes and 28 ST types were identified, with serotypes 2 and 3 comprising 50.8% of the isolates, and sequence types ST353 and ST117 accounting for 23.7%. Clustering analysis based on known virulence-associated factors (VAFs) resulted in the identification of four distinct clusters, and virulence was assessed using animal models, including a unique, highly virulent cluster designated as cluster I. Drug susceptibility testing indicated that 97.7% of the isolates were multidrug-resistant. A total of 26 resistance-associated genes were identified within the genome, 18 of which were associated with integrative and conjugative elements (ICEs) and/or integrative mobilizable elements (IMEs). Nevertheless, our understanding of suis virulence in terms of phylogeny remains incomplete. This study contributes to the understanding of the population structure and genetic characteristics of suis, provides a framework and novel partitioning approach for future investigations into its virulence and pathogenicity, and complements the data on antibiotic resistance.

Keywords: Streptococcus suis; antimicrobial resistance; genomics; virulence.

Figure 1

Phylogenetic tree of 177 Streptococcus suis isolates. This phylogenetic tree was generated utilizing genome-wide SNPs. The legends, arranged from the innermost to the outermost ring, include the following information: ST type, serotype, isolation time, and tissue source. Those containing at least one mismatched gene are marked with an asterisk.

Figure 2

Phylogenetic tree (unrooted) showing the clades of 177 isolates of Streptococcus suis isolates, with HAC denoted in blue, HPC in yellow, DPC in red, and the remaining isolates classified as an unknown clade, indicated by the absence of color.

Figure 3

(A) Virulence associated factors (VAFs) in 177 isolates of Streptococcus suis. The heatmap illustrates the presence or absence of 104 previously identified virulence associated factors (VAFs) across 177 isolates of Streptococcus suis. The color coding indicates presence in orange and absence in grey. The right column delineates the clades and serotypes of the isolates, which are categorized into four distinct clusters (clusters Ⅰ–Ⅳ) based on their VAFs. (B) The mouse infection model was generated via intraperitoneal injection, involving a total of 20 isolates, which included 5 isolates from cluster Ⅰ, 4 from cluster II, 7 from cluster III, and 4 from cluster Ⅳ.

Figure 4

Bacterial load and lung tissue of mice infected with suis of cluster I, cluster III. and cluster IV in HPC. The mice were injected peritoneally with 5 × 10⁸ CFU for 12 h. Bacterial loads in (A) blood and (B) lungs. (C) Histological changes in the lungs. (D) Cytokines and chemokines in cluster I, cluster III, and cluster IV of HPC Streptococcus suis-infected mice. Mice (n = 3) were injected peritoneally with 5 × 10⁸ CFUs, and IL-6, TNF-α, IFN-γ, and CXCL1 levels were quantified via ELISA 12 h later. Each dot represents one mouse. In the figure, ‘*’ represents p < 0.05, ‘**’ represents p < 0.01, ‘***’ represents p < 0.001 and ‘* ***’ represents p < 0.0001.

Figure 5

(A) Antibiotic resistance upset plot for Streptococcus suis, with horizontal bars showing antibiotic species and the number of isolates. The colored circles represent resistance to one antibiotic. Vertical bars represent the number of isolates with a particular combination of resistance. (B) Resistance ratios (black), mediator ratios (grey), and susceptibility ratios (light grey) are shown for each antibiotic drug. (C) Resistance phenotypes for each of the clades. Resistant = 2, mediator = 1, and sensitive = 0. The vertical axis is the sum of the values. A single asterisk (*) indicates p < 0.05 and double asterisks (**) indicates p < 0.01.

Figure 6

(A) Heatmap showing the presence (blue) or absence (grey) of resistance genes. The horizontal axis represents the drug resistance genes. (B) Resistance genes carried by ICE and IME. The columns on the right represent serotypes.