Abstract:[Objective] Streptococcus suis is a zoonotic pathogen that can cause diseases in pigs and humans. Healthy pigs in slaughterhouses often carry diverse serotypes of S. suis, which can be a major source of infections for susceptible animals and humans. The outbreaks of S. suis occurred in Sichuan and Guangxi, resulting in severe illness and deaths of pigs and humans. Therefore, it is crucial to investigate the infection rate of S. suis in healthy pigs in slaughterhouses and unveil the pathogenic characteristics of S. suis in these two areas. [Methods] We isolated S. suis from the tonsils of healthy pigs collected from slaughterhouses in Guangxi and Sichuan during 2021–2022 and performed serotype-specific PCR for serotyping the isolates. Furthermore, we examined the virulence of the isolates in zebrafish and mice and performed genome sequencing and multilocus-sequence typing (MLST) on the virulent strains to explore their pathogenic characteristics. [Results] The positive rate of S. suis was 84.21% (48/57) in the 57 tonsil samples collected from Guangxi. Among the 60 strains isolated from Guangxi, serotype 31 (16.67%, 10/60) had the highest isolation rate, followed by serotype 9 (11.67%, 7/60), serotype 4 (10.00%, 6/60), and serotype 12 (8.33%, 5/60). The tonsil samples carrying at least two serotypes of strains accounted for 33.33% (16/48) in Guangxi. The positive rate of S. suis in 250 tonsil samples collected from Sichuan was 10.8% (27/250). Among the 41 strains isolated from Sichuan, serotype 31 (34.15%, 14/41) had the highest isolation rate, followed by serotype 16 (17.07%, 7/41), serotype 9 (12.20%, 5/41), and serotype 28 (9.76%, 4/41). The tonsil samples carrying at least 2 serotypes of strains accounted for 33.33% (9/27) in Sichuan. Zebrafish infection experiments with 28 strains from Guangxi and 16 strains from Sichuan showed that five strains were highly virulent, causing the mortality rates ranging from 70% to 100% in the zebrafish challenged with the dose of 3×106 CFU/fish. The five strains included three strains from Guangxi (serotypes 2, 9 and NCL18) and two strains from Sichuan (serotypes 2 and 9). Furthermore, the 5 strains were used to infect mice, with four strains causing the mortality rates ranging from 80% to 100% and 1 strain causing the mortality rate of 60%, which were consistent with the results of the zebrafish infection experiments. MLST and virulence gene analysis revealed that the two strains of serotype 2 belonged to ST1 and exhibited the virulence genotypes mrp+, epf+, and sly+, showing the potential as zoonotic pathogens. The two strains of serotype 9 had the virulence genotypes mrp-, epf-, and sly- and belonged to ST1198 and ST2104, respectively. The NCL18 strain was typed as ST2102 and had the virulence genotypes mrp+, epf-, and sly-. [Conclusion] The S. suis infection rates differed between slaughterhouses in Guangxi and Sichuan, and the isolation rate was higher in Guangxi. The slaughterhouses in both Guangxi and Sichuan harbor serotype 2 ST1 strains with zoonotic potential that are widespread worldwide, warranting attention.