Molecular epidemiological and phenotypic characteristics of Streptococcus suis isolated in Hainan Island of China

• Serotypes 16 and 2 predominated among the 298 S. suis isolates, while 17.79% of the strains belonged to non-classical serotypes. • Two novel NCL subtypes (NCL3-3, NCL29-2) discovered in S. suis from diseased pigs in Hainan. • High-virulence isolates from healthy pigs showed a high genetic similarity to the Chinese epidemic strains 98HAH33 and 05ZYH33. Streptococcus suis ( S. suis ) is an important global zoonotic pathogen that can cause meningitis, arthritis, and even death in humans and pigs. Hainan, as the only tropical island in China, experiences a year-round prevalence of S. suis in swine and a high risk of human infection. This work aimed to investigate the molecular epidemiological and phenotypic characteristics of S. suis isolates from pigs in Hainan. Between 2022 and 2024, a total of 298 S. suis isolates were recovered from 639 samples (629 from healthy pigs and 10 from sick pigs) collected across Hainan Island. Serotype 16 (22.15%) and 2 (11.74%) strains exhibited the highest prevalence, followed by serotypes 7 (6.04%) and 31 (5.37%), while 17.79% of the strains belonged to non-classical serotypes. Whole-genome sequencing was conducted on 63 representative strains, and the genome data showed that 65.08% of the strains belonged to novel sequence types, which reflects the distinctive evolutionary relationships of strains originating from Hainan. Notably, D74-2 and D77-1, isolated from healthy pigs, exhibited high virulence with 106 virulence-associated genes (VAGs), and had the closest evolutionary relationship to the human strains 98HAH33 and 05ZYH33, which were responsible for two human outbreaks in China. Further, two new NCL subtypes (NCL3-3, NCL29-2) were identified from diseased pig-derived strains. Furthermore, 98.41% of sequenced strains exhibited multidrug resistance, irrespective of whether they originated from healthy or diseased pigs. Interestingly, all SS2/ST1 and SS7/ST29 strains were classified as highly virulent, whereas all SS16 strains were categorized as lowly virulent in zebrafish infection experiments. Nevertheless, our data showed that some strains lacking combinations of virulence markers ( mrp/sly/epf, srtF/ofs , and NisR/K ) still exhibited high virulence. In conclusion, the results presented above illustrate the diverse molecular epidemiological and phenotypic characteristics of S. suis in Hainan, providing a targeted scientific basis for the development of prevention and control strategies for this zoonotic pathogen in the Chinese tropical region.