New insights into the epidemiology of Streptococcus suis in pig production systems using whole genome sequencing.

Streptococcus suis (S. suis) is a major pathogen for pigs, causing large economic losses to the swine industry. Moreover, this bacterium has a zoonotic potential, being capable of infecting humans in close contact with pigs or, less frequently, through contact with pork products. Given its importance in both veterinary and public health, S. suis remains a key topic of research. This study explores the genetic characteristics of 154 S. suis isolates obtained from clinical samples collected from pigs between 2018 and 2022. Whole genome sequencing (WGS) allowed a comprehensive analysis of the S. suis population in Spain, including detection of serotype, sequence type (ST), antimicrobial resistance genes, and virulence-associated genes. This approach also explored the vertical transmission of this pathogen through vertically integrated pyramids, as evidenced by associations between grandmother and mother sow farms, and phylogenetic groups, serotypes, and STs. Our analysis revealed that serotype 9 was the most prevalent in our strain collection, predominantly associated with ST123. Notably, the three most significant virulence genes, encoding the extracellular protein factor (EPF), the muramidase-release protein (MRP), and suilysin (SLY), were not consistently present in all clinical isolates. Regarding antimicrobial resistance, no phenotypic resistance was observed to ceftiofur or florfenicol, while observing low resistance to ampicillin (0.6 %) and enrofloxacin (2.6 %), intermediate resistance to penicillin (22.1 %), and high percentage of non-wild-type isolates to trimethoprim-sulfamethoxazole (57.1 %), and doxycycline (96.1 %). The most prevalent antimicrobial resistance genes (ARGs) were tet(O) (85.1 %) and erm(B) (86.4 %), conferring resistance to tetracyclines and macrolides, respectively, although macrolides were not included in the phenotypic testing. Overall, this study provides key epidemiological insights into this significant systemic pathogen within the Spanish swine population. The findings underscore the importance of understanding sample origins, such as grandmother and mother sow farms, to develop an effective antimicrobial stewardship program for managing S. suis-associated diseases.