Characterization of neurologic disease-associated <i>Streptococcus suis</i> strains within the United States swine herd and use of diagnostic tools

<i>Streptococcus suis</i> negatively impacts swine health, posing diagnostic and preventative challenges. <i>S. suis</i> can induce disease and also quietly reside on mucosal surfaces. The limited use of diagnostic tools to identify disease-associated strains and rule out differential diagnoses, alongside the complex ecology of <i>S. suis</i>, poses significant challenges in comprehending this important pathogen and defining pathotypes. This study evaluated 2,379 <i>S</i>. <i>suis</i> central nervous system (CNS) isolates from diagnostic submissions between 2015 and 2019. Isolates originating from submissions with histologic evidence of CNS infection (<i>n</i> = 1,032) were further characterized by standard and advanced diagnostic techniques. We identified 29 <i>S</i>. <i>suis</i> serotypes and 4 reclassified serotypes as putative causes of CNS disease. Among these, serotypes 1 and 7 emerged as the predominant putative causes of CNS infection (32% of submissions). Furthermore, 51 sequence types (STs), of which 15 were novel, were detected with ST1 predominating. Through whole-genome sequencing of 145 isolates, we observed that five commonly used virulence-associated genes (VAGs; <i>epf</i>, <i>mrp</i>, <i>sly</i>, <i>ofs</i>, and <i>srtF</i>) were not present in most disease-associated isolates, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) yielded false-positive results in 7% of isolates. These data indicate that (i) clinical signs and site of isolation alone are insufficient for defining a pathotype, (ii) <i>S. suis</i> serotypes and STs associated with CNS infection are more diverse than previously reported, (iii) MALDI-TOF MS may need to be supplemented with additional diagnostic tools for precise <i>S. suis</i> identification, and (iv) VAGs remain an unreliable means for identifying isolates associated with CNS disease.IMPORTANCE<i>Streptococcus suis</i> is an important and complex systemic bacterial pathogen of swine. Characterization of <i>S. suis</i> strains originating from pigs with histologic confirmation of neurologic disease is limited. Review of swine diagnostic submissions revealed that fewer than half of cases from which <i>S. suis</i> was isolated from the brain had histologic evidence of neurologic disease. This finding demonstrates that clinical signs and site of isolation alone are not sufficient for identifying a neurologic disease-associated strain. Characterization of strains originating from cases with evidence of disease using classic and advanced diagnostic techniques revealed that neurologic disease-associated strains are diverse and commonly lack genes previously associated with virulence.