Genomic re-evaluation of clinical isolates reveals a structured <i>Streptococcus suis</i> complex

Several new species closely related genetically to <i>Streptococcus suis</i> have recently been formally recognized or proposed, raising the possibility that they form a broader, previously unrecognized <i>S. suis</i> complex. Yet most clinical laboratories still report such isolates simply as <i>S. suis</i>, due to the limited resolution of current diagnostic tools. Here, we show that two widely used methods, MALDI-TOF MS and a <i>recN</i>-based PCR used for molecular confirmation of MALDI-TOF MS results, can misidentify <i>S. suis</i>-like isolates. We analyzed 61 isolates from diseased swine and three from cows: all were classified as <i>S. suis</i> by MALDI-TOF MS but tested negative by the <i>recN</i> PCR. Exposing a major gap in current diagnostic frameworks, whole-genome sequencing revealed that most isolates were not <i>S. suis</i> sensu stricto but instead belonged to other recognized or recently proposed <i>Streptococcus</i> species. Most swine isolates were recovered from normally sterile sites, suggesting potential but unconfirmed pathogenic relevance. We provide genomic evidence supporting the proposal of a structured <i>S. suis</i> complex and identify <i>S. suis</i> sensu stricto-specific markers that may inform improved molecular diagnostics in the future. Our findings emphasize the need to modernize diagnostics to account for the true diversity and potential importance for animal health of this expanding group of taxa.