Streptococcus pneumoniaeis capable of randomly switching their genomic DNA methylation pattern between six distinct bacterial subpopulations (A-F) via recombination of a type 1 restriction-modification locus,spnIII. These pneumococcal subpopulations exhibit phenotypic changes which favor carriage or invasive disease. In particular, thespnIIIBallele has been associated with increased nasopharyngeal carriage and the downregulation of theluxSgene. The LuxS/AI-2 QS system represent a universal language for bacteria and has been linked to virulence and biofilm formation inS. pneumoniae. In this work, we have explored the link betweenspnIIIalleles, theluxSgene and virulence in two clinical pneumococcal isolates from the blood and cerebrospinal fluid (CSF) of one pediatric meningitis patient. The blood and CSF strains showed different virulence profiles in mice. Analysis of thespnIIIsystem of these strains recovered from the murine nasopharynx showed that the system switched to different alleles commensurate with the initial source of the isolate. Of note, the blood strain showed high expression ofspnIIIBallele, previously linked with less LuxS protein production. Importantly, strains with deletedluxSdisplayed different phenotypic profiles compared to the wildtype, but similar to the strains recovered from the nasopharynx of infected mice. This study used clinically relevantS. pneumoniaestrains to demonstrate that the regulatory network betweenluxSand the type 1 restriction-modification system play a key role in infections and may support different adaptation to specific host niches.