Serotype-independent inhibition of S. pneumoniae by SMiTE, a commensal-derived bacteriocin

Abstract

ABSTRACT Streptococcus pneumoniae remains a leading cause of disease despite widespread vaccination, highlighting the need for serotype-independent strategies. We recently identified commensal streptococci that produce bacteriocins with anti-pneumococcal activity. Here, we evaluate these bacteriocins as candidates for pneumococcal control. Using cell-free protein synthesis, we screened 58 bacteriocins, the majority of which absent in available pneumococcal genomes, and identified SMiTE as the most potent. Purified SMiTE disrupted pneumococcal membrane integrity, as shown by confocal, transmission, and scanning electron microscopy, induced ATP leakage, and triggered transcriptional responses consistent with envelope stress and metabolic remodeling. In a mouse nasopharyngeal colonization model, intranasal SMiTE treatments reduced pneumococcal loads by 65-fold with no significant weight loss. SMiTE inhibited a broad range of serotypes, with the strongest activity against serotype 3, which is poorly controlled by current vaccines, while sparing most oral and upper respiratory tract commensals. Repeated sub-inhibitory exposure did not select resistant mutants in line with the membrane-targeting mechanism. These findings establish SMiTE as a commensal-derived strategy for serotype-independent, microbiota-sparing pneumococcal decolonization. IMPORTANCE Streptococcus pneumoniae is a bacterium that can cause serious infections such as pneumonia, meningitis, and bloodstream infections. Although vaccines have greatly reduced disease, they do not protect against all strains, making new approaches urgently needed. In this study, we discovered a natural antimicrobial molecule, called SMiTE, produced by harmless bacteria that normally live in the human mouth. SMiTE effectively kills pneumococci by damaging their protective membrane, preventing them from surviving. In mice, a simple nasal treatment with SMiTE dramatically reduced the amount of pneumococci in the nose, where these bacteria first establish themselves before spreading or causing disease. Importantly, SMiTE was active against many different pneumococcal strains, including serotype 3, which is poorly controlled by current vaccines, while leaving most beneficial bacteria unharmed. Because it did not readily trigger resistance, SMiTE represents a promising new strategy to prevent pneumococcal carriage, transmission, and disease, regardless of serotype.