Abstract
In a world facing the unprecedented threat of antibiotic-resistant bacteria, targeted approaches to control colonization and prevent disease caused by common pathobionts offer a promising solution. Streptococcus pneumoniae (pneumococcus) is a leading cause of infections worldwide, affecting both children and adults despite available antimicrobials and vaccines. Colonization, which occurs in the form of a biofilm in the upper respiratory tract, is frequent and a prerequisite for disease and transmission. The use of live bacterial strains as biotherapeutics for infectious diseases is actively being explored. Here, we investigated the potential of commensal streptococci to control S. pneumoniae. Screening of over 300 human isolates led to the identification of seven strains (one Streptococcus oralis and six Streptococcus mitis, designated A22 to G22) with inhibitory activity against S. pneumoniae of multiple serotypes and genotypes. Characterization of A22 to G22 cell-free supernatants indicated the involvement of secreted proteins or peptides in the inhibitory effect of all S. mitis isolates. Genome analyses revealed the presence of 64 bacteriocin loci, encoding 70 putative bacteriocins, several of which are novel and absent or rare in over 7,000 publicly available pneumococcal genomes. Deletion mutants indicated that bacteriocins partially or completely explained the anti-pneumococcal activity of the commensal strains. Importantly, strains A22 to G22 were further able to prevent and disrupt pneumococcal biofilms, a proxy for nasopharyngeal colonization. These results highlight the intricacy of the interactions among nasopharyngeal colonizers and support the potential of strains A22 to G22 to be used as live biotherapeutics, alone or in combination, to control S. pneumoniae colonization. IMPORTANCE: Streptococcus pneumoniae (pneumococcus) infections remain a major public health issue despite the use of vaccines and antibiotics. Pneumococci asymptomatically colonize the human upper respiratory tract, a niche shared with several commensal Streptococcus species. Competition for space and nutrients among species sharing the same niche is well documented and tends to be more intense among closely related species. Based on this rationale, a screening of several commensal streptococci isolated from the human upper respiratory tract led to the identification of strains of Streptococcus mitis and Streptococcus oralis capable of inhibiting most pneumococcal strains, across diverse serotypes and genotypes. This inhibition was partially or wholly linked to the expression of novel bacteriocins. The selected S. mitis and S. oralis strains significantly disrupted pneumococcal biofilms, indicating a potential for using commensals as biotherapeutics to control pneumococcal colonization, a key step in preventing disease and transmission.