Tracing of streptococcal strains from infant stools across human body sites links site-specific prevalence to adhesins

Streptococci colonize various human body sites, both as commensals and as pathogens. They are early gut colonizers, but we lack strain-level information about the origin and persistence of streptococci in the non-diseased gut. To gain a greater insight into commensal streptococci in the infant gut and their presence in other body habitats, we analyzed samples from mother-infant pairs collected from multiple body sites (stool, oral cavity, vagina, breast milk). We performed whole-metagenome sequencing and isolated streptococci from 100 infant stool samples (collected at 10 days of age). To trace the streptococci at the strain level, we designed selective quantitative PCR (qPCR) primers for seven streptococcal strains, which were then used to screen the corresponding samples from the other body sites of the infants and their mothers. We found that two of the strains investigated, one <i>Streptococcus parasanguinis</i> strain and one <i>Streptococcus vestibularis</i> strain, were highly prevalent in stool samples obtained from infants and their mothers. Interestingly, the screening revealed that another <i>S. parasanguinis</i> strain, closely related to the stool-prevalent strain, displayed a completely different prevalence pattern, being most prevalent in vaginal swabs, breast milk, and oral swabs. A genotypic comparison of these two <i>S</i>. <i>parasanguinis</i> strains revealed major differences in genes encoding adhesins, suggesting that host surface attachment could be a key factor for the observed differences in body site specificity. Together, our extensive tracing of streptococci across the body sites of 100 infants and their mothers provides strain-level insight into patterns of distribution and identifies streptococcal strains prevalent in stool.IMPORTANCEStreptococci thrive on mucosal surfaces and colonize multiple human body sites, including the gut. To understand how streptococci colonize and spread between body site habitats, strain-level information about their prevalence is required; however, such knowledge is currently lacking. In this study, we isolate streptococci and perform metagenome sequencing and quantitative PCR (qPCR) on samples from a large cohort of mother-infant pairs to trace streptococcal strains in different habitats. We demonstrate how different strains prefer specific habitats. For example, we show that two closely related strains, both isolated from stool, are distributed differently across the human body, with one of them prevalent in stool samples and the other more prevalent in other samples. These results emphasize the necessity of strain-level analysis for the identification of true colonizers of a habitat.