Strain-level genomic variation of Streptococcus mutans and early childhood caries in preschool children from Northern Arizona and Hawai‘i

Background. Early childhood caries (ECC) is the most common chronic disease of childhood, with especially high prevalence in Arizona and Hawai‘i where several racial and ethnic groups experience disproportionate burden. Although ECC is a polymicrobial disease, Streptococcus mutans plays a central role in its development, and evidence suggests that strain-level genetic variation influences its cariogenic potential. Understanding whether specific S. mutans lineages are associated with higher ECC risk and whether these lineages are more common in disproportionately affected groups is an important step toward identifying biological contributors to ECC outcomes. Methods. We conducted a cross-sectional study of 408 preschool-aged children (1– 6 years) from Arizona and Hawai‘i. Saliva samples were tested for S. mutans using quantitative polymerase chain reaction (qPCR), and positive samples were genotyped using a custom amplicon sequencing assay. Logistic regression was used to evaluate associations between demographic factors (race, ethnicity, age, and sex), S. mutans colonization, and ECC status. To assess whether certain S. mutans genotypes were associated with ECC risk, we calculated a K-nearest-neighbor-smoothed risk score for each genotype based on patristic distances. Genetic markers of ECC risk were identified using a pseudo-genome-wide association approach. Results. ECC odds increased with age and were higher among Native Hawaiian/Pacific Islander, Asian, American Indian, and Hispanic children compared to non-Hispanic White children, although estimates for some groups were imprecise due to limited subgroups sizes. S. mutans colonization increased ECC odds by 361%, but colonization rates did not significantly differ across groups. Genotypes from Arizona and Hawai‘i showed no evidence of geographic clustering but ECC risk was non-randomly distributed across the phylogeny with multiple localized regions of higher risk genotypes. Native Hawaiian/Pacific Islander children were significantly more likely to carry higher-risk strains. Genetic markers linked with ECC risk mapped to genes involved in cariogenic processes—many of which were previously shown to be upregulated in caries-active plaque. Conclusions. The observed correlation between S. mutans genotype and ECC risk, together with the finding that higher-risk genotypes were more prevalent among at least one disproportionately affected group, suggests that strain-level variation may contribute to population-level disparities. The identification of functional markers linked to ECC risk further supports biologically meaningful strain-specific effects and warrants further investigation. These findings highlight the value of incorporating microbial genetic diversity into ECC risk frameworks, while recognizing that fully disentangling microbial contributions will require studies that integrate social, behavioral, and dietary determinants.