Biological Drivers of Early Childhood Caries in Preschool Children of Northern Arizona and Hawaii

BackgroundEarly childhood caries (ECC) is the most prevalent chronic childhood disease, disproportionately affecting children from specific racial/ethnic groups. While ECC is a multifactorial disease influenced by demographic, behavioral, and environmental factors, it is also widely associated with the presence of Streptococcus mutans in the oral microbiome.MethodsTo better understand the interplay between demographic and microbial factors and ECC risk, we collected saliva samples from 408 preschool children aged 1-6 years, including 266 from northern Arizona and 142 from Hawaii, representing racially and geographically diverse populations. We examined demographic features (race, ethnicity, age, and sex) and caries status (number of cavities) to identify factors associated with increased ECC risk. Saliva samples were tested for S. mutans using a qPCR assay, and positive samples were further genotyped using a multiplexed targeted amplicon sequencing assay. To identify genetic predictors of caries risk, we conducted a pseudo-genome-wide association study to analyze the presence of strain-specific genetic markers associated with caries risk.ResultsLogistic regression showed that ECC risk increased 80.1% per year of age, and was significantly higher in Native Hawaiian/Pacific Islander (330.9%), Native American (282.4%), and Hispanic (245.2%) children compared to Non-Hispanic White children. Oral S. mutans colonization increased ECC odds by 360.5%. Phylogenetic analysis showed high genetic diversity in S. mutans between and within populations, with no evidence of geographic clustering. Some S. mutans clades were associated with up to a 33-fold increase in ECC odds, with only Native Hawaiian/Pacific Islander children more likely to carry strains from higher-risk clades. We identified genetic markers in genes involved in carbohydrate metabolism, pH regulation, and biofilm formation that were associated with high-risk S. mutans strains.ConclusionsThis study highlights the increased ECC risk among Native Hawaiian/Pacific Islander, Native American, and Hispanic children compared to Non-Hispanic White children, emphasizing demographic disparities in disease susceptibility. We demonstrate that S. mutans strains are highly diverse, lack geographic clustering, and contribute to caries risk, with specific clades showing higher pathogenic potential. Additionally, we identify novel genetic markers distinguishing high- and low-risk clades, providing insights into strain-specific factors that may drive S. mutans virulence.