Genetic Classification of Severe Early Childhood Caries Using 1 Subtracted DNA

1 Streptococcus mutans is one of several members of the oral indigenous biota linked with severe 2 early childhood caries (S-ECC). Because most humans harbor S. mutans, but not all manifest 3 disease, it has been proposed that the strains of S. mutans associated with S-ECC are 4 genetically distinct from those found in caries free (CF) children. The objective of this study was 5 to identify common DNA fragments from S. mutans present in S-ECC but not in CF children. 6 Using suppressive subtractive hybridization (SSH), we found a number of DNA fragments 7 (biomarkers) present in 88 to 95% of the S-ECC S. mutans strains, but not in CF S. mutans 8 strains. We then applied machine learning techniques including support vector machines and 9 neural networks to identify those biomarkers with the most predictive power for disease status, 10 achieving a 92% accurate classification of the strains into either S-ECC-or CF-associated. The 11 presence of these gene fragments in 90 to 100% of the 26 S-ECC isolates tested suggested 12 their possible functional role in the pathogenesis of S. mutans associated with dental caries.