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Journal of Clinical Microbiology, September 2008, p. 2868-2873, Vol. 46, No. 9
0095-1137/08/$08.00+0     doi:10.1128/JCM.01000-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Genetic Classification of Severe Early Childhood Caries by Use of Subtracted DNA Fragments from Streptococcus mutans{triangledown}

Deepak Saxena,1* Page W. Caufield,2,4 Yihong Li,1 Stuart Brown,4 Jinmei Song,2 and Robert Norman3

Department of Basic Science and Craniofacial Biology,1 Department of Cariology and Comprehensive Care,2 Department of Epidemiology and Health Promotion, College of Dentistry,3 School of Medicine, New York University, New York, New York 100104

Received 23 May 2008/ Returned for modification 6 June 2008/ Accepted 22 June 2008

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

* Corresponding author. Mailing address: Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E. 24th Street, Rm. 921B, New York, NY 10010. Phone: (212) 998-9256. Fax: (212) 998-4087. E-mail: ds100{at}nyu.edu

{triangledown} Published ahead of print on 2 July 2008.

Journal of Clinical Microbiology, September 2008, p. 2868-2873, Vol. 46, No. 9
0095-1137/08/$08.00+0     doi:10.1128/JCM.01000-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.





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