A bstract Background and aim The therapeutic procedures used in the treatment of caries do not always eliminate all the microorganisms. Persisting cariogenic bacteria can cause recurrent caries and failure of restoration. Incorporation of an antimicrobial agent in the restorative material may be of paramount significance. The purpose of this study was to evaluate and compare the antibacterial effect of glass ionomer cement (GIC) containing CHX and miswak extract on Streptococcus mutans and Streptococcus sobrinus in ECC children using polymerase chain reaction (PCR). Materials and methods Forty-five children with ECC in the age-group 3–6 years were selected. The children were randomly allocated into three groups. Supragingival plaque samples (S1) were collected from sound buccal or labial surfaces of primary teeth. Cavity preparation was done and the teeth were restored according to the group to which the child had been allotted. The second plaque sample (S2) was collected 1 month and the final sample after 3 months of restoring all the decayed teeth. All the samples were sent for PCR analysis. Results Intergroup analysis was done using Kruskal–Wallis test followed by Mann–Whitney post hoc test showed statistically significant difference in S. mutans and S. sobrinus count between group I (CHX) and group III (control) and group II (miswak) and group III (control) but no statistically significant difference between group I (CHX) and group II (miswak) in S. mutans and S. sobrinus count. Conclusion 1% chlorhexidine digluconate and aqueous extract of miswak are equally effective against S. mutans and S. sobrinus . Miswak can be used as an alternative herbal antimicrobial that can be incorporated in anhydrous GIC. How to cite this article Kalpavriksha AJ, Siddaiah SB, Bilichodmath S, et al. Comparative Evaluation of Antibacterial Effect of GIC Containing Chlorhexidine and Miswak on Streptococcus mutans and Streptococcus sobrinus in Early Childhood Caries Children: A PCR Study. Int J Clin Pediatr Dent 2021;14(2):229–234.
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