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Introduction: Regenerative endodontic treatment (RET) aims to promote root maturation in necrotic immature teeth, where effective microbial disinfection is crucial for treatment success. This study evaluated the effect of calcium hydroxide (CH) and 2% chlorhexidine gluconate (CHD) as intracanal medicaments and their impact on bacterial loads and RET outcomes.

Methods: The material consisted of bacterial samples from 41 patients who participated in a previously conducted randomized controlled clinical trial comparing CH and CHD during RET. A total of 123 microbial samples were analyzed using real-time quantitative polymerase chain reaction (qPCR). Bacterial loads were assessed at three time points: before root canal disinfection (S1), after root canal disinfection (S2), and after intracanal dressing (S3). The microbial composition was evaluated at the kingdom (Eubacteria), phylum (Actinomycetota), and species (Enterococcus faecalis) levels.

Results: Significant reductions in bacterial loads were observed after root canal disinfection (S2) in both CH and CHD subgroups, regardless of treatment outcome. Further reductions after intracanal dressing (S3) occurred exclusively in the successful cases. Actinomycetota loads significantly decreased after root canal disinfection in the successful cases but remained unchanged after intracanal medication. The presence of E. faecalis after intracanal dressing was associated with failed RET (OR = 9.778; p = 0.0432), although no significant differences in the effectiveness of the intracanal medicaments were found.

Conclusion: Both CH and CHD effectively reduced bacterial loads, with greater reductions linked to successful outcomes. The association between E. faecalis and failed RET suggests that this species may play a role in treatment outcomes. Further research, including microbiome profiling, is desirable to identify potential prognostic markers for failed RET.