Bacterial Profile Changes During Root Canal Treatment With 5.25% and 3% Sodium Hypochlorite Irrigation and Calcium Hydroxide Medicament Assessed by 16S rRNA PCR

Chronic apical abscess is associated with complex multispecies biofilms in the root canal that can differ between populations and are not fully characterized by conventional culture methods. This study focuses on adult patients with necrotic molar teeth and chronic apical abscess treated at the Dental and Oral Hospital, Faculty of Dentistry, Hasanuddin University. The main objective is to describe how the root canal bacterial community profile changes during different phases of routine root canal treatment using 16S rRNA PCR and sequence analysis.

The study uses a descriptive and analytic repeated-measures design. At least 24 adult outpatients with necrotic pulp and chronic apical abscess who meet the inclusion and exclusion criteria will be recruited and provide written informed consent. After rubber dam isolation, access cavity preparation, and working length determination, the first root canal sample (S1) is collected from the distal canal using a sterile Hedström file and transferred into a tube containing DNA preservative solution. Mechanical preparation is then performed with rotary instruments. Patients are randomly assigned by clinic staff, who are blinded to the investigator, to one of two irrigation regimens: 5.25 percent sodium hypochlorite or 3 percent sodium hypochlorite, each followed by sterile distilled water, 17 percent EDTA, and a final rinse with sterile distilled water. A second sample (S2) is collected from the same canal after irrigation. Calcium hydroxide intracanal medicament is then placed and the tooth is temporized.

After approximately two weeks, the temporary restoration and calcium hydroxide are removed, and a third sample (S3) is collected from the same canal using a sterile Hedström file. All samples are stored in DNA preservative solution and analyzed by 16S rRNA PCR followed by DNA sequencing to characterize the bacterial community composition and diversity. The study will compare bacterial taxa and community profiles at S1, S2, and S3 and between the two sodium hypochlorite concentrations in order to explore how root canal irrigation and calcium hydroxide medicament are associated with changes in the bacterial community.