Introduction The present study evaluated bacterial reduction promoted by the WaveOne system (Dentsply Maillefer, Ballaigues, Switzerland) and ProTaper Gold system (PTG; Dentsply Maillefer) in human extracted central incisors. Methods Sixty-two maxillary central incisors that were infected with Enterococcus faecalis (ATCC 51299) were sterilized with ethylene oxide for 21 days, and then root canal initial bacterial sample was collected with paper points and plated on M-Enterococcus agar. The specimens were randomly divided into two groups according to instrumentation: WaveOne Gold group (n = 30) and PTG group (n = 30). Each group was further subdivided into subgroup A (n = 15) where no activation of the irrigant was performed, and subgroup B (n = 15) where passive ultrasonic activation (PUI) was applied. The other two specimens without contamination were control asepsis. After instrumentation, samples were collected with the use of paper points. The bacterial reduction was calculated using colony-forming unit and quantitative real-time polymerase chain reaction. Data were collected and statistically analyzed. Results All techniques significantly reduced the number of bacteria in the root canal (p < 0.05), in which PTG showed superior bacterial reduction than WaveOne Gold (p > 0.05). The aseptic control group did not show any bacterial growth. PUI showed a significant bacterial reduction with the WaveOne Gold group. Conclusion It can be concluded that the single-file system, WaveOne Gold with the aid of passive ultrasonic irrigation, significantly reduce the bacterial number in the root canal similar to the multifile system, PTG.
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