Clinical Trial Details
— Status: Completed
Administrative data
| NCT number |
NCT05690763 |
| Other study ID # |
Microbial analysis |
| Secondary ID |
|
| Status |
Completed |
| Phase |
N/A
|
| First received |
|
| Last updated |
|
| Start date |
February 7, 2022 |
| Est. completion date |
December 2, 2022 |
Study information
| Verified date |
May 2023 |
| Source |
Istanbul Medipol University Hospital |
| Contact |
n/a |
| Is FDA regulated |
No |
| Health authority |
|
| Study type |
Interventional
|
Clinical Trial Summary
Aim of the present study was to determine the intraradicular microbiota of previously root
canal-treated teeth with apical periodontitis using droplet digital polymerase chain reaction
(ddPCR) and to investigate the antibacterial effectiveness of different irrigation activation
methods [ XP-endo Finisher and EndoActivator ] that will make classical chemomechanical
preparation more effective. This superiority, parallel, randomized clinical trial was
conducted in the clinic of the Endodontic Department, Faculty of Dentistry, Istanbul Medipol
University, Istanbul. 20 patients with posttreatment apical periodontitis (one tooth each)
were randomly allocated into two groups according to the used (n=10, for each): the EA group
(A) or the XPF group (B). Total bacterial loads, as well as the amount of Enterococcus
faecalis (E.faecalis) were determined before (S1) and after (S2) chemomechanical preparation
and finally, after intracanal medication (S3) by means of ddPCR.
Description:
Eligibility criteria The study population consisted of 20 patients (9 women and 11 men, aged
19-66 years) presenting to the endodontic clinic at Istanbul Medipol University Dental
School, for nonsurgical endodontic retreatment of teeth with apical periodontitis lesions. 20
previously root canal-treated teeth exhibiting clinical and radiographic evidence of chronic
apical periodontitis lesions were included in this study. Radiographically, the diameter of
the periapical radiolucency ranged from 2 to 7 mm. Teeth with post-treatment apical
periodontitis had endodontic therapy completed more than 2 years earlier and required
retreatment. Termini of the root canal fillings ranged from 0-4 mm short of the radiographic
apex, with no overfilling. The teeth had intact coronal restorations, with no obvious
exposure of the root-filling material to the oral cavity. Selected teeth had enough crown
structure for adequate isolation with a rubber dam and showed an absence of periodontal
pockets or attachment level deeper than 4 mm. Exclusion criteria were also applied, as
follows: teeth from patients who had received antibiotics within the previous 3 months or who
had any general disease, teeth that could not be properly isolated with rubber dam, teeth
with absence of coronary sealing, teeth with periodontal pocket depth >4 mm; and teeth with
crown/root fracture. Only one tooth was included from each patient.
Root canal treatment procedures and sampling Rubber dam and an aseptic technique were used
throughout the endodontic retreatment. After plaque removal and rubber dam isolation, the
operative field was cleaned with 3% hydrogen peroxide and disinfected with 2.5% NaOCl
solution. Then, all coronal restorations, posts and carious defects were removed and access
preparation was completed when the root canal filling was properly exposed. Afterwards, the
tooth (including the pulp chamber), clamp, and adjacent rubber dam were once again
disinfected with 2.5% NaOCl, followed by inactivation with 10% sodium thiosulfate in order to
avoid interference with bacteriological sampling. Sterility control samples (SR1) were taken
from the tooth surface with a sterile Omni Swab (Whatman FTA, Sigma-Aldrich) with an
ejectable head. Paper points were transferred to cryotubes containing phosphate buffered
saline (PBS) solution stored at -20°C. In each case, a single root canal was sampled in order
to confine the microbial evaluation to a single ecological environment. In multirooted teeth,
the root with the periapical lesion was selected. If there were periapical lesions in all
roots, the wider canal was selected. Two of the canals included in this study were from
single-rooted teeth, 3 were buccal canals in maxillary premolars, 1 palatal canal in
maxillary molar, and 10 distal canals in mandibular molars.
Old root fillings were removed using Gates-Glidden drills (Dentsply Maillefer, Ballaigues,
Switzerland) and endodontic files without the use of chemical solvents. The working length
(WL) was established 1-mm short of the apical foramen with an apex locator (Raypex6; VDW
GmbH, Munich, Germany), and then periapical radiographs were taken to ensure that all filling
material was removed. Irrigation with sterile saline solution was performed in order to
remove any remaining materials and to moisten the canal prior to sample collection. Next, the
canal was left filled with saline, and a small hand instrument was placed at the WL and used
to gently file the canal walls. An initial microbiologic sample (S1) was taken from the root
canal with sterile paper points consecutively placed at the WL. Three sterile paper points
were inserted into the root canal for sampling. Each paper point was left in the canal for
about 1 minute. Both the paper points and the endodontic hand instrument, without the handle,
were transferred to cryotubes containing 300 μl of PBS solution stored at -20°C. The samples
were transferred to genetic analysis laboratory for further analysis in cold chain.
Root canals were prepared by using the Revo S files and irrigated with 2.5% NaOCl. The canals
were apically enlarged to size 35 (AS35) at the working length. Between each instrument
change, the root canal was irrigated with 5 ml of 2.5% NaOCl solution by using 30-gauge
side-vented needle, which was placed 1 to 2 mm short of working length. Hence, a total of 30
mL of the irrigating solution was used. After instrumentation was completed, the smear layer
was removed with 2 mL 17% EDTA, which was left in the canal for 3 min, followed by 2.5%
NaOCl. The root canal was dried with sterile paper points and flushed with 2 ml of 10% sodium
thiosulfate for 1 min to inactivate the NaOCl solution. Next, a sample (S2) was taken from
the canals as described for S1. Following this, the NaOCl was agitated/activated as described
below.
XPF group: The instrument XP-Endo Finisher (FKG Dentaire, size #25, taper .00) was cooled
down (Endo-Frost; Roeko, Langenau, Germany) in order to keep it straight and measure the WL.
The canals were flushed with 2.5 mL 2.5% NaOCl for 30 s and activated by a XPF instrument
that was placed in the canal to 1 mm short of the WL and powered by the motor at 800 rpm (1
N-cm torque) for 30 s according to the manufacturer's instructions (in slow up-and-down
movements at approximately 7-mm amplitude in continuous rotation). Then the canals were
rinsed with 2.5 mL of 2.5% NaOCl, followed by activation of the substance with the XPF
instrument for 30 seconds, the same way as above. A new XP-endo Finisher file was used for
each canal.
EA group: The root canals were irrigated with 2.5 mL of 2.5% NaOCl for 30 s, followed by
sonic activation of this solution with EndoActivator red tip size #25/0.04 (EA; Dentsply
Tulsa Dental Specialties, Tulsa, OK), inserted into the root canal 1 mm short of the WL, at
10,000 cpm/min. for 30 seconds. The EA polymer tip moved vertically from apical to coronal
part of the canal during activation. Then the same procedure was repeated once more (sonic
activation of 2.5 mL of 2.5% NaOCl for 30 seconds) so that the total irrigation with NaOCl
and irrigation agitation time with the test devices were 1 min. The total volume of NaOCl
used per canal in both groups was 35 mL. In both groups, 5 mL of NaOCl was used and activated
for one minute.
Finally, the canals in both groups were dried and rinsed with 2 mL 10% sodium thiosulfate for
1 min. The post activation sample (S3) was obtained in the same way as the pre-activation
sample was collected and sent for the PCR analysis. Completion of the root canal treatment
proceeded with root filling using lateral condensation of gutta-percha. Access cavities were
restored with composite resin, and a final radiograph was taken. All the root canal and
microbial sampling procedures were performed by a single experienced endodontist. Total
bacterial loads, as well as the amount of Enterococcus faecalis were determined before
instrumentation, after instrumentation and use of the irrigation activation systems, by means
of droplet digital polymerase chain reaction (ddPCR).
Total bacterial loads, as well as the amount of Enterococcus faecalis were determined before
instrumentation, after instrumentation and use of the intracanal medicaments, by means of
ddPCR.
Genomic DNA isolation and measurement of DNA concentration DNA was extracted using the QIAamp
DNA Mini Kit (Qiagen, Germany) following the protocol recommended by the manufacturer. Before
DNA isolation, samples (the tubes with paper points) were digested at 50-60°C BY vortexING
for 30s in every 10 min in order to ensure disaggregation of all bacteria into the PBS
solution. Afterwards, the paper points were aseptically removed from the suspension and, the
bacterial suspension was pelleted by centrifugation for 10 min at 5000 g. The pellet was then
resuspended in 180 µl buffer ATL supplied by QIAamp DNA Mini Kit (QIAGEN GmbH, Hilden,
Germany) and 20 µl proteinase K (20 mg/ml) was added. Samples were incubated for 3 h at 56°C.
Subsequently, total bacterial genomic DNA was isolated according to the protocol of the
QIAamp DNA Mini Kit. The final volume of DNA solution of each sample was 150 μL and was taken
into account during calculation. DNA concentration (absorbance at 260 nm) was determined with
a spectrophotometer (Promega Quantifluor).
Amplification of 16S rRNA genes Primers for Universal and Enterococcus 16S rRNA genes were
designed in this study. After DNA extraction of samples with QIAamp DNA Mini Kit, 700-800 bp
of 16S rRNA sequences were amplified by using universal E8F forward primer
(5'-AGAGTTTGATCCTGGCTCAG-3') and universal E1115R reverse primer (5'-AGGGTTGCGCTCGTTG-3') 59.
The final volume of PCR reactions for each isolated bacterial strain was adjusted to 25 µl.
The amplification reactions of 16S rRNA genes were performed with the following conditions. 1
cycle of predenaturation at 95°C for 3 minutes, 35 cycles of 95°C for 30 seconds, 55°C for 30
seconds, and 72°C for 30 seconds which continue with a final extension step at 72°C for 10
minutes.
The PCR products were analyzed by electrophoresis using 2% agarose gel (containing ethidium
bromide) in Tris/BoratE/EDTA (TBE) buffer, with gels being analyzed under ultraviolet light
(at 140V for 20 minutes). Their images were visualized under ultraviolet illumination. In
addition, the control and optimization of primers to be used for ddPCR was also done in
conventional PCR.
Purification and Sequencing of the 16S rRNA Gene After the PCR reactions, the purification of
PCR products is done by hydrolyzing the excess primers and nucleotides with ExoSap-IT
(Thermo, PN: 78201.1.ML) containing Exonuclease I and Alkaline Phosphatase enzymes. 2 µl of
ExoSap-IT was mixed with 5 µl of PCR product for each sample. The ExoSap reaction is
performed at 37 °C for 15 minutes (enzyme activation) followed by 15 minutes (inactivation)
at 80 °C. Sequencing reactions were performed by using Bigdye™ Terminator v3.1 cycle
sequencing kit (Thermo). The reactions were performed according to the kit manual for all
isolated strains.
After purification of the products with Exosap, the sequence reaction was performed with
BigDye Terminator v3.1 Cycle Sequencing Kit (Thermo) under the following conditions. After
the sequence PCR, BigDye products were purified by colon method. Zymo ZR DNA Sequencing
Clean-up Kit (Zymo Research, USA) was used for this process. All samples were purified in
accordance with the protocol given in the kit and executed on the 3130XL genetic analyzer.
Droplet Digital PCR (ddPCR) Droplet Digital PCR (ddPCR) was performed using primers designed
according to the 16S rRNA region specific to the total bacteria and Enterococcus faecalis
species, after sequencing, absolute quantitation from the bacterial species found in the
paper-point sample. Primer pairs were 16S-F-5'-AGGGAATCTTCSGCAATGGG-3' and
16S-R-5'-ACGCCCAATAAATCCGGACA-'3 for total bacteria and ENT-F-5'-CGCTTCTTTCCTCCCGAGT-3' and
ENT-R-5'-GCCATGCGGCATAAACTG-3' primer pairs for Enterococcus Faecalis. In the PCR reaction,
amplicons amplified with unmarked primer pairs were analyzed by labeling with Eva-Green dye.
For absolute quantitation of Enterococcus and total 16S rRNA, PCR was performed with two
primer pairs from the same sample. 20 µL of PCR mix containing 10 µL of 2X ddPCR EvaGreen
Supermix (Bio-Rad, cat. no. 1864034), 9 µL of nuclease-free water, 0.25 µL of both forward
and reverse primer and 2 ng of DNA from each sample Thermal cycling conditions were: 95◦C for
5 min, then 40 cycles of 95◦C for 30 s and 60◦C for 1 min and two final steps at 4◦C for 5
minutes and 90◦C for 5minutes with a 4◦C infinite hold. After PCR was completed, the sealed
plate was transferred into the plate holder of the QX200 Droplet Reader (Bio-Rad, cat. no.
1864003).
