Comparison of rRNA-based reverse transcription PCR and rDNA-based PCR for the detection of streptococci in root canal infections

Abstract Objective The rDNA-based method is unable to distinguish between alive and dead cells. Alternatively, bacterial viability can be assessed by molecular methods based on ribosomal RNA (rRNA). Therefore, this study aimed to detect viable streptococci in root canal samples using rRNA-based reverse transcription polymerase chain reaction (RT-PCR), compared to an rDNA-based PCR assay. Methodology Microbiological root canal samples were obtained from 32 teeth with primary endodontic infections before (S1) and after chemomechanical preparation (S2), and after removal of intracanal medication (S3). RNA and DNA were extracted, and complementary DNA (cDNA) was synthesized from RNA using RT reaction. cDNA and genomic DNA were subjected to PCR with primers complementary to the 16S rRNA sequences of Streptococcus spp. McNemar's test was used to compare the detection rate of both assays (P<0.05). Results Streptococci were detected in 28.12% (9/32) and 37.5% (12/32) of S1 samples using rRNA- and rDNA-based PCR assays, respectively. In contrast, they were detected in only 6.25% (2/32) of S2 samples using rRNA-based RT-PCR, compared to 15.62% (5/32) using rDNA-based PCR. Finally, in S3 samples, streptococci were not detected by rRNA, whereas rDNA-based PCR still detected the bacteria in 12.5% (4/32) of the samples. The total number of PCR-positive reactions in the rDNA-based PCR was higher than in the rRNA-based assay (P<0.05). Conclusions The rRNA-based RT-PCR showed a lower detection rate of streptococci when compared to the rDNA-based PCR, suggesting that the latter may have detected dead cells of streptococci in root canal samples.

Estudo in vivo da susceptibilidade de bactérias Gram-positivas após procedimentos químico-cirúrgico e medicação intracanal pelo método de reação de cadeia de polimerase baseado em DNA e RNA / In vivo study of the susceptibility of Gram-positive bacteria after chemosurgical preparation and intracanal medication by RNA and DNA-based polymerase chain reaction

Este estudo identificou a presença e a viabilidade de Streptococcus spp., Propionibacterium acnes e Enterococcus faecalis antes e após os procedimentos endodônticos, utilizando o método de reação de cadeia de polimerase (PCR) baseado em RNA ribossômico (rRNA) e seus respectivos genes (rDNA). Foram coletadas amostras de 20 dentes com infecção primária antes (S1) e após o preparo químico-cirúrgico (S2), e depois do emprego do Ca(OH)2 como medicação intracanal (S3). DNA e RNA foram extraídos da mesma amostra de canal radicular e utilizados como moldes para reação de PCR com iniciadores específicos para a região 16S rRNA das espécies analisadas. Streptococcus espécies foram detectados em 20% e 25% das amostras S1 utilizando os métodos baseados em rRNA e rDNA, respectivamente; enquanto P. acnes foi detectado apenas pela análise de rRNA, estando presente em 10% das amostras S1. Após o preparo químico-cirúrgico, Streptococcus spp. foram detectado em 10% das amostras S2 quando se utilizou rDNA, porém não foi detectado pelo método baseado em rRNA, indicando ausência de células viáveis. Por outro lado, P. acnes foi detectado por ambos os métodos nas amostras S2, com prevalência de 10% e 5% quando se utilizou rRNA e rDNA como molde para PCR, respectivamente. Nas amostras S3, P. acnes foi a única espécie detectada nos ensaios baseados em rRNA, presente em 10% dos casos, enquanto o método baseado em rDNA falhou em detectar essa espécie. Por sua vez, E. faecalis não foi detectado em nenhuma amostra pelos métodos utilizados. Portanto, concluise que a suscetibilidade bacteriana aos procedimentos endodônticos varia entre as espécies Gram-positivas. Enquanto Streptococcus spp. foram suscetíveis, P. acnes persistiu ativo em canais radiculares após o preparo químico-cirúrgico e medicação intracanal. Esses dados sugerem que há necessidade de novas estratégias para a eliminação de espécies resisitentes ao tratamento endodôntico.

This study identified the presence and viability of Streptococcus spp., Enterococcus faecalis and Propionibacterium acnes before and after endodontic procedures, using the polymerase chain reaction (PCR) based on ribosomal RNA (rRNA) and their genes (rDNA ). Samples of 20 teeth with primary infection were collected before (S1) and after chemical-surgical preparation (S2), and after Ca(OH)2 as temporary dressing (S3). DNA and RNA were extracted from the same root canal sample and used as templates for PCR with specific primers for 16S rRNA region of the analyzed species. Streptococcus species were detected in 20% and 25% of the S1 samples using methods based on rRNA and rDNA, respectively; while P. acnes was only detected by analysis of rRNA, present in 10% of the samples S1. After chemicalsurgical preparation, Streptococcus spp. were detected in 10% of S2 samples when using rDNA as template, but they were not detected by the method based on rRNA, indicating the absence of viable cells. Furthermore, P. acnes was detected by both methods in samples S2, with a prevalence of 10% and 5% when using as template rRNA and rDNA for PCR, respectively. In S3 samples, P. acnes was the only species detected in assays based on rRNA, present in 10% of cases, while the rDNA-based method failed to detect this species. E. faecalis was not detected in any sample by the methods used. Therefore, it is concluded that bacterial susceptibility to endodontic procedures may vary among Gram-positive species. While Streptococcus spp. were susceptible, P. acnes persisted active in root canals after chemicalsurgical preparation and dressing. These data suggest the need for new strategies to eliminate resisitant species to endodontic treatment.