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.

Efeito da irrigação ultrassônica e da medicação intracanal com hidróxido de cálcio na quantidade e no metabolismo de bactérias que persistiram após o preparo dos canais radiculares de dentes com periodontite apical / Effect of ultrasonic irrigation and calcium hydroxide intracanal medication on the levels and metabolism of bacteria that persisted after root canal preparation of teeth with apical periodontitis

Estudos moleculares ressaltam as limitações do protocolo endodôntico tradicional em eliminar bactérias dos canais radiculares. Apesar do preparo químico-cirúrgico (PQC) promover uma drástica redução bacteriana, muitos canais continuam infectados após essa etapa do tratamento. Dessa forma, estudos apontam para a necessidade de complementação técnica para potencializar a desinfecção dos canais radiculares após o PQC. Assim, o objetivo deste estudo clínico foi avaliar, por métodos moleculares baseados em DNA e RNA, o efeito dos métodos complementares ao preparo na desinfecção dos canais radiculares. Coletas microbiológicas dos canais de 20 dentes unirradiculares com periodontite apical foram feitas em diferentes etapas do tratamento endodôntico: previamente ao preparo (S1); após o PQC realizado com sistema Reciproc associado à irrigação com NaOCl 2,5% (S2); após a irrigação ultrassônica passiva, denominada PUI (S3); e após a medicação intracanal à base de hidróxido de cálcio (S4). As amostras foram submetidas à extração de DNA e RNA. O RNA foi submetido à reação de transcrição reversa (RT-PCR) para confecção da fita dupla de DNA complementar (cDNA). DNA e cDNA foram submetidos a reações de qPCR, com iniciadores universais para a região 16S rRNA do domínio Bacteria. A atividade metabólica das bactérias foi verificada através da relação entre os níveis de rRNA e rDNA determinados pelos ensaios de qPCR. Os dados foram analisados pelo teste de Wilcoxon para amostras pareadas (p < 0,05). As amostras S1 dos 20 casos apresentaram altos níveis de rDNA (mediana: 1,25 x 105, intervalo 1,83 x 104 - 9,2 x 106) e rRNA bacteriano (mediana: 5,47 x 105, intervalo 7,8 x 104 - 5,95 x 107). Dezessete canais (85%) apresentaram reações qPCR positivas para rDNA nas amostras pós-preparo (S2). A redução de rDNA após o preparo foi estatisticamente significativa (p = 0,0003), com mediana de 2,5 x 104 (intervalo 2,26 x 103 - 9,52 x 104) cópias de rDNA em S2. Por sua vez, os níveis de rRNA (mediana: 7,84 x 104, intervalo 2,91 x 103 - 1,09 x 106) foram maiores que os níveis de rDNA (p = 0,01), sugerindo que essas bactérias estavam metabolicamente ativas em S2. Após a PUI, o número de amostras S3 com resultados positivos para rDNA caiu para 12, representando uma redução significativa em relação às amostras S2 (p = 0,008). Além disso, a PUI promoveu uma redução significativa dos níveis de rDNA (mediana 2,94 x 103, intervalo 2,70 x 103 - 1,09 x 105) em relação à amostras S2 (p = 0,01). Na análise baseada em rRNA, os níveis em S3 (mediana: 03 x 104, intervalo 1,82 x 103 - 1,39 x 105) não apresentaram diferença significativa em comparação aos níveis de rDNA (p = 0,07), sugerindo que houve uma redução do metabolismo bacteriano após a PUI. Em S4, o número de casos positivos para rDNA bacteriano (n = 13) e os níveis de rDNA (mediana: 3,73 x 104, intervalo 1,98 x 103 - 3,21 x 105) foram ligeiramente maiores quando comparados aos valores das amostras S3, porém sem diferenças significativas. Entretanto, os níveis de rRNA (mediana: 1,08 x 105, intervalo 3,41 x 103 - 1,60 x 106) foram maiores que os de rDNA (p = 0,02) nas amostras S4, sugerindo que as bactérias retomaram sua atividade metabólica apesar do uso da medicação intracanal. Portanto, foi possível concluir que a irrigação ultrassônica passiva contribuiu para a desinfecção dos canais radiculares, promovendo uma redução do número e do metabolismo de bactérias. Por outro lado, as bactérias persistiram ativas nos canais radiculares após o uso do hidróxido de cálcio como medicação intracanal em dentes com periodontite apical.

New host record of five Flavobacterium species associated with tropical fresh water farmed fishes from North India

Abstract Yellow pigmented, filamentous, Gram-negative bacteria belonging to genus Flavobacterium are commonly associated with infections in stressed fish. In this study, inter-species diversity of Flavobacterium was studied in apparently healthy freshwater farmed fishes. For this, ninety one yellow pigmented bacteria were isolated from skin and gill samples (n = 38) of three farmed fish species i.e. Labeo rohita, Catla catla and Cyprinus carpio. Among them, only twelve bacterial isolates (13.18%) were identified as Flavobacterium spp. on the basis of morphological, biochemical tests, partial 16S rDNA gene sequencing and phylogenetic analysis. On the basis of 16S rDNA gene sequencing, all the 12 isolates were 97.6-100% similar to six different formally described species of genus Flavobacterium. The 16S rDNA based phylogenetic analysis grouped these strains into six different clades. Of the 12 isolates, six strains (Fl9S1-6) grouped with F. suncheonense, two strains (Fl6I2, Fl6I3) with F. indicum and the rest four strains (Fl1A1, Fl2G1, Fl3H1 and Fl10T1) clustered with F. aquaticum, F. granuli, F. hercynium and F. terrae, respectively. None of these species except, F. hercynium were previously reported from fish. All the isolated Flavobacterium species possessed the ability of adhesion and biofilm formation to colonize the external surface of healthy fish. The present study is the first record of tropical freshwater farmed fishes as hosts to five environmentally associated species of the Flavobacterium.

Characterizations of a new Cordyceps cicadae isolate and production of adenosine and cordycepin

Cordyceps is a fastidious pathogenic fungus infecting insects, and recent years have witnessed rapid progress in its medical properties. In this study, a wild isolate, C. cicadae MP12, was characterized through in vitro cultivation and its nuclear small-subunit (SSU) ribosomal DNA (rDNA) data. In vitro culture of C. cicadae MP12 was established by growing its fruiting bodies in a solid matrix. C. cicadae MP12 was inoculated into Cryptotympana atrata cicada pupae for in vivo culture, where the fungi developed its fruiting body as well. The contents of adenosine and cordycepin in dried fruiting bodies after culture were 1421.45µg/g and 1398.12 µg/g, respectively. Therefore, the established cultures from this study could be used for the production of various medically important metabolic substances.

The presence of Helicobacter pylori in the liver depends on the Th1, Th17 and Treg cytokine profile of the patient

The hypothesis that Helicobactermight be a risk factor for human liver diseases has arisen after the detection of Helicobacter DNA in hepatic tissue of patients with hepatobiliary diseases. Nevertheless, no explanation that justifies the presence of the bacterium in the human liver has been proposed. We evaluated the presence of Helicobacterin the liver of patients with hepatic diseases of different aetiologies. We prospectively evaluated 147 patients (106 with primary hepatic diseases and 41 with hepatic metastatic tumours) and 20 liver donors as controls. Helicobacter species were investigated in the liver by culture and specific 16S rDNA nested-polymerase chain reaction followed by sequencing. Serum and hepatic levels of representative cytokines of T regulatory cell, T helper (Th)1 and Th17 cell lineages were determined using enzyme linked immunosorbent assay. The data were evaluated using logistic models. Detection of Helicobacter pylori DNA in the liver was independently associated with hepatitis B virus/hepatitis C virus, pancreatic carcinoma and a cytokine pattern characterised by high interleukin (IL)-10, low/absent interferon-γ and decreased IL-17A concentrations (p < 10-3). The bacterial DNA was never detected in the liver of patients with alcoholic cirrhosis and autoimmune hepatitis that are associated with Th1/Th17 polarisation. H. pylori may be observed in the liver of patients with certain hepatic and pancreatic diseases, but this might depend on the patient cytokine profile.

18S-rDNA Sequencing, enzyme patterns and morphological characterization of trichophyton isolates

Dermatophytes, capable to use keratin of the host for nutrition, belong to one of the major groups of pathogenic fungi. Since dermatophytes are a closely related group they share various common features, and the morphology of isolates of a given species can be atypical, making species identification and differentiation even more difficult. Many methods have been explored in attempts to distinguish dermatophytes, but the combined use of different approaches for the investigation of the intraspecific and interspecific variability of Trichophyton continues to be scarce. Some studies have shown that amplified fragments of the small ribosomal DNA subunit 18S contains variable regions which can be used to discriminate between medically relevant yeast species, indicating that these regions could also be used for differentiation between dermatophytes. In our study, sequence analysis of the 18S-rDNA gene was combined with morphological and biochemical criteria in order to detect genetic differences between seven Trichophyton isolates and estimate their phylogenetic relationships. The results show that the isolates investigated belong to the Trichophyton group, which potentially contains the Trichophyton rubrum cluster.

Molecular cloning and characterization of the ribosomal RNA genes of the cestode Echinococcus granulosus

The analysis of total protoscolex DNA and some rDNA recombinats of Echinococcus granulosus by restriction endonuclease mapping and hybridization to rDNA probes indicated the complex organization of the ribosomal RNA genes and that some repeat units are larger than 15 kb. The nontranscribed spacer can be up to 13 kb in length in some repeat units. Restriction site polymorphisms was detected mainly in the nontranscribed spacer regions although some polymorphisms was also observed in the 28S rRNA coding region. On the basis of Southern blot hybridization using EcoRi-digested genomic DNA, we conclude that the repeat units containing an extra EcoRI site are present almost in the same proportion as the repeat units without the extra EcoRi site in the 28S rRNA coding region