Nested PCR for detection of mutans streptococci in dental plaque

A View on Polymerase Chain Reaction as an Outstanding Molecular Diagnostic Technique in Periodontology

Objectives

This study presents a discussion on the fundamentals of polymerase chain reaction (PCR) and its use as a diagnostic tool in periodontology.

Materials and Methods

A computer-aided as well as hand-made search in PubMed and Scopus indexed journals (relevant to the topic) was done by keywords of molecular technique in periodontology, PCR, applications of PCR, and PCR in periodontics. Only the papers in the English language and outlining PCR and its association with periodontology were collected and utilized to provide a succinct review. There was no limitation for publication time.

Results

The results of our search showed that PCR has turned into a standard in diagnosis in the field of periodontology. A variety of researches has demonstrated that its sensitive, and specific characteristics make it a quick and effective technique of recognition, identification, and quantification of microorganisms. Identification of various immunoinflammatory markers at the mRNA expression level as well as ascertaining gene-related polymorphisms can also be performed.

Conclusions

The mechanisms of periodontal disease can further become clarified using PCR. Clinical Relevance. PCR as a diagnostic method can play a main part in the validation of the clinical diagnosis of periodontal disease indicating the reason, pathogenesis, clinical steps, progress, and prognosis of the disease.

Association between S. mutans and S. sanguinis in Severe Early childhood Caries and Caries-Free Children A Quantitative Real-Time PCR Analysis

OBJECTIVES

To identify S. mutans and S. sanguinis in initial and overnight plaque between 2 groups and to analyze the association between them and caries-related factors.

STUDY DESIGN

Collected supra gingival plaque from 140 Thai children aged 2-6 years old (S-ECC = 68, caries-free=72). Recorded plaque and gingival indices, dmft score, salivary mutans streptococci level, pH and buffer capacity. Firstly, the overnight plaque was collected, then, 4 hrs. after a thorough prophylaxis, the initial plaque was collected. Accessed parent's attitude and behavior in children's oral hygiene care and diet practice using a questionnaire. A quantitative real-time PCR was performed.

RESULTS

For initial plaque, S. sanguinis was higher in caries-free. S. mutans (0.011) and S. mutans/S. sanguinis ratio (0.005) were higher in S-ECC. S. sanguinis amount was inverse correlated with dmft (0.00), gingival index (0.044), and plaque index (0.011). For overnight plaque, S. mutans (0.00) and S. mutans/S. sanguinis ratio (0.005) were also higher in S-ECC. S. mutans, S. mutans/S. sanguinis ratio were positive correlated to dmft (0.00). Parent education levels (0.004) and bottle feeding (0.011) between 2 groups were different.

CONCLUSION

S. sanguinis, S. mutans and their ratio in initial and overnight plaque, low family income and bottle feeding are strongly associated with S-ECC.

Streptococcus mutans and Streptococcus sobrinus colonization and caries experience in 3- and 5-year-old Thai children

OBJECTIVES

The aim of this study was to examine the colonization of Streptococcus mutans and Streptococcus sobrinus in supra-gingival plaque samples and to determine their correlation with the prevalence of early childhood caries (ECC) in Thai children.

MATERIALS AND METHODS

A total of 344 Thai children, ages 3 and 5 years, were invited to participate in this study. Caries status of the children was examined. Supra-gingival plaque samples were collected. Quantitative real-time PCR was performed to evaluate DNA levels of S. mutans and S. sobrinus.

RESULTS

Eighty-five percent of the children were colonized by S. mutans and 50.9% of them were colonized by S. sobrinus. The prevalence of ECC was 43.8% and 56.2% among 3- and 5-year-old children, respectively, and was significantly associated with the presence of S. mutans and S. sobrinus. The severity of ECC was significantly correlated with increased DNA levels of the two bacteria. Children who were positive for S. mutans and S. sobrinus (Sm+/Sb+) were 8 times or 44 times more likely to experience ECC than children who were Sm-/Sb + or were Sm-/Sb-.

CONCLUSIONS

The study evidence further suggest that children colonized by both S. mutans and S. sobrinus are at the higher risk for ECC.

CLINICAL RELEVANCE

Molecular-based qPCR can be used to detect and quantify S. mutans and S. sobrinus colonization for epidemiological and clinical studies for ECC risk assessment.

Rapid and sensitive PCR-dipstick DNA chromatography for multiplex analysis of the oral microbiota

A complex of species has been associated with dental caries under the ecological hypothesis. This study aimed to develop a rapid, sensitive PCR-dipstick DNA chromatography assay that could be read by eye for multiplex and semiquantitative analysis of plaque bacteria. Parallel oligonucleotides were immobilized on a dipstick strip for multiplex analysis of target DNA sequences of the caries-associated bacteria, Streptococcus mutans, Streptococcus sobrinus, Scardovia wiggsiae, Actinomyces species, and Veillonella parvula. Streptavidin-coated blue-colored latex microspheres were to generate signal. Target DNA amplicons with an oligonucleotide-tagged terminus and a biotinylated terminus were coupled with latex beads through a streptavidin-biotin interaction and then hybridized with complementary oligonucleotides on the strip. The accumulation of captured latex beads on the test and control lines produced blue bands, enabling visual detection with the naked eye. The PCR-dipstick DNA chromatography detected quantities as low as 100 pg of DNA amplicons and demonstrated 10- to 1000-fold higher sensitivity than PCR-agarose gel electrophoresis, depending on the target bacterial species. Semiquantification of bacteria was performed by obtaining a series of chromatograms using serial 10-fold dilution of PCR-amplified DNA extracted from dental plaque samples. The assay time was less than 3 h. The semiquantification procedure revealed the relative amounts of each test species in dental plaque samples, indicating that this disposable device has great potential in analysis of microbial composition in the oral cavity and intestinal tract, as well as in point-of-care diagnosis of microbiota-associated diseases.

Sensitive deep-sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism

With 29 individual antiretroviral drugs available from six classes that are approved for the treatment of HIV-1 infection, a combination of different phenotypic and genotypic tests is currently needed to monitor HIV-infected individuals. In this study, we developed a novel HIV-1 genotypic assay based on deep sequencing (DeepGen HIV) to simultaneously assess HIV-1 susceptibilities to all drugs targeting the three viral enzymes and to predict HIV-1 coreceptor tropism. Patient-derived gag-p2/NCp7/p1/p6/pol-PR/RT/IN- and env-C2V3 PCR products were sequenced using the Ion Torrent Personal Genome Machine. Reads spanning the 3' end of the Gag, protease (PR), reverse transcriptase (RT), integrase (IN), and V3 regions were extracted, truncated, translated, and assembled for genotype and HIV-1 coreceptor tropism determination. DeepGen HIV consistently detected both minority drug-resistant viruses and non-R5 HIV-1 variants from clinical specimens with viral loads of ≥1,000 copies/ml and from B and non-B subtypes. Additional mutations associated with resistance to PR, RT, and IN inhibitors, previously undetected by standard (Sanger) population sequencing, were reliably identified at frequencies as low as 1%. DeepGen HIV results correlated with phenotypic (original Trofile, 92%; enhanced-sensitivity Trofile assay [ESTA], 80%; TROCAI, 81%; and VeriTrop, 80%) and genotypic (population sequencing/Geno2Pheno with a 10% false-positive rate [FPR], 84%) HIV-1 tropism test results. DeepGen HIV (83%) and Trofile (85%) showed similar concordances with the clinical response following an 8-day course of maraviroc monotherapy (MCT). In summary, this novel all-inclusive HIV-1 genotypic and coreceptor tropism assay, based on deep sequencing of the PR, RT, IN, and V3 regions, permits simultaneous multiplex detection of low-level drug-resistant and/or non-R5 viruses in up to 96 clinical samples. This comprehensive test, the first of its class, will be instrumental in the development of new antiretroviral drugs and, more importantly, will aid in the treatment and management of HIV-infected individuals.

Prevalence of Streptococcus mutans and Lactobacillus fermentum and their association with caries and dietary habits in preschool Thai children

AIMS

To detect the prevalence of Streptococcus mutans and Lactobacillus fermentum in plaque obtained from severe early childhood caries (S-ECC) and caries-free (CF) groups and to assess any association between their prevalence, feeding habits and oral hygiene practices within each group.

STUDY DESIGN

Sixty-four supra-gingival plaque samples were collected from S-ECC and CF groups (CF = 30, S-ECC = 34). All participants were asked about feeding habits and oral hygiene care behaviour by direct questionnaire.

METHODS

After DNA extraction, S. mutans and L. fermentum were amplified using standard PCR. Nested PCR was performed as a second identification method for S. mutans.

RESULTS

Mean age in CF and S-ECC was 2.29 ± 0.42 and 2.49 ± 0.41 years, respectively. Mean dmft in S-ECC was 4.51 ± 0.72. By standard PCR, no S. mutans was detected in CF group, while 10 % was detected in S-ECC group. By nested PCR, S. mutans was detected for 48 and 50 % in CF and S-ECC, respectively. L. fermentum was detected for 16 and 40 % in CF and S-ECC, respectively.

CONCLUSION

Nested PCR gave a higher detection frequency than standard PCR but not significant (p ≤ 0.05). The prevalence of S. mutans was not different between the two groups, while the prevalence of L. fermentum was significantly associated with S-ECC (p ≤ 0.05).

Diet and caries-associated bacteria in severe early childhood caries

Frequent consumption of cariogenic foods and bacterial infection are risk factors for early childhood caries (ECC). This study hypothesized that a short diet survey focused on frequency of foods, categorized by putative cariogenicity, would differentiate severe ECC (S-ECC) from caries-free children. Children's diets were obtained by survey and plaque bacteria detected by PCR from 72 S-ECC and 38 caries-free children. S-ECC children had higher scores for between-meal juice (p < 0.01), solid-retentive foods (p < 0.001), eating frequency (p < 0.005), and estimated food cariogenicity (p < 0.0001) than caries-free children. S-ECC children with lesion recurrence ate fewer putative caries-protective foods than children without new lesions. Streptococcus mutans (p < 0.005), Streptococcus sobrinus (p < 0.005), and Bifidobacteria (p < 0.0001) were associated with S-ECC, and S. mutans with S. sobrinus was associated with lesion recurrence (p < 0.05). S. mutans-positive children had higher food cariogenicity scores. Food frequency, putative cariogenicity, and S. mutans were associated with S-ECC individually and in combination.

Detection of oral streptococci in dental biofilm from caries-active and caries-free children

This work correlated the presence of oral streptococci in dental biofilm with clinical indexes of caries and oral hygiene in caries-active and caries-free children. S. mutans and/or S. sobrinus in the dental biofilm does not indicate a direct risk for developing dental caries.

A novel method for the identification of saliva by detecting oral streptococci using PCR

We have used DNA amplification methods to detect common oral bacterial strains to test for the presence of saliva in forensic samples. Streptococcus salivarius and Streptococcus mutans were detected in various forms of saliva samples, whereas these streptococci were not detected in semen, urine, vaginal fluid, or on skin surfaces. Therefore, we demonstrated that these streptococci are promising new marker for the forensic identification of saliva. Our data indicated that S. salivarius is more reliable than S. mutans as an indicator of saliva presence, because the detection rates for S. salivarius and S. mutans by this method were 100% and 90%, respectively. Furthermore, S. salivarius was detected in all saliva stain samples, whereas S. mutans was only identified in 60% of the stains. Finally, using this method we were able to successfully detect S. salivarius and S. mutans in mock forensic samples. We therefore suggested that this method is useful for the identification of saliva in forensic science.

Overestimation of Streptococcus mutans prevalence by nested PCR detection of the 16S rRNA gene

This study was carried out in order to compare two PCR-based methods in the detection of Streptococcus mutans. The first PCR method was based on primers for the 16S rRNA gene and the second method was based on specific primers that targeted the glucosyltransferase gene (gtfB). Each PCR was performed with eight different streptococci from the viridans group, five other streptococci and 17 different non-streptococcal bacterial strains. Direct use of the S. mutans 16S rRNA gene-specific primers revealed that Streptococcus gordonii and Streptococcus infantis were also detected. After amplifying the 16S rRNA gene with universal primers and subsequently performing nested PCR, the S. mutans-specific nested primers based on the 16S rRNA gene detected all tested streptococci. There was no cross-reaction of the gtfB primers after direct PCR. Our results indicate that direct PCR and nested PCR based on 16S rRNA genes can reveal false-positive results for oral streptococci and lead to an overestimation of the prevalence of S. mutans with regards to its role as the most prevalent causative agent of dental caries.

Detection frequency of periodontitis-associated bacteria by polymerase chain reaction in subgingival and supragingival plaque of periodontitis and healthy subjects

The aim of this study was to compare the detection frequencies of 25 bacterial species in subgingival and supragingival plaque of 18 untreated periodontitis subjects and 12 periodontally healthy subjects. Genomic DNA was extracted from subgingival and supragingival plaque samples, and bacterial detection was performed by polymerase chain reaction of the 16S rRNA genes. Fourteen bacteria showed no relationship with periodontitis, and 11 of these 14 species were frequently detected (> or =50%) in subgingival plaque in both periodontitis and healthy subjects. Nine bacteria such as Eubacterium saphenum, Prevotella intermedia, and Treponema denticola seemed to be related to periodontitis; their detection frequencies in subgingival plaque samples were higher in periodontitis than in healthy subjects, but these differences were not statistically significant by multiple comparisons (0.002< or =P<0.05). Two species (Mogibacterium timidum and Porphyromonas gingivalis) were detected significantly more frequently in subgingival plaque of periodontitis subjects than of healthy subjects (P<0.002), with P. gingivalis being detected only in periodontitis subjects, suggesting that these two species are closely related to periodontitis. There were no significant differences in the detection frequencies of the 25 bacteria between subgingival and supragingival plaque, suggesting that the bacterial flora of supragingival plaque reflects that of subgingival plaque.

A Method for Mapping the Distribution Pattern of Cariogenic Streptococci within Dental Plaque in vivo

This study was carried out to develop a method for mapping the distribution of cariogenic oral streptococci, Streptococcus mutans and Streptococcus sobrinus, from the outermost to the innermost plaque. Ten consenting subjects were asked to form plaque by abstaining from tooth brushing over 3 days within in situ plaque-generating devices, which were placed on the upper molars. The plaque formed in the devices was separated into 8-10 layered fractions (100 microm thick). Genomic DNA was extracted from each plaque fraction by a commercial DNA purification kit and used for the amplification of the 16S ribosomal RNA gene sequences by polymerase chain reaction (PCR) with universal primers. The products were then amplified by PCR with S. mutans- or S. sobrinus-specific nested primers. The final products were separated on agarose gels, stained and photographed to confirm the existence of S. mutans and S. sobrinus. The results showed that S. mutans was detected in the plaque obtained from all of the 10 subjects and S. sobrinus in the plaque of 7 subjects. However, the distribution patterns of fractions positive for S. mutans and S. sobrinus varied among the subjects, with a tendency for frequent detection of both species in the outer to middle layers of dental plaque. There were no plaque fractions in which only S. sobrinus was found. This method could be useful to map the distribution of cariogenic microorganisms and to estimate the bacterial ecology for oral biofilm.