Identification and genetic characterisation of melibiose-negative isolates of Streptococcus mutans

Oral Microbiome and Dental Caries Development

Dental caries remains the most prevalent oral disease worldwide. The development of dental caries is highly associated with the microbiota in the oral cavity. Microbiological research of dental caries has been conducted for over a century, with conventional culture-based methods and targeted molecular methods being used in order to identify the microorganisms related to dental caries. These methods’ major limitation is that they can identify only part of the culturable microorganisms in the oral cavity. Introducing sequencing-based technology and bioinformatics analysis has boosted oral microbiome research and greatly expanded the understanding of complex oral microbiology. With the continuing revolution of molecular technologies and the accumulated sequence data of the oral microbiome, researchers have realized that microbial composition alone may be insufficient to uncover the relationship between caries and the microbiome. Most updated evidence has coupled metagenomics with transcriptomics and metabolomics techniques in order to comprehensively understand the microbial contribution to dental caries. Therefore, the objective of this article is to give an overview of the research of the oral microbiome and the development of dental caries. This article reviews the classical concepts of the microbiological aspect of dental caries and updates the knowledge of caries microbiology with the results of current studies on the oral microbiome. This paper also provides an update on the caries etiological theory, the microorganisms related to caries development, and the shifts in the microbiome in dental caries development.

Methods of Biotyping of Streptococcus mutans Species with the Routine Test as a Prognostic Value in Early Childhood Caries

Purpose

In order to investigate the suitability of Streptococcus mutans species biotyping by measuring the activity of selected enzymes from a commercial test, criteria were established for biotyping clinical strains from children with dental caries. In addition, the relationships between the selected biotypes, sensitivity to commonly used antibiotics, and early childhood caries were determined.

Methods

A total of 142 S. mutans isolates from dental plaque of children with caries were divided into different biotypes. Patients were divided into two groups: noncavitated (1-2 in ICDAS) and cavitated (5-6 in ICDAS) lesions. Biotyping criteria were determined based on both the arbitrary method and the clusterization method. The susceptibility of the strains to amoxicillin, cefazolin, erythromycin, and teicoplanin was studied by diluting a solid medium.

Results

Biotype I was the most common. Mean MIC values showed that the strains belonging to biotypes II and IV were the most sensitive to amoxicillin. For predetermined biotypes, observed differences were dependent on the severity of dental caries.

Conclusions

The proposed method of S. mutans strains biotyping is relatively quick and simple to use, provided the application of suitable biotyping criteria, and may contribute to the effective prevention of dental caries induced by S. mutans.

Development of species-specific primers for detection of Streptococcus mutans in mixed bacterial samples

Streptococcus mutans is the major microbial pathogen associated with dental caries in children. The objectives of this study were to design and evaluate species-specific primers for the identification of S. mutans. Validation of the best primer set, Sm479F/R, was performed using seven S. mutans reference strains, 48 ATCC non-S. mutans strains, 92 S. mutans clinical isolates, DNA samples of S. mutans-Streptococcus sobrinus or S. mutans-Streptococcus sanguinis, and mixed bacterial DNA of saliva samples from 33 18-month-old children. All of the S. mutans samples tested positive, and no PCR products were amplified from members of the other streptococci or nonstreptococci strains examined. The lowest detection level for PCR was 10(-2) ng of S. mutans DNA (c. 4.6 x 10(3) copies) in the test samples. The results of this study suggest that the Sm479F/R primer pair is highly specific and sensitive for identification of S. mutans in either purified or mixed DNA samples.

Comparative genome hybridization of Streptococcus mutans strains

The basis for genotypic and phenotypic variation within Streptococcus mutans is poorly understood but the availability of the genome sequence of strain UA159 provides an opportunity for comparative studies. Genomic DNA prepared from nine strains of S. mutans was used to probe a microarray consisting of oligonucleotides representing 1948 open reading frames of S. mutans UA159. A total of 385 (20%) of the UA159 open reading frames were found to be absent from one or more of the test strains. Absent open reading frames frequently occurred in blocks of adjacent open reading frames and represented regions previously experimentally detected by polymerase chain reaction, predicted genomic islands and insertion sequence elements as well as novel open reading frames. Approximately half appear to involve foreign DNA acquired by horizontal transmission. The results indicate the existence of distinct core and dispensable genomes and may help explain the phenotypic and genotypic variation within S. mutans.

In vitro growth and acid production by mutans streptococci on traditional African foods

The growth rate and production of acids by mutans streptococci (MS) are influenced by their ability to ferment different dietary carbohydrates. This suggests that the nutrient environment in the oral cavity affects bacterial virulence. The aim of this study was to investigate the effect of maize, samp and brown bread on the growth and acidogenicity of this species. Six laboratory references and five clinical strains isolated from the dental plaque of South African black and 'colored' (historical race classification) children were studied in batch culture on maize, samp (coarsely ground maize), brown bread and compared against a 3% sucrose control. The doubling time of bacterial strains was prolonged in maize (1.9-17.5 h) and samp (2.4-18.4 h), and the number of cell divisions was low. Staple foods accounted for 25% (F=5.98; P=0.0007) and MS strains 30.78% (F=2.84; P=0.009) of the total variance. The fermentation of samp and maize showed the least drop in pH of the culture medium, ranging between 0.54 and 1.06 and 0.69 and 2.28 pH units respectively, with variation between strains most significant in maize (F=33.62; P<0.0001). The total mean concentration of acids produced was highest in bread (25.13 mM/mL) and samp (17.00 mM/mL) which was comparable to Brain Heart Infusion broth (16.49 mM/mL) and a basal synthetic medium (17.96 mM/mL) containing 3% sucrose, but the yield of lactate, acetate and formate was low during the fermentation of samp (0.50 mM/mL), BHI+3% sucrose (4.12 mM/mL) and brown bread (0.06 mM/mL) respectively. Results indicated that maize and samp do not optimally support the growth or acid production by MS, and the varying response of test strains demonstrates the strain variability of this species to different carbohydrate sources in the diet.

Genomic variation in Streptococcus mutans: deletions affecting the multiple pathways of β-glucoside metabolism

The genome of Streptococcus mutans UA159 contains two phospho-beta-glucosidase genes, bglA and celA, which occur in operon-like arrangements along with genes for components of phosphotransferase transport systems and a third phospho-beta-glucosidase encoded by the arb gene, which does not have its own associated transport system but relies on uptake by the bgl or cel systems. Targeted inactivation of each of the phospho-beta-glucosidase genes revealed that bglA is involved in aesculin hydrolysis, celA is essential for utilisation of cellobiose, amygdalin, gentobiose and salicin, and arb is required for utilisation of arbutin. Inactivation of genes for the phosphotransferase systems revealed an overlap of specificity for transport of beta-glucosides and also indicated that further, unidentified transport systems exist. The cel and arb genes are subject to catabolite repression by glucose, but the regM gene is not essential for catabolite repression. Screening a collection of isolates of S. mutans revealed strains with deletions affecting the msm, bgl and/or cel operons. The phenotypes of these strains could largely be explained on the basis of the results obtained from the knockout mutants of S. mutans UA159 but also indicated the existence of other pathways apparently absent from UA159. The extensive genetic and phenotypic variation found in beta-glucoside metabolism indicates that there may be extensive heterogeneity in the species.

Characterization of Streptococcus mutans diversity by determining restriction fragment-length polymorphisms of the gtfB gene of isolates from 5-year-old children and their mothers

The diversity between Streptococcus mutans clinical isolates from 5-year-old children and their mothers in two South African ethnic groups was investigated. The gtfB gene encoding for glucosyltransferase (EC 2.4.1.5), an enzyme responsible for the synthesis of extracellular polysaccharides was characterized by PCR-RFLP with HaeIII restriction enzyme digestion. Forty-seven children were examined for dental caries and 128 S. mutans clinical isolates cultured from samples of their saliva and plaque and from the saliva of their mothers. Thirty-three children had active caries (70%) and the remainder (n = 14) were caries-free. Caries prevalence was significantly different (p = 0.02) between black African and coloured children, but no differences were found between gtfB amplitypes by caries or ethnic grouping. Thirty-four (27%) of the S. mutans clinical isolates investigated did not ferment melibiose. Melibiose-negative phenotypes (n = 10) isolated from four families showed gtfB RFLP patterns identical to each other. Mothers and children harboured between one and three amplitypes. GtfB amplitypes were identical in 17 families (17/47), of which nine only were identical to S. mutans reference strains. The percentage match between S. mutans amplitype from mothers and their children was low (13%) in the caries-free group compared to children with caries (44%). RFLP analysis of the gtfB gene showed the diversity of S. mutans genotypes within two South African populations that were acquired from mothers and other sources.

A novel glucan-binding protein with lipase activity from the oral pathogen Streptococcus mutans

Streptococcus mutans produces extracellular glucosyltransferases (GTFs) that synthesize glucans from sucrose. These glucans are important in determining the permeability properties and adhesiveness of dental plaque. GTFs and the GbpA glucan-binding protein are characterized by a binding domain containing a series of 33-amino-acid repeats, called 'A' repeats. The S. mutans genome sequence was searched for ORFs containing 'A' repeats, and one novel gene, gbpD, which appears to be unique to the mutans group of streptococci, was identified. The GbpD sequence revealed the presence of three 'A' repeats, in the middle of the protein, and a novel glucan-binding assay showed that GbpD binds to dextran with a K(D) of 2-3 nM. Construction of truncated derivatives of GbpD confirmed that the 'A' repeat region was essential for binding. Furthermore, a gbpD knockout mutant was modified in the extent of aggregation induced by polymers derived from sucrose. The N-terminus of GbpD has a signal sequence, followed by a region with no homologues in the public databases, while the C-terminus has homology to the alpha/beta hydrolase family (including lipases and carboxylesterases). GbpD contains the two regions typical of these enzymes: a GxSxG active site 'lipase box' and an 'oxyanion hole'. GbpD released free fatty acids (FFAs) from a range of triglycerides in the presence of calcium, indicating a lipase activity. The glucan binding/lipase bifunctionality suggested the natural substrate for the enzyme may be a surface macromolecule consisting of carbohydrate linked to lipid. The gbpD mutant was less hydrophobic than wild-type and pure recombinant GbpD reduced the hydrophobicity of S. mutans and another plaque bacterium, Streptococcus sanguinis. GbpD bound to and released FFA from lipoteichoic acid (LTA) of S. sanguinis, but had no effect on LTA from S. mutans. These results raise the intriguing possibility that GbpD may be involved in direct interspecies competition within the plaque biofilm.

Genetic studies on reference strains of mutans streptococci

Twenty four reference strains (serotype a-h) belonging to the mutans group of streptococci were compared for DNA fragment patterns of rDNA after treatment with Hind III. It was shown that Streptococcus cricetus (serotype a), S. rattus (serotype b), and S. downei (serotype h) reveals comparatively homogeneous patterns while S. mutans (serotype c, e and f) exhibits differences between the different serotypes as well as within single serotypes. S. sobrinus had an intermediary diversity. These data support the previous findings that S. mutans is heterogeneous at the serological, biochemical and genetical level.

DNA probes and primers in dental practice

In clinical microbiology, molecular genetic techniques are increasingly being used to detect and/or differentiate uncultivable, anaerobic, or fastidious microorganisms. During the past decade, DNA probe hybridization and in vitro amplification by polymerase chain reaction have also been introduced to detect oral pathogens. The present review describes experiences with methods and commercial test systems for the detection of pathogens in periodontitis and caries.

Identification of mutans streptococcal species by the PCR products of the dex genes

A pair of polymerase chain reaction (PCR) primers was designed on the basis of the nucleotide sequence homology of dextranase genes (dex) of Streptococcus mutans, S. sobrinus and S. downei. The primer pair amplified a 530-bp DNA fragment on the dex genes of mutans streptococcal species: S. mutans, S. sobrinus, S. downei, S. rattus and S. cricetus. HaeIII digestion of the 530-bp fragments generated species-specific subfragments, which were easily distinguishable from each other by agarose gel electrophoresis. These results suggest that the PCR-amplification of the dex gene followed by the HaeIII digestion is useful for rapid identification of the five species of mutans streptococci.

Construction of a new integration vector for use in Streptococcus mutans

A new integration vector, pBGK, was constructed for delivery of heterologous DNA into the chromosome of Streptococcus mutans. A kanamycin resistance element (OmegaKm), which is flanked by transcriptional and translational terminators and which is selectable in both Escherichia coli and streptococci, was inserted into a 2.4-kb EcoRI fragment carrying the S. mutans gtfA gene. A unique SmaI site flanking OmegaKm is available for cloning of promoter:reporter gene fusions or foreign genes, which can then be integrated into the S. mutans chromosome by allelic exchange with the gtfA gene. The vector was used to analyze the activity of an S. mutans promoter by fusing it to a chloramphenicol acetyltransferase gene. The reporter fusions could readily be cloned into the vector at a unique SmaI site and the vector and passenger DNA were stable in E. coli. DNAs flanked by gtfA sequees integrated efficiently into the chromosome of S. mutans and were stably maintained in the absence of selective pressure. Expression levels of the reporter gene were consistent regardless of orientation or repeated subculturing.

A DNA probe specific to Streptococcus sobrinus

Three DNA fragments (SSB-1, -2 and -3) in the dextranase gene (dex) of Streptococcus sobrinus were amplified by polymerase chain reaction and used as DNA probes. The probes were examined for the specificity and the sensitivity of hybridization with DNA of oral streptococcal species. While probes SSB-1 and SSB-2 were specific to both S. sobrinus and Streptococcus downei, SSB-3 was specific only to S. sobrinus. SSB-3 was able to detect 5 ng of chromosomal DNA purified from S. sobrinus NIDR6715 and DNA extracted from 1 x 10(5) cells of the strain. In addition, SSB-3 could differentiate clinical isolates of S. sobrinus from Streptococcus mutans. These results suggest that SSB-3 is an effective DNA-probe to detect and to identify S. sobrinus.

Arbitrarily primed polymerase chain reaction fingerprinting for the genotypic identification of mutans streptococci from humans

Determining whether two strains of bacteria are unique, identical or clonally related depends upon comparisons of phenotypic and/or genotypic traits. Individual isolates can then be grouped according to differences or similarities among those traits. One method of genotyping strains of bacteria is commonly referred to as chromosomal DNA fingerprinting. Previously, we generated chromosomal DNA fingerprints of mutans streptococci to study the transmission of this organism within families. Here, we developed and evaluated an arbitrarily primed polymerase chain reaction (AP-PCR) method for the genotypic characterization of mutans streptococci. Results were compared to those derived from the more conventional chromosomal DNA fingerprinting method. First, we showed that randomly selected clinical isolates displayed a unique banding profile by both methods; the mean similarity indices between DNA fragment patterns were 0.69 for chromosomal DNA fingerprinting and 0.74 for AP-PCR. This indicated that AP-PCR demonstrated less diversity than chromosomal DNA fingerprinting. Subsequently, we tested the agreement between chromosomal DNA fingerprinting and AP-PCR in determining genotypic similarities among 21 mutans streptococci strains obtained from 10 mother-child pairs, and 5 mutans streptococci strains from 5 fathers. The Kappa value for agreement was 0.88. We conclude that AP-PCR, which generates patterns of 8 to 12 amplicons, is capable of distinguishing strains of mutans streptococci among non-related individuals. Moreover, AP-PCR can discern both homogeneity and heterogeneity of mutans streptococci genotypes among mother and child pairs. Overall, we found that AP-PCR gave results comparable to those of chromosomal DNA fingerprinting.

Organization and nucleotide sequence of the Streptococcus mutans galactose operon

The galactose operon encoding a repressor and genes for the Leloir pathway for galactose metabolism (galactokinase, galactose-1-phosphate-uridyl transferase and UDP glucose-4-epimerase) was located adjacent to the multiple sugar metabolism (msm) operon on the chromosome of Streptococcus mutans Ingbritt (serotype c) and the complete nucleotide sequence of this 5-kilobase region was determined. The Leloir pathway was induced by the presence of galactose in the growth medium or following the release of intracellular galactose after uptake and cleavage of alpha-galactosides by the multiple sugar metabolism system. Analysis of the mechanism of galactose transport confirmed the absence of a galactose-specific phosphotransferase system and suggested the presence of an inducible galactose permease. Evidence is presented that galactose transport is independent of the proton motive force and may be ATP-dependent.

Typing of mutans streptococci by arbitrarily primed polymerase chain reaction

The discriminative power of the arbitrarily primed polymerase chain reaction (AP-PCR) in differentiating between Streptococcus mutans and Strep. sobrinus species, serotypes and clones was investigated. Mutans streptococcal isolates (12(7)) obtained from 65 individuals (1-10 isolates per individual) were AP-PCR typed separately with two random primers, OPA-05 and OPA-13. Bacterial cell lysates were used as a template in PCR reactions, which made AP-PCR easy and fast to perform. Eighty-one isolates from 19 individuals were also ribotyped to compare the discriminative ability of ribotyping and AP-PCR techniques. AP-PCR performed with the two primers differentiated between Strep. mutans and Strep. sobrinus isolates, but neither primer detected serotype-specific amplification products. OPA-05 distinguished two main AP-PCR patterns among Strep. mutans isolates and one main pattern among Strep. sobrinus isolates, whereas OPA-13 found one main AP-PCR pattern among Strep. mutans isolates and two main patterns among Strep. sobrinus isolates. Ribotyping and AP-PCR revealed 40 and 33 different types among 81 selected isolates, respectively. Both techniques detected intra-individual heterogeneity in 16 out of 19 participants. The results indicate that AP-PCR has good discriminative ability in differentiating between mutans streptococcal clones and that the technique is suitable for epidemiological studies on mutans streptococci.