Genetic classification of severe early childhood caries by use of subtracted DNA fragments from Streptococcus mutans

Determination of salivary concentrations of leptin and adiponectin, ability to reduce ferric ions and total antioxidant capacity of saliva in patients with severe early childhood caries

INTRODUCTION

One of the most common oral diseases affecting children is early childhood caries (ECC). The link between oxidative stress and ECC has been proven in numerous clinical studies. Technical and biological variability were so high in most of the studies that none of the markers have yet been proven suitable for routine clinical use. This study aimed to evaluate the antioxidant status and the levels of leptin and adiponectin in saliva of children with severe early childhood caries (S-ECC).

METHODS

Morning unstimulated saliva samples were collected from children (n = 40, 0-6 years old) for the evaluation of oxidative stress which were measured by total antioxidant capacity (TAC), and by the ferric reducing antioxidant power (FRAP) assays, as well as to assess the salivary levels of leptin and adiponectin. FRAP, TAC, leptin and adiponectin concentrations were evaluated in S-ECC group (n = 31) and caries free group CF (n = 9). All results were analyzed based on age and sex.

RESULTS

Overall median salivary leptin and adiponectin levels were 5.59 pg/mL and 24.86 ng/mL, respectively. Significantly lower leptin levels were observed in saliva of caries free children (4.66 pg/mL) than in the S-ECC group (6.64 pg/mL, p < 0.01). No significant difference was observed for adiponectin levels (S-ECC and CF, 25.31 and 23.2 ng/mL, respectively, p = 0.961). TAC and FRAP values of saliva had similar values in children with S-ECC and caries free children. TAC and FRAP values also remained stable with the age of the children, without significant differences with respect to sex.

CONCLUSION

The increased concentrations of leptin in saliva of children with S-ECC suggests that leptin may play a role in inflammatory and immune responses in the development of early childhood caries.

An Automated Machine Learning Classifier for Early Childhood Caries

Purpose: The purpose of the study was to develop and evaluate an automated machine learning algorithm (AutoML) for children's classification according to early childhood caries (ECC) status. Methods: Clinical, demographic, behavioral, and parent-reported oral health status information for a sample of 6,404 three- to five-year-old children (mean age equals 54 months) participating in an epidemiologic study of early childhood oral health in North Carolina was used. ECC prevalence (decayed, missing, and filled primary teeth surfaces [dmfs] score greater than zero, using an International Caries Detection and Assessment System score greater than or equal to three caries lesion detection threshold) was 54 percent. Ten sets of ECC predictors were evaluated for ECC classification accuracy (i.e., area under the ROC curve [AUC], sensitivity [Se], and positive predictive value [PPV]) using an AutoML deployment on Google Cloud, followed by internal validation and external replication. Results: A parsimonious model including two terms (i.e., children's age and parent-reported child oral health status: excellent/very good/good/fair/poor) had the highest AUC (0.74), Se (0.67), and PPV (0.64) scores and similar performance using an external National Health and Nutrition Examination Survey (NHANES) dataset (AUC equals 0.80, Se equals 0.73, PPV equals 0.49). Contrarily, a comprehensive model with 12 variables covering demographics (e.g., race/ethnicity, parental education), oral health behaviors, fluoride exposure, and dental home had worse performance (AUC equals 0.66, Se equals 0.54, PPV equals 0.61). Conclusions: Parsimonious automated machine learning early childhood caries classifiers, including single-item self-reports, can be valuable for ECC screening. The classifier can accommodate biological information that can help improve its performance in the future.

Effect of SrtA on Interspecies Adherence of Oral Bacteria

This study aimed to study whether the Sortase A (srtA) gene helps mediate coaggregation and co-adherence between Streptococcus mutans (S. mutans) and other salivary bacteria. S. mutans UA159 and srtA-deficient mutant served as "bait" in classical co-aggregation assays and membrane-based co-adherence assays were used to examine interactions of S. mutans with Fusobacterium nucleatum (F. nucleatum), Streptococcus mitis (S. mitis), Streptococcus gordonii (S. gordonii), Streptococcus sanguis (S. sanguis), Actinomyces naeslundii (A. naeslundii) and Lactobacillus. Co-adherence assays were also performed using unfractionated saliva from healthy individuals. Co-adhering partners of S. mutans were sensitively detected using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Both UA159 and its srtA-deficient mutant bound to F. nucleatum but not to any of the other five salivary bacteria. The srtA-deficient mutant showed lower co-adherence with F.nucleatum. The two S. mutans strains also showed similar co-adherence profiles against unfractionated salivary bacteria, except that UA159 S. mutans but not the srtA-deficient bound to a Neisseria sp. under the same conditions. Deleting srtA reduces the ability of S. mutans to bind to F.nucleatum, but it does not appear to significantly affect the binding profile of S. mutans to bulk salivary bacteria.

Relationship between the genetic polymorphisms of vicR and vicK Streptococcus mutans genes and early childhood caries in two-year-old children

Background

The VicRK two-component signalling system regulates virulence and cariogenicity in Streptococcus mutans (S. mutans). The purpose of this study was to explore the genetic polymorphisms of the vicR and vicK genes, which are associated with dental caries in children with S. mutans.

Methods

In this study, 121 (from each group) clinical S. mutans strains were isolated from caries-free children and children with high-severity caries to sequence the vicR and vicK genes. Genomic DNA was extracted from S. mutans strains and amplified using PCR. The PCR products were purified and sequenced. A chi-squared test and ABI Variant Reporter software were used to analyse the sequencing results.

Results

The 242 clinically isolated S. mutans strains contained the full-length vicR and vicK genes. No nucleotide sequence insertions or deletions were observed in the two genes. Four silent point mutations were identified in the vicR genes, and no missense mutations could be detected. Forty-one mutations were identified in the vicK genes. In addition to 32 silent mutations, 9 missense mutations at the 173, 337, 470, 1051, 1132, 1258, 1260, 1277, and 1348 bp positions were found. The distribution frequencies of the missense mutations were not significantly different between the groups, except for the C470T mutation. The frequency of the C470T missense mutation was higher in the high-severity caries group than in the caries-free group.

Conclusions

vicR sequences are highly conserved in S. mutans clinical isolates. The locus 470 missense mutation of the vicK gene may be related to caries in children with S. mutans.

Genotypic characterization and comparison of Streptococcus mutans in American Indian and Southeast Iowa children

Early childhood caries is a complex health care issue that has a multifactorial etiology. One aspect of this etiology is the colonization and propagation of acidogenic bacteria at an early age. There have been several bacterial species associated with caries but 1 common species is Streptococcus mutans. Here, we describe genotypic diversity and commonality of Streptococcus mutans recovered from children representing 2 groups with similar socioeconomic demographics: a Northern Plains American Indian Tribe and a Southeast Iowa population. Forty 36‐month‐old American Indian children were selected from a cohort of 239 mothers and children, and forty 2‐ to 5‐year‐old children from Southeast Iowa were selected to compare the genotypic profiles of Streptococcus mutans recovered from each child's plaque. S. mutans isolates were selected from whole mouth plaque samples; DNA was extracted and amplified via AP‐PCR to show specific genotype patterns. These patterns were compared with GelComparIIv6.5 gel analysis software. We found 18 distinct genotypes from 524 isolates; 13 of which were common between the 2 communities. Five genotypes were unique to only the American Indian children while the Southeast Iowa children harbored no unique genotypes. Although the American Indian children had some genotypes that were not present in the Southeast Iowa children, these were not widely distributed among the community. Furthermore, the levels of genotypic diversity and commonality were similar between the 2 populations. This study sets the groundwork for a comprehensive comparison of genotypes and caries among larger subsections of both populations.

Comparative genomics of oral isolates of Streptococcus mutans by in silico genome subtraction does not reveal accessory DNA associated with severe early childhood caries

Comparative genomics is a popular method for the identification of microbial virulence determinants, especially since the sequencing of a large number of whole bacterial genomes from pathogenic and non-pathogenic strains has become relatively inexpensive. The bioinformatics pipelines for comparative genomics usually include gene prediction and annotation and can require significant computer power. To circumvent this, we developed a rapid method for genome-scale in silico subtractive hybridization, based on blastn and independent of feature identification and annotation. Whole genome comparisons by in silico genome subtraction were performed to identify genetic loci specific to Streptococcus mutans strains associated with severe early childhood caries (S-ECC), compared to strains isolated from caries-free (CF) children. The genome similarity of the 20 S. mutans strains included in this study, calculated by Simrank k-mer sharing, ranged from 79.5% to 90.9%, confirming this is a genetically heterogeneous group of strains. We identified strain-specific genetic elements in 19 strains, with sizes ranging from 200 to 39 kb. These elements contained protein-coding regions with functions mostly associated with mobile DNA. We did not, however, identify any genetic loci consistently associated with dental caries, i.e., shared by all the S-ECC strains and absent in the CF strains. Conversely, we did not identify any genetic loci specific with the healthy group. Comparison of previously published genomes from pathogenic and carriage strains of Neisseria meningitidis with our in silico genome subtraction yielded the same set of genes specific to the pathogenic strains, thus validating our method. Our results suggest that S. mutans strains derived from caries active or caries free dentitions cannot be differentiated based on the presence or absence of specific genetic elements. Our in silico genome subtraction method is available as the Microbial Genome Comparison (MGC) tool, with a user-friendly JAVA graphical interface.

Dynamics of oral microbial community profiling during severe early childhood caries development monitored by PCR-DGGE

OBJECTIVE

To monitor the longitudinal changes in oral microbial diversity of children with severe early childhood caries (S-ECC) compared to caries free (CF) controls.

METHODS

Dental plaque samples of 12 children in each group at 8, 14, 20, 26 and 32 months of age were analysed. Total microbial genomic DNA was isolated from each sample, and PCR-denaturing gradient gel electrophoresis (DGGE) analyses were carried out.

RESULTS

The number of bands was significantly higher in the CF group (18.17±4.91 bands) than in the S-ECC group (14.54±5.56 bands) at 32 months of age (P<0.05). A total of 21 genera were identified in all subjects, and there were no significant differences between the two groups at genus level. DGGE profiles showed that most of the clusters were constructed from one individual over time in the both groups.

CONCLUSIONS

The onset of S-ECC is accompanied by a decrease in microbial diversity. The overall composition of the microbiota is highly similar within an individual over time.

Short communication: polymicrobial community in teeth associated with severe early-childhood caries

AIM

This was to characterise the microbial diversity in the complex dental plaque of children with severe early-childhood caries (S-ECC), using the denaturing gel gradient electrophoresis (DGGE) technique.

METHODS

The DGGE technique was used as a diagnostic tool to analyse samples from the oral cavity of a patient with S-ECC. Dental plaque samples from a 3-year-old child with S-ECC were taken from the primary central maxillary incisor (biofilm on vestibular surface), primary maxillary molar (biofilm on vestibular surface), primary central maxillary incisor (dentine), primary maxillary molar (dentine) and saliva and then analysed by PCR-DGGE.

RESULTS

Three bands occurred in all samples, moreover, 86% of similarity was observed in the pattern of bands between incisor and molar teeth biofilm samples, including four similar bands.

CONCLUSION

DGGE is a valuable tool for differentiating the microbial composition of the oral plaque in S-ECC children.

Distribution of putative virulence genes in Streptococcus mutans strains does not correlate with caries experience

Streptococcus mutans, a member of the human oral flora, is a widely recognized etiological agent of dental caries. The cariogenic potential of S. mutans is related to its ability to metabolize a wide variety of sugars, form a robust biofilm, produce copious amounts of lactic acid, and thrive in the acid environment that it generates. The remarkable genetic variability present within the species is reflected at the phenotypic level, notably in the differences in the cariogenic potential between strains. However, the genetic basis of these differences is yet to be elucidated. In this study, we surveyed by PCR and DNA hybridization the distribution of putative virulence genes, genomic islands, and insertion sequences across a collection of 33 strains isolated from either children with severe early childhood caries (S-ECC) or those who were caries free (CF). We found this genetically diverse group of isolates to be remarkably homogeneous with regard to the distribution of the putative virulence genes and genetic elements analyzed. Our findings point to the role of other factors in the pathogenesis of S-ECC, such as uncharacterized virulence genes, differences in gene expression and/or enzymatic activity, cooperation between S. mutans strains or with other members of the oral biota, and host factors.

Resemblance of salivary protein profiles between children with early childhood caries and caries-free controls

Although prolonged bottle feeding with a carbohydrate-rich content is commonly agreed to be the main etiologic factor for early childhood caries (ECC), in recent years additional endogenous factors, including the composition of saliva, have been suspected as predisposing factors in children for the development of this aggressive form of dental caries. As a basis for investigating the putative involvement of salivary proteins in the etiology of ECC, a qualitative comparison of major salivary protein profiles between children with ECC and caries-free controls was performed. Saliva was collected from 30 children with ECC and, after separation by sodium dodecyl sulphate-polyacrylamide gel electrophoresis, was compared with saliva from 20 caries-free controls for the general composition of proteins by means of silver staining, glycoprotein staining, and lectin blotting. Gels and blots were analysed using densitometry, and the protein-banding patterns resulting from the individuals' samples were compared by image analysis for the presence or absence of protein bands. Dendrograms obtained after comparison of all samples showed a high degree of similarity for the experimental groups. In summary, the results attest a uniform expression of the major protein components in children's saliva, regardless of the clinical manifestation of ECC, and thus pave the way for further detailed investigations of more subtle differences in the salivary proteome.