Assessment of two multilocus sequence typing (MLST) schemes available for Streptococcus mutans

Intraspecies interactions of Streptococcus mutans impact biofilm architecture and virulence determinants in childhood dental caries

Early childhood dental caries (ECC) is the most common chronic disease among children, especially among low socioeconomic populations. Streptococcus mutans is most frequently associated with initiation of ECC. Although many studies report children with multiple S. mutans strains (i.e., genotypes) have greater odds of developing ECC, studies investigating intraspecies interactions in dental caries are lacking. This study investigates the impact of intraspecies interactions on cariogenic and fitness traits of clinical S. mutans isolates using in vitro and in vivo approaches. Association analysis evaluated if presence of multiple S. mutans genotypes within the first year of colonization was associated with caries. Initially, clinical S. mutans isolates from 10 children were evaluated. S. mutans strains (G09 and G18, most prevalent) isolated from one child were used for subsequent analysis. Biofilm analysis was performed for single and mixed cultures to assess cariogenic traits, including biofilm biomass, intra-polysaccharide, pH, and glucan. Confocal laser scanning microscopy (CLSM) and time-lapse imaging were used to evaluate spatial and temporal biofilm dynamics, respectively. A Drosophila model was used to assess colonization in vivo. Results showed the mean biofilm pH was significantly lower in co-cultured biofilms versus monoculture. Doubling of S. mutans biofilms was observed by CLSM and in vivo colonization in Drosophila for co-cultured S. mutans. Individual strains occupied specific domains in co-culture and G09 contributed most to increased co-culture biofilm thickness and colonization in Drosophila. Biofilm formation and acid production displayed distinct signatures in time-lapsed experiments. This study illuminates that intraspecies interactions of S. mutans significantly impacts biofilm acidity, architecture, and colonization.IMPORTANCEThis study sheds light on the complex dynamics of a key contributor to early childhood dental caries (ECC) by exploring intraspecies interactions of different S. mutans strains and their impact on cariogenic traits. Utilizing clinical isolates from children with ECC, the research highlights significant differences in biofilm architecture and acid production in mixed versus single genotype cultures. The findings reveal that co-cultured S. mutans strains exhibit increased cell density and acidity, with individual strains occupying distinct domains. These insights, enhanced by use of time-lapsed confocal laser scanning microscopy and a Drosophila model, offer a deeper understanding of ECC pathogenesis and potential avenues for targeted interventions.

Intraspecies interactions of Streptococcus mutans impact biofilm architecture and virulence determinants in childhood dental caries

Early childhood dental caries (ECC) is the most common chronic disease among children with a heavy disease burden among low socioeconomic populations. Streptococcus mutans is most frequently associated with initiation of ECC. Many studies report children with multiple S. mutans strains (i.e., genotypes) having greater odds of developing ECC, studies investigating intraspecies interactions in dental caries are lacking. In this study, the impact of intraspecies interactions on cariogenic and fitness traits of clinical S. mutans isolates are investigated using in-vitro and in-vivo approaches. Initially clinical S. mutans isolates of 10 children from a longitudinal epidemiological study were evaluated. S. mutans strains (G09 and G18, most prevalent) isolated from one child were used for subsequent analysis. Association analysis was used to determine if presence of multiple S. mutans genotypes within the first-year of colonization was associated with caries. Biofilm analysis was performed for single and mixed cultures to assess cariogenic traits, including biofilm biomass, intra-polysaccharide, pH, and glucan. Confocal Laser Scanning Microscopy (CLSM) and time-lapse imaging were used to evaluate spatial and temporal biofilm dynamics, respectively. A Drosophila model was used to assess colonization in-vivo. Mean biofilm pH was significantly lower in co-cultured biofilms as compared with monoculture biofilms. Doubling of S. mutans in-vitro biofilms was observed by CLSM and in-vivo colonization in Drosophila for co-cultured S. mutans. Individual strains occupied specific domains in co-culture and G09 contributed most to increased co-culture biofilm thickness and colonization in Drosophila. Biofilm formation and acid production displayed distinct signatures in time-lapsed experiments.

Genetic variation in the glucosyltransferase-B gene of Streptococcus mutans and its relationship with caries experience in children from Córdoba, Argentina, and with strains from other countries

BACKGROUND

Caries is a worldwide distributed oral disease of multifactorial nature, with Streptococcus mutans being the most commonly isolated bacterial agent. The glycosyltransferases of this bacterium would play an essential role in the aetiology and pathogenesis of caries.

AIM

We explored how the glucosyltransferase-B (gtf-B) gene variability of S. mutans from children in central Argentina correlated with their caries experience and how these strains were genetically related to those of other countries.

DESIGN

Dental examinations were performed on 59 children; dmft and DMFT indexes were calculated. From stimulated saliva, S. mutans was grown and counted (CFU/mL). From bacterial DNA, the gtf-B gene was amplified and sequenced. Alleles were identified and their genealogical relationships established. Clinical, microbiological, and genetic variables were correlated with caries experience. Our sequences were included in a matrix with those from 16 countries (n = 358); genealogical relationships among alleles were obtained. Population genetic analyses were performed for countries with >20 sequences.

RESULTS

The mean dmft + DMFT was 6.45. Twenty-two gtf-B alleles were identified here, which showed low genetic differentiation in the network. Caries experience was correlated with CFU/mL, but not with allele variation. Low differentiation was found among the 70 alleles recovered from the 358 sequences and among the countries analyzed.

CONCLUSION

In this study, caries experience in children was correlated with the number of CFU/mL of S. mutans but not with the gtf-B gene variability. Combined genetic analyses of worldwide strains support the theory that this bacterium experienced population expansions, probably associated with agriculture development and/or food industrialization.

[Association of sepM gene mutation with mutacin Ⅳ production by Streptococcus mutans]

OBJECTIVE

To investigate the types of sepM gene mutations and their distribution in clinical isolates of Streptococcus mutans (S. mutans) and explore the association of sepM gene mutation with the capacity of mutacin Ⅳ production by S. mutans.

OBJECTIVE

We assessed the capacity of mutacin Ⅳ production in 80 clinical isolates of S. mutans using an inhibition zone assay. The minimum spanning tree and phylogenetic tree of these isolates were constructed using core genome multilocus sequence typing and maximum likelihood method, respectively. GeneMarkS software was used to predict the coding genes of these isolates, and the predicted genes were blasted against the sepM gene sequence of the reference genome UA159 to determine sepM gene mutations and their distribution characteristics in the clinical isolates. The mutation types affecting mutacin Ⅳ production were identified by analyzing the differentially distributed mutations between mutacin Ⅳ-producing isolates and mutacin Ⅳ-free isolates and by comparing the inhibition zones between isolates with sepM gene mutations and those without mutations.

OBJECTIVE

Among the 80 clinical isolates of S. mutans, 25 isolates were capable of mutacin Ⅳ production and 55 did not produce mutacin Ⅳ. The minimum spanning tree showed that the allelic differences were less among the mutacin Ⅳproducing isolates than among the mutacin Ⅳ-free isolates, and the origins of the mutacin Ⅳ-producing isolates were similar. We identified a total of 34 single base mutations in the 80 clinical isolates, and among them, C31T (P=0.001), G533A (P < 0.001), C756T (P=0.025), and C1036T (P=0.003) showed significant differential distributions between the mutacin Ⅳ-producing and mutacin Ⅳ-free isolates. These differentially distributed mutations were positively correlated with the capacity of mutacin Ⅳ production of the bacteria.

OBJECTIVE

sepM gene mutations that affect the capacity of mutacin Ⅳ production are present in the clinical strains of S. mutans.

Phenotypic and genetic characteristics of Streptococcus mutans isolates from site-specific dental plaque in China

Introduction. Streptococcus mutans is an important cariogenic microbe.Hypothesis/Gap Statement. The potential characteristics of S. mutans isolates from site-specific dental plaque are still not clear.Aim. This study aimed to investigate the phenotypic and genetic characteristics of S. mutans isolates from site-specific dental plaque in China.Methodology. We used S. mutans isolated from children with early-childhood caries (ECC) and caries-free children to compare the phenotypic and genetic characteristics of S. mutans from site-specific dental plaque samples. The ECC subjects presented two sites: a cavitated lesion and a sound surface. The caries-free subjects presented one sound surface. Growth pattern, biofilm, decrease in pH, extracellular polysaccharide, expression levels of virulence-related genes, multilocus sequence typing (MLST) and phylogenetic trees were evaluated among these three sites.Results. The phenotypes detected between the cavitated and sound surfaces of ECC children were similar. However, the capacity for biofilm formation, pH drop and expression levels of genes (gtfB and spaP) of S. mutans in the caries-free group were lower compared with those of the ECC group. We identified 44 new alleles and 77 new sequence types. More than 90 % of the children with ECC shared an identical sequence type. The distribution of sequence types among different subjects showed diversity, and child-to-child transmission was detected.Conclusions. This is the first report of MLST on site-specific dental plaques in a single subject, and indicates that S. mutans isolated from site-specific dental plaque of a single subject showed similar phenotypes as a result of the isolates were closely related.

A Core Genome Multilocus Sequence Typing Scheme for Streptococcus mutans

Streptococcus mutans is one of the primary pathogens responsible for the development of dental caries. Recent whole-genome sequencing (WGS)-based core genome multilocus sequence typing (cgMLST) approaches have been employed in epidemiological studies of specific human pathogens. However, this approach has not been reported in studies of S. mutans Here, we therefore developed a cgMLST scheme for S. mutans We surveyed 199 available S. mutans genomes as a means of identifying cgMLST targets, developing a scheme that incorporated 594 targets from the S. mutans UA159 reference genome. Sixty-eight sequence types (STs) were identified in this cgMLST scheme (cgSTs) in 80 S. mutans isolates from 40 children that were sequenced in this study, compared to 35 STs identified by multilocus sequence typing (MLST). Fifty-six cgSTs (82.35%) were associated with a single isolate based on our cgMLST scheme, which is significantly higher than in the MLST scheme (11.43%). In addition, 58.06% of all MLST profiles with ≥2 isolates were further differentiated by our cgMLST scheme. Topological analyses of the maximum likelihood phylogenetic trees revealed that our cgMLST scheme was more reliable than the MLST scheme. A minimum spanning tree of 145 S. mutans isolates from 10 countries developed based upon the cgMLST scheme highlighted the diverse population structure of S. mutans This cgMLST scheme thus offers a new molecular typing method suitable for evaluating the epidemiological distribution of this pathogen and has the potential to serve as a benchmark for future global studies of the epidemiological nature of dental caries.IMPORTANCE Streptococcus mutans is regarded as a major pathogen responsible for the onset of dental caries. S. mutans can transmit among people, especially within families. In this study, we established a new epidemiological approach to S. mutans classification. This approach can effectively differentiate among closely related isolates and offers superior reliability relative to that of the traditional MLST molecular typing method. As such, it has the potential to better support effective public health strategies centered around this bacterium that are aimed at preventing and treating dental caries.

Transmission patterns of Streptococcus mutans demonstrated by a combined rep-PCR and MLST approach

OBJECTIVE

Clinical typing methods of the oral pathogen Streptococcus mutans with molecular analysis can be very specific, but expensive. Repetitive extragenic palindromic PCR (rep-PCR) is a relatively inexpensive pre-screening alternative for isolate selection for additional analyses. This study evaluated the prediction accuracy of using rep-PCR to identify S. mutans multilocus sequence typing (MLST) sequence types (ST) among children and their family members. Potential S. mutans strain sources were evaluated for evidence of transmission.

MATERIAL AND METHODS

Ten dendrograms (rep-PCR), with 20 isolates each of the 10 most common S. mutans genotypes, were generated from different subjects. Using a cut-off of 98% similarity, 7-11 isolates of each genotype were selected for MLST analysis to determine ST match/no-match.

RESULTS

Overall, rep-PCR was 75% effective at determining MLST ST match/no-match and 90% effective when applied to related individuals. Most genotypes were further differentiated by MLST. MLST ST diversity was greatest for one genotype (genotype 12, G12) and evidence of transmission among children and their family members was identified by rep-PCR and MLST. Younger children (6 months to 4 years old) shared ST with their mothers but 50% of older children (5-9 years old) had ST not identified in their mother. Six ST were shared between different families and probable source members were identified.

CONCLUSION

This study confirms that rep-PCR offers an affordable option to predict diverse isolates for downstream applications.

CLINICAL RELEVANCE

Using a combined rep-PCR and MLST approach, it is possible to track probable transmission and strain sources for S. mutans genotypes.

Assessment of MultiLocus Sequence Analysis As a Valuable Tool for the Classification of the Genus Salinivibrio

The genus Salinivibrio includes obligatory halophilic bacteria and is commonly isolated from hypersaline habitats and salted food products. They grow optimally between 7.5 and 10% salts and are facultative anaerobes. Currently, this genus comprises four species, one of them, S. costicola, with three subspecies. In this study we isolated and characterized an additional 70 strains from solar salterns located in different locations. Comparative 16S rRNA gene sequence analysis identified these strains as belonging to the genus Salinivibrio but could not differentiate strains into species-like groups. To achieve finer phylogenetic resolution, we carried out a MultiLocus Sequence Analysis (MLSA) of the new isolates and the type strains of the species of Salinivibrio based on the individual as well as concatenated sequences of four housekeeping genes: gyrB, recA, rpoA, and rpoD. The strains formed four clearly differentiated species-like clusters called phylogroups. All of the known type and subspecies strains were associated with one of these clusters except S. sharmensis. One phylogroup had no previously described species coupled to it. Further DNA–DNA hybridization (DDH) experiments with selected representative strains from these phylogroups permitted us to validate the MLSA study, correlating the species level defined by the DDH (70%) with a 97% cut-off for the concatenated MLSA gene sequences. Based on these criteria, the novel strains forming phylogroup 1 could constitute a new species while strains constructing the other three phylogroups are members of previously recognized Salinivibrio species. S. costicola subsp. vallismortis co-occurs with S. proteolyticus in phylogroup 4, and separately from other S. costicola strains, indicating its need for reclassification. On the other hand, genome fingerprinting analysis showed that the environmental strains do not form clonal populations and did not cluster according to their site of cultivation. In future studies regarding the classification and identification of new Salinivibrio strains we recommend the following strategy: (i) initial partial sequencing of the 16S rRNA gene for genus-level identification; (ii) sequencing and concatenation of the four before mentioned housekeeping genes for species-level discrimination; (iii) DDH experiments, only required when the concatenated MLSA similarity values among a new isolate and other Salinivibrio strains are above the 97% cut-off.

Relationship between Pyruvate Kinase Activity and Cariogenic Biofilm Formation in Streptococcus mutans Biotypes in Caries Patients

Streptococcus mutans (MS) and its biotype I are the strains most frequently found in dental plaque of young children. Our results indicate that in children pyruvate kinase (PK) activity increases significantly in dental plaque, and this corresponds with caries progression. The MS strains isolated in this study or their main glycolytic metabolism connected with PK enzymes might be useful risk factors for studying the pathogenesis and target points of novel therapies for dental caries. The relationship between PK activity, cariogenic biofilm formation and selected biotypes occurrence was studied. S. mutans dental plaque samples were collected from supragingival plaque of individual deciduous molars in 143 subjects. PK activity was measured at different time points during biofilm formation. Patients were divided into two groups: initial stage decay, and extensive decay. Non-parametric analysis of variance and analysis of covariance were used to determine the connections between S. mutans levels, PK activity and dental caries biotypes. A total of 143 strains were derived from subjects with caries. Biotyping data showed that 62, 23, 50, and 8 strains were classified as biotypes I, II, III, IV, respectively. PK activity in biotypes I, II, and IV was significantly higher in comparison to that in biotype III. The correlation between the level of S. mutans in dental plaque and PK activity was both statistically significant (p < 0.05) and positive. The greater the level of S. mutans in the biofilm (colony count and total biomass), the higher the PK activity; similarly, a low bacterial count correlated with low PK activity.

Genetic Diversity and Evidence for Transmission of Streptococcus mutans by DiversiLab rep-PCR

This two-part study investigated the genetic diversity and transmission of Streptococcus mutans using the DiversiLab repetitive extragenic palindromic PCR (rep-PCR) approach. For children with S. mutans and participating household members, analysis for evidence of unrelated child-to-child as well as intra-familial transmission was evaluated based on commonality of genotypes. A total of 169 index children and 425 household family members from Uniontown, Alabama were evaluated for genetic diversity using rep-PCR. Thirty-four unique rep-PCR genotypes were observed for 13,906 S. mutans isolates. For transmission, 117 child and household isolates were evaluated for shared genotype (by child and by genotype cases, multiple matches possible for each child). Overall, children had 1-9 genotypes and those with multiple genotypes were 2.3 times more likely to have caries experience (decayed, missing and filled teeth/surfaces>0). Only 28% of children shared all genotypes within the household, while 72% had at least 1 genotype not shared with anyone in the household. Children had genotype(s) not shared with any household members in 157 cases. In 158 cases children and household members shared a genotype in which 55% (87/158 cases) were shared with more than one family member. Children most frequently shared genotypes with their mothers (54%; 85/158), siblings (46%; 72/158) and cousins (23%; 37/158). A reference library for S. mutans for epidemiological surveillance using the DiversiLab rep-PCR approach is detailed. The genetic diversity of S. mutans in this population demonstrated frequent commonality of genotypes. Evidence for both child-to-child and intra-familial transmission of S. mutans was observed by rep-PCR.

Assessment of clonality and serotypes of Streptococcus mutans among children by multilocus sequence typing

Studies using multilocus sequence typing (MLST) have demonstrated that Streptococcus mutans isolates are genetically diverse. Our laboratory previously demonstrated clonality of S. mutans using MLST but could not discount the possibility of sampling bias. In this study, the clonality of randomly selected S. mutans plaque isolates from African-American children was examined using MLST. Serotype and the presence of collagen-binding proteins (CBPs) encoded by cnm/cbm were also assessed. One-hundred S. mutans isolates were randomly selected for MLST analysis. Sequence analysis was performed and phylogenetic trees were generated using start2 and mega. Thirty-four sequence types were identified, of which 27 were unique to this population. Seventy-five per cent of the isolates clustered into 16 clonal groups. The serotypes observed were c (n = 84), e (n = 3), and k (n = 11). The prevalence of S. mutans isolates of serotype k was notably high, at 17.5%. All isolates were cnm/cbm negative. The clonality of S. mutans demonstrated in this study illustrates the importance of localized population studies and are consistent with transmission. The prevalence of serotype k, a recently proposed systemic pathogen, observed in this study, is higher than reported in most populations and is the first report of S. mutans serotype k in a United States population.