Multiplex polymerase chain reaction assay for simultaneous detection of black-pigmented Prevotella species in oral specimens

Simultaneous detection and evaluation of Prevotella intermedia, Prevotella nigrescens, Prevotella loescheii, and Prevotella melaninogenica in subgingival plaque samples of chronic periodontitis and healthy individuals through multiplex polymerase chain reaction

Background

Prevotella is a Gram-negative anaerobic bacilli. The phenotypic characteristics of the various species of Prevotella are similar, which often makes it difficult in routine differentiation and identification of all the species.

Aim

The purpose of the study was to detect and compare presence of Prevotella intermedia, Prevotella nigrescens, Prevotella melaninogenica, and Prevotella loescheii in subgingival plaque samples of chronic periodontitis and healthy individuals.

Materials and Methods

Two hundred and thirty-six subjects were considered consisting of chronic periodontitis (128) and healthy (108) individuals. Subgingival plaque sample was collected in reduced transport fluid and analyzed. DNA extraction and polymerase chain reaction (PCR) were performed for genus Prevotella followed by positive samples were considered for the detection of selected species through multiplex PCR using specific primers.

Results

Out of 236 samples, 94.1% were positive for genus Prevotella. Out of 222 cases P. nigrescens showed the highest number of cases positive (59.5%) followed by P. melaninogenica (57.2%), P. intermedia (55.4%), and P. loescheii (40.1%). Species were analyzed individually between chronic periodontitis and healthy, P. intermedia, P. nigrescens, and P. loescheii showed greater positivity in healthy compared to chronic periodontitis. Positivity for P. melaninogenica was high in chronic periodontitis compared to healthy.

Conclusion

The number of positive cases for species, when correlated with clinical parameters showed an increase in mean score for all clinical parameters assessed, suggesting the presence of variation in the prevalence of Prevotella species and geographic variation do exist in oral microflora. Findings suggest that they can be normal commensals and opportunistic.

Efficacy of virginiamycin for the control of periodontal disease in calves

ABSTRACT: Periodontal diseases are multifactorial infectious processes caused by complexes of microorganisms, with damage to health, production, and animal welfare. The aim of the present study was to evaluate the efficacy of virginiamycin in the prevention and control of two early forms of periodontal disease: gingivitis and necrotizing gingivitis. Ten weaned calves, aged four to six months, were permanently kept in a single lot under the same rotational grazing regime in a newly reformed area of Panicum maximum. Five of the calves were orally administered 340mg of virginiamycin (Virginiamycin Group) daily for a period of 18 weeks, while the remaining five calves (Control Group) remained under the same food management but did not receive virginiamycin. During this period, animals underwent 18 weekly evaluations regarding periodontal health, with monitoring and recording of clinical parameters of the eight deciduous incisor teeth on the labial and lingual faces. At approximately two-week intervals, nine collections of subgingival sulcus material from five sites of the four right incisor teeth of each animal were performed and subjected to microbiological evaluation using polymerase chain reaction with primers of 25 microorganisms considered potentially pathogenic. After 1440 periodontal clinical evaluations of incisor teeth of the 10 calves, a total of 395 episodes of gingivitis were recorded, of which 267 occurred in the Control Group and 128 in the Virginiamycin Group. Similarly, 89 episodes of necrotizing gingivitis were recorded; 58 in the Control Group and 31 in the Virginiamycin Group. Comparison of between-group means found significant differences for teeth with gingivitis and necrotizing gingivitis (t test; p<0.05). The total number of teeth with gingivitis (p<0.01) and necrotizing gingivitis (p<0.01) in Control Group was significantly higher than that of gingivitis (p<0.01) and necrotizing gingivitis (p<0.05) in the Virginiamycin Group. There was a positive correlation between total occurrence of gingivitis and necrotizing gingivitis in the Virginiamycin Group by Pearson’s test. Virginiamycin had a protective effect on treated animals compared with the Control Group (OR = 0.36: CI (95%) = 0.27-0.43). In the Control Group, Actinomyces israelli (4.74%), domain Archaea (1.58%), Eikenella corrodens (1.05%), Fusobacterium nucleatum (27.37%), class Mollicutes (5.26%); Porphyromonas endodontalis(5.26%); Porphyromonas gulae(0.53%), Prevotella buccae (6.32%), Prevotella loescheii (3.68%), Prevotella nigrescens (8.42%), Prevotella oralis (1.58%), Tannerella forsythia (0.53%), and Treponema denticola (4.21%) were detected at healthy sites, and gingivitis or necrotizing gingivitis samples. In the Virginiamycin Group, A. israelli (3.41%), domain Archaea (0.98%), F. nucleatum (9.27%), class Mollicutes(4.39%), P. endodontalis (4.39%), P. gulae (0.49%), P. buccae (8.29%), P. loescheii (6.83%), P. nigrescens (15.61%), P. oralis (1.46%), Selenomonas sputigena (0.49%), T. forsythia (0.49%), and T. denticola (2.44%) were detected. In conclusion, virginiamycin administered at a dosage of 340mg/animal/day significantly reduced the occurrence of gingivitis and necrotizing gingivitis in cattle maintained on reformed pastures, and was revealed to have action against periodontal bacterial microbiota considered to be potentially pathogenic.

Quantifying known and emerging uterine pathogens, and evaluating their association with metritis and fever in dairy cows

Metritis is caused by polymicrobial infection; however, recent metagenomic work challenges the importance of known pathogens such as Escherichia coli and Trueperella pyogenes while identifying potential new pathogens such as Bacteroides pyogenes, Porphyromonas levii and Helcococcus ovis. This study aims to quantify known and emerging uterine pathogens, and to evaluate their association with metritis and fever in dairy cows. Metritis was diagnosed at 6 ± 2 days postpartum, a uterine swab was collected and rectal temperature was measured. 39 cows were classified into three groups: Healthy (n = 14), Metritis without fever (MNoFever; n = 12), and Metritis with fever (MFever; n = 13). Absolute copy number was determined for total bacteria and for 8 potentially pathogenic bacteria using droplet digital PCR. Both MNoFever and MFever cows had higher copy number of total bacteria, Fusobacterium necrophorum, Prevotella melaninogenica, Bacteroides pyogenes, Porphyromonas levii, and Helcococcus ovis than Healthy cows. MNoFever and MFever groups were similar. There was no difference among groups in copy number of Escherichia coli, Trueperella pyogenes, and Bacteroides heparinolyticus, and they all had low copy numbers. Our work confirms the importance of some bacteria identified by culture-based studies in the pathogenesis of metritis such as Fusobacterium necrophorum and Prevotella melaninogenica; however, it challenges the importance of others such as Escherichia coli and Trueperella pyogenes at the time of metritis diagnosis. Additionally, Bacteroides pyogenes, Porphyromonas levii, and Helcococcus ovis were recognized as emerging pathogens involved in the etiology of metritis. Furthermore, fever was not associated with the total bacterial load or specific bacteria.

Modulation of the immune system during postpartum uterine inflammation

Postpartum uterine inflammation (endometritis) in the dairy cow is associated with lower fertility at both the time of infection and after the inflammation has resolved. We hypothesized that aberrant DNA methylation may be involved in the subfertility associated with uterine inflammation. The objective of this study was to characterize genome-wide DNA methylation and gene expression in the endometrium of dairy cows with subclinical endometritis (SCE). Endometrial tissues were obtained at 29 days postpartum ( n = 12), and microarrays were used to characterize transcription and DNA methylation. Analyses revealed 1,856 probes differentially expressed in animals with SCE ( n = 6) compared with controls (CON, n = 6, P < 0.05, Storey Multiple testing correction) and 2,976 probes with significant correlation between gene expression and bacteriology score. No significant associations among DNA methylation and gene expression were detected. Analysis of transcription data using the Database for Annotation, Visualization, and Integrated Discovery and Gene Set Enrichment Analysis identified several pathways and processes enriched in SCE cows, with the majority related to the immune response. Furthermore, the top ontology terms enriched in genes that had expression data correlated to bacteriology score were: Defense response, inflammatory response, and innate immune response. Gene expression profiles in cows with subclinical endometritis in this study indicate that the immune response is activated, potentially resulting in a local proinflammatory environment in the uterus. If this period of inflammation is prolonged it could result in tissue damage or failure to complete involution of the uterus, which may create a suboptimal environment for future pregnancy.

Biofilms of black tooth stains: PCR analysis reveals presence of Streptococcus mutans

This study investigated the presence of the black-pigmented bacteria Prevotella nigrescens and Prevotella intermedia, the non-black-pigmented bacteria Actinomyces spp and particularly the cariogenic pathogen Streptococcus mutans in the dental biofilms of patients with or without black extrinsic tooth stains, using the multiplex polymerase chain reaction (PCR) technique. Analysis of the dental biofilms of patients with (n=26) or without (n=26) black tooth stains was performed using duplex PCR for the 16S ribosomal RNA gene (P. nigrescens, P. intermedia, Actinomyces spp) and glucosyltransferase-I gene for S. mutans. P. nigrescens and S. mutans were the most frequent bacteria detected in both groups. The least frequently detected were P. intermedia and Actinomyces spp. The similar bacterial composition of dental biofilms of black tooth stains and healthy tooth surfaces indicates that black tooth stains are not free of cariogenic bacteria.

Association of periodontitis with increased colonization by Prevotella nigrescens

AIM

To estimate differences in the prevalence of Prevotella intermedia and Prevotella nigrescens in the subgingival plaque of patients with periodontitis (including aggressive and advanced chronic periodontitis) compared to healthy controls, and to search for significant associations with clinical status.

METHODS

Sixteen patients and 16 healthy controls were enrolled in this study. Interproximal plaque index, oral hygiene index, gingival index, bleeding on probing, probing depth, and clinical attachment level were recorded. Samples of subgingival plaque were taken with paper points from four teeth of each individual and immediately plated on appropriate supplemented Columbia agar. Black pigmented colonies were identified with the Rapid ID32 A system, and further differentiated using matrix-assisted laser desorption ionization-time of flight mass spectrometry. For the statistical analysis, chi-squared test and the Mann-Whitney U-test were used.

RESULTS

Prevotella nigrescens was isolated from 10 patients and three controls, while P. intermedia was isolated from only two patients. P. nigrescens was found more frequently in the subgingival plaque of patients (P = 0.029), and was significantly associated with high values of clinical indices (P ≤ 0.025). Significant differences for P. intermedia were not found.

CONCLUSIONS

Periodontitis seems to be associated with increased colonization with P. nigrescens. Whether or not it is a major pathogen needs to be determined.

The identification of genes specific to Prevotella intermedia and Prevotella nigrescens using genomic subtractive hybridization

Prevotella intermedia and Prevotella nigrescens, which are often isolated from periodontal sites, were once considered two different genotypes of P. intermedia. Although the genomic sequence of P. intermedia was determined recently, little is known about the genetic differences between P. intermedia and P. nigrescens. The subtractive hybridization technique is a powerful method for generating a set of DNA fragments differing between two closely related bacterial strains or species. We used subtractive hybridization to identify the DNA regions specific to P. intermedia ATCC 25611 and P. nigrescens ATCC 25261. Using this method, four P. intermedia ATCC 25611-specific and three P. nigrescens ATCC 25261-specific regions were determined. From the species-specific regions, insertion sequence (IS) elements were isolated for P. intermedia. IS elements play an important role in the pathogenicity of bacteria. For the P. intermedia-specific regions, the genes adenine-specific DNA-methyltransferase and 8-amino-7-oxononanoate synthase were isolated. The P. nigrescens-specific region contained a Flavobacterium psychrophilum SprA homologue, a cell-surface protein involved in gliding motility, Prevotella melaninogenica ATCC 25845 glutathione peroxide, and Porphyromonas gingivalis ATCC 33277 leucyl-tRNA synthetase. The results demonstrate that the subtractive hybridization technique was useful for distinguishing between the two closely related species. Furthermore, this technique will contribute to our understanding of the virulence of these species.

PCR-based identification of selected pathogens associated with endodontic infections in deciduous and permanent teeth

OBJECTIVE

The aim of the present study was to evaluate the presence of the selected pathogens in samples from deciduous and permanent tooth root canals by using PCR method and to determine the association of these organisms with clinical symptoms.

STUDY DESIGN

A total of 145 children, 5 to 13 years old, were involved in this study. The presence of selected pathogens (Actinomyces israelii, Candida albicans, Enterococcus faecalis, Fusobacterium nucleatum, Porphyromonas endodontalis, Porphyromonas gingivalis, Prevotella intermedia, Streptococcus intermedius, Treponema denticola, Parvimonas micra, Tannerella forsythensis, Enterococcus faecium, Prevotella melaninogenica) in infected root canals was studied using PCR.

RESULTS

T. denticola (P = .012, .02) and E. faecalis (P = .012, .04) were highly associated with periapical radiolucency and previous pain, while P. gingivalis was associated with tenderness to percussion in both deciduous and permanent teeth (P = .01, .015).

CONCLUSION

The results of the present study confirm that certain species of microorganisms are associated with clinical signs and symptoms of endodontic disease in both deciduous and permanent teeth.

The prevalence of periodontopathogenic bacteria in saliva is linked to periodontal health status and oral malodour

This study investigated whether an improvement in periodontal health resulted in changes in the prevalence of periodontopathogenic bacteria in saliva and tongue coatings and a reduction in volatile sulfur compounds (VSCs: H2S and CH3SH) linked to oral malodour. The subjects were 35 patients who visited the breath odour clinic of Kyushu Dental College, Japan. Their mean age was 51.2±18.3 years (mean±sd). A clinical examination performed at baseline and 2 months after periodontal treatment assessed VSCs in mouth air using gas chromatography, periodontal probing depth and bleeding on probing (BOP) in all subjects; saliva and tongue coatings were also collected. Genomic DNA was isolated from the samples, and the proportions of five periodontopathogenic bacteria (Porphyromonas gingivalis, Tannerella forsythensis, Treponema denticola, Prevotella intermedia and Prevotella nigrescens) were investigated using quantitative real-time PCR. The subjects were classified into four groups based on the presence of a periodontal pocket of more than 4 mm (PD) and VSCs above the organoleptic threshold level (VSCT) as follows: –PD/–VSCT group, subjects without PD or VSCT; –PD/+VSCT group, those without PD but with VSCT; +PD/–VSCT group, those with PD but without VSCT; and +PD/+VSCT group, those with PD and VSCT. Although the mean PD values in the +PD/–VSCT and +PD/+VSCT groups, BOP in the +PD/+VSCT group, and H2S and CH3SH concentrations in the –PD/+VSCT and +PD/+VSCT groups were greater than in the other groups at baseline, we found no significant difference among the four groups after periodontal treatment. The proportion of periodontopathogenic bacteria in saliva was higher in the +PD/–VSCT and +PD/+VSCT groups than in the –PD/–VSCT and –PD/+VSCT groups at baseline and after treatment, but the proportions of bacteria in saliva after treatment were reduced compared to the baseline. Furthermore, the differences in the proportions of the five target bacteria in the tongue coating were not as apparent as those in saliva at baseline or after treatment. The prevalence of periodontopathogenic bacteria in saliva may reflect periodontal health status and influence VSC levels in mouth air.

Getting the most out of fluorescent amplified fragment length polymorphism

Amplified fragment length polymorphism (AFLP™) is one of the most widely applied molecular marker detection systems used today. Among the reasons for its popularity are its reproducibility, capacity to generate large numbers of data points in a single assay, and “off-the-shelf” universal applicability. The original AFLP protocol was developed using radioactive detection. The transfer of this technique to fluorescent detection on automated DNA fragment analysers not only removed the undesirable requirement for radioactivity but also provided the possibility for increased effectiveness and detection throughput. Unfortunately, a number of problems are frequently encountered with fluorescent AFLPs, particularly failure to amplify high molecular-weight fragments and generation of nonuniform peak distributions. Here, we describe an improved generic protocol for fluorescent AFLPs achieved mainly thorough optimization of the multiplexed selective amplification reaction. This improved protocol gives increased production of valuable high molecular-weight markers and uniform peak intensities, facilitating unambiguous scoring. The protocol has been successfully applied, without further optimization, to species of Salix and Populus (Salicaceae), Melampsora (Melampsoraceae, rust fungi) and Heracleum (Apiaceae), as well as sugar beet ( Beta vulgaris L. subsp. vulgaris , Amaranthaceae), the endangered species Ranunculus kadzunensis Makino (Ranunculaceae), and to Aphidius ervi Haliday (Braconidae), a parasitoid wasp.