The impact of 16S ribosomal RNA-based phylogeny on the taxonomy of oral bacteria

Comparative Evaluation of L-PRF and Ofloxacin Incorporated L-PRF as an Adjunctive to SRP-A Split-Mouth Randomized Clinical Trial

Aim and Objectives

To compare and evaluate the clinical efficacy of "ofloxacin incorporated L-PRF" and "L-PRF alone" when used as an adjuvant to non-surgical periodontal therapy.

Materials and Methods

A split-mouth study was conducted in 50 patients diagnosed as chronic periodontitis with pocket depth ≥6 with at least one site in each quadrant. All patients underwent scaling and root planning. Test site received with ofloxacin incorporated L-PRF and control site received L-PRF alone. Clinical parameters pocket depth (PD), plaque index (PI), and gingival bleeding index (GBI) were recorded at baseline and 1 month after scaling and root planning.

Results

In total, 100 sites were treated (50 test group and 50 control group) with no uneventful healing effects. Statistically significant decreases in PD (P = .0001 for both test and control groups), PI (P = .001), GBI (P = .001 for both groups), between pre-treatment and 1 month post-treatment were noted in both test and control groups. For intergroup comparisons, there was a statistically significant difference in all clinical indices (P > .005).

Conclusion

Use of L-PRF with ofloxacin as an adjuvant to non-surgical periodontal therapy showed better improvements in clinical parameters.

Bacteria in the cavity-restoration interface after varying periods of clinical service - SEM description of distribution and 16S rRNA gene sequence identification of isolates

OBJECTIVES

To use extracted human teeth with amalgam (n = 26) or GIC (n = 3) restorations in service up to 20 years to evaluate microbiota at the cavity/restoration interface by SEM or culture.

MATERIALS AND METHODS

Extracted teeth with intracoronal restorations (n = 20) of known history (2-20 years) were fixed, split, and prepared for SEM to ascertain the pattern and structure of bacterial aggregates on cavity and restoration surfaces. Another 9 teeth were anaerobically decontaminated, split and sampled (cavity/restorations), and cultured (anaerobically, aerobically); recovered isolates were identified by 16S rRNA gene sequencing.

RESULTS

SEM showed rods, cocci, and filaments in 11/20 teeth (55%) on cavity and corresponding restoration surfaces; 4/20 (20%) on neither surface; 1/20 (5%) on just cavity; and 4/20 (20%) on just restoration. Microbial growth extended from marginal openings into the deeper interfacial microspace to varying extents but was not always evident. Restoration size or age did not predict bacterial presence. Bacteria-free surfaces (cavity/amalgam) showed possible calcification. Cultivation yielded 160 isolates, mainly Gram-positive (86%) and facultative (81%); and morphotypes of rods (43%), cocci (36%), and cocco-bacilli (18%) belonging to Actinobacteria (45%) and Firmicutes (50%). The most frequent genera were Staphylococcus, Streptococcus, Actinomyces, and Lactobacillus. Biofilms on cavity and restoration appeared independent of each other.

CONCLUSIONS

Cavity and amalgam surfaces were independently colonised and some not. The penetration of microbiota into marginal gaps varied; resembled root caries and was dominated by Gram-positive species.

CLINICAL RELEVANCE

Marginal gaps around restorations are unavoidable but are not always colonised by bacteria after long-term clinical service. Calcification of biofilms in the restorative interface may prevent further colonisation. The viable microbiota in the restorative interface resembled root caries and may be subject to ecological fluxes of activity and arrest and therefore preventative management.

Evaluation and association of periodontal status with levels of Porphyromonas gingivalis in chronic periodontitis with and without Type 2 diabetes mellitus following nonsurgical periodontal therapy using quantitative polymerase chain reaction: An interventional study

Background:

The aim of the present study was to detect and correlate the levels of Porphyromonas gingivalis with clinical parameters after nonsurgical periodontal therapy (NSPT) in chronic periodontitis patients with or without Type 2 diabetes mellitus (T2DM), using quantitative polymerase chain reaction (Q-PCR) method.

Materials and Methods:

Sixty patients equally divided into three groups, i.e., periodontally healthy (Group I), chronic periodontitis (CP) (Group II), and CP with T2DM patients (Group III) were assessed through clinical parameters of probing pocket depth (PPD) and clinical attachment level (CAL) and were correlated for the presence of P. gingivalis in the respective groups. PPD, CAL, and saliva samples for microbiological evaluation were assessed at baseline, 1-, and 3-month post-NSPT.

Results:

Significant reduction of PPD was found 1.26 ± 0.22 versus 0.43 ± 0.33 mm in Group I, 4.62 ± 0.78 versus 2.58 ± 0.60 mm in Group II, and 6.28 ± 1.52 versus 4.01 ± 1.38 mm in Group III post-NSPT at 3 months. Similarly, a notable reduction of CAL was exhibited in both Group II (5.28 ± 0.80 vs. 3.12 ± 0.77 mm) and Group III (7.14 ± 1.59 vs. 4.51 ± 1.38 mm) patients after NSPT at 3 months. A greater reduction of P. gingivalis concentrations was observed in both Group II and Group III at 3-month post-NSPT.

Conclusion:

The substantial improvement of clinical parameters was found to be in correlation with the load of P. gingivalis, which was reduced more in Group II than in Group III, emphasizing the applicability and sensitivity of Q-PCR method for its assessment.

Characterization of biofilm formed by multidrug resistant Pseudomonas aeruginosa DC-17 isolated from dental caries

The present work reports with the screening of biofilm-producing bacteria from the dental caries. The dental pathogens showed resistance against various antibiotics and biofilm forming ability at various levels. Among the bacterial strain, Pseudomonas aeruginosa DC-17 showed enhanced biofilm production. Extracellular polymeric substance (EPS) was synthesized by the selected bacterial isolate considerably and contributed as the major component of biofilm. EPS composed of eDNA, proteins and lipids. The total protein content of the EPS was found to be 1.928 mg/mL and was the major component than carbohydrate and DNA. Carbohydrate content was 162.3 mg/L and DNA content of EPS was 4.95 μg/mL. These macromolecules interacted in the matrix to develop dynamic and specific interactions to signalling biofilm to differentiating various environments. Also, the isolated bacteria showed resistant against various commercially available antibiotics. The isolates showed more resistance against penicillin (98%) and were sensitive against amoxicillin. Among the factors, temperature, pH and sugar concentration influenced biofilm formation. Biofilm forming ability of the selected bacterial stain was tested at various pH values and alkaline pH was favoured for biofilm production. Biofilm production was found to be maximum at 40 °C and 8% sucrose enhanced biofilm formation. Biofilm formed by P. aeruginosa DC-17 was resistant against various tested antimicrobials and chemicals.

Herpesvirus-bacteria synergistic interaction in periodontitis

The etiopathogenesis of severe periodontitis includes herpesvirus-bacteria coinfection. This article evaluates the pathogenicity of herpesviruses (cytomegalovirus and Epstein-Barr virus) and periodontopathic bacteria (Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis) and coinfection of these infectious agents in the initiation and progression of periodontitis. Cytomegalovirus and A. actinomycetemcomitans/P. gingivalis exercise synergistic pathogenicity in the development of localized ("aggressive") juvenile periodontitis. Cytomegalovirus and Epstein-Barr virus are associated with P. gingivalis in adult types of periodontitis. Periodontal herpesviruses that enter the general circulation may also contribute to disease development in various organ systems. A 2-way interaction is likely to occur between periodontal herpesviruses and periodontopathic bacteria, with herpesviruses promoting bacterial upgrowth, and bacterial factors reactivating latent herpesviruses. Bacterial-induced gingivitis may facilitate herpesvirus colonization of the periodontium, and herpesvirus infections may impede the antibacterial host defense and alter periodontal cells to predispose for bacterial adherence and invasion. Herpesvirus-bacteria synergistic interactions, are likely to comprise an important pathogenic determinant of aggressive periodontitis. However, mechanistic investigations into the molecular and cellular interaction between periodontal herpesviruses and bacteria are still scarce. Herpesvirus-bacteria coinfection studies may yield significant new discoveries of pathogenic determinants, and drug and vaccine targets to minimize or prevent periodontitis and periodontitis-related systemic diseases.

In vitro study on the activity of essential oil and methanolic extract from Algerian Nigella sativa L. Seeds on the growth kinetics of micro-organisms isolated from the buccal cavities of periodontal patients

An in vitro evaluation of the antimicrobial activity of essential oil (EO) and methanol extract (ME) from Algerian Nigella sativa L. seeds against microbial strains isolated from the oral cavities of periodontal patients was performed. Twelve Gram-positive bacteria, eleven Gram-negative bacteria and three microscopic fungi strains were isolated and identified. The antimicrobial activities of EO and ME were tested against Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumoniae, Enterococcus faecalis, Klebsiella pneumoniae, Proteus sp., Acinetobacter baumannii/calcoaceticus, Porphyromonas sp., Veillonella sp., Candida sp. and Saccharomyces sp.. The total polyphenol and flavonoids contents of ME were higher than those of EO. Thin layer chromatography showed that catechin, gallic acid and quercetin were most likely present in the extracts. Fourier transform infrared spectrometry analysis (FT-IR) indicated the presence of bands from the CO groups of acids, alcohols, phenols, and ethers and the C Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]>O band of aldehydes. Analysis of the antimicrobial activity of N. sativa extracts obtained by the microdilution method showed excellent bactericidal activity of the essential oil and moderate efficiency of the ME against all the microbes tested. Staphylococcus epidermidis and Porphyromonas sp. were the most sensitive to EO (minimum bactericidal concentration (MBC): 16,500 μg/ml) at 48 h of incubation and, 125,000 μg/ml of ME was the most active against all the microbes tested. However, after18 or 24 h, this efficiency was decreased in some strains. In addition, Saccharomyces sp. and Candida albicans were more sensitive to EO than ME during the incubation, while this efficiency was clearly not visible with the agar well method, and most microbes tested presented remarkable resistance to these extracts.

Development of an Analysis Pipeline Characterizing Multiple Hypervariable Regions of 16S rRNA Using Mock Samples

Objectives

There is much speculation on which hypervariable region provides the highest bacterial specificity in 16S rRNA sequencing. The optimum solution to prevent bias and to obtain a comprehensive view of complex bacterial communities would be to sequence the entire 16S rRNA gene; however, this is not possible with second generation standard library design and short-read next-generation sequencing technology.

Methods

This paper examines a new process using seven hypervariable or V regions of the 16S rRNA (six amplicons: V2, V3, V4, V6-7, V8, and V9) processed simultaneously on the Ion Torrent Personal Genome Machine (Life Technologies, Grand Island, NY). Four mock samples were amplified using the 16S Ion Metagenomics Kit^™ (Life Technologies) and their sequencing data is subjected to a novel analytical pipeline.

Results

Results are presented at family and genus level. The Kullback-Leibler divergence (D_KL), a measure of the departure of the computed from the nominal bacterial distribution in the mock samples, was used to infer which region performed best at the family and genus levels. Three different hypervariable regions, V2, V4, and V6-7, produced the lowest divergence compared to the known mock sample. The V9 region gave the highest (worst) average D_KL while the V4 gave the lowest (best) average D_KL. In addition to having a high D_KL, the V9 region in both the forward and reverse directions performed the worst finding only 17% and 53% of the known family level and 12% and 47% of the genus level bacteria, while results from the forward and reverse V4 region identified all 17 family level bacteria.

Conclusions

The results of our analysis have shown that our sequencing methods using 6 hypervariable regions of the 16S rRNA and subsequent analysis is valid. This method also allowed for the assessment of how well each of the variable regions might perform simultaneously. Our findings will provide the basis for future work intended to assess microbial abundance at different time points throughout a clinical protocol.

Biofilm forming ability of a new bacterial isolate from dental caries: An atomic force microscopic study

Background:

Dental plaque being one of the most-studied biofilm communities, is particularly complex because it consists of thousands of bacterial species, and new species are still being isolated and characterized. The aim of the present study is to characterize surface topography of the biofilm formed by a new bacterial isolate, obtained from the dental caries lesion using atomic force microscopy.

Materials and Methods:

Ten clinical isolates were obtained from five teeth with carious lesions involving dentine. Quantification of the biofilm forming ability of the clinical isolates was performed using microtiter plate assay. Bacterial isolate exhibiting maximum biofilm formation was subjected to phylogenetic analysis based on 16S rRNA gene sequencing and atomic force microscopic analysis.

Results:

The bacterial strain JKAS-CD2 displayed the highest similarity to 16S rRNA gene sequences of members of the family Streptococcaceae. It shared 95.3-99.3% similarity to the type strains of genus Streptococcus and 99.9% sequence similarity to the type strain Streptococcus infantarius. Atomic Force Microscopic analysis confirmed that the sucrose dependent bacterial adhesion for stable biofilm development has increased over a time-span on the thin film of enamel. Major structural components of plaque such as clumping of colonies and slime layer were clearly visualized by surface image of JKAS-CD2 cells grown on the enamel powder coated glass surface.

Conclusion:

JKAS-CD2 emerged as an obligate biofilm forming microbe under sucrose-dependent condition; a mechanism for adherence that determines the survival and persistence of the bacteria in the oral cavity and thus implicated with the dental caries.

Using Plant Source as a Buffering Agent to Manipulating Rumen Fermentation in an In vitro Gas Production System

The objective of this study was to investigate the effect of banana flower powder (BAFLOP) supplementation on gas production kinetics and rumen fermentation efficiency in in vitro incubation with different ratios of roughage to concentrate in swamp buffalo and cattle rumen fluid. Two male, rumen fistulated dairy steers and swamp buffaloes were used as rumen fluid donors. The treatments were arranged according to a 2×2×3 factorial arrangement in a Completely randomized design by using two ratios of roughage to concentrate (R:C; 75:25 and 25:75) and 3 levels of BAFLOP supplementation (0, 2 and 4% of dietary substrate) into two different kinds of rumen fluid (beef cattle and swamp buffalo). Under this investigation, the results revealed that the rumen ecology was affected by R:C ratio. The pH declined as a result of using high concentrate ratio; however, supplementation of BAFLOP could buffer the pH which led to an improvement of ruminal efficiency. BAFLOP supplementation affected acetic acid (C2) when the proportion of concentrate was increased. However, there were no effect on total volatile fatty acid (TVFA) and butyric acid (C4) by BAFLOP supplementation. The microbial community was affected by BAFLOP supplementation, especially the bacterial population. As revealed by real-time PCR, the populations of F. succinogenes and R. albus were reduced by the high concentrate treatments while that of R. flavafaciens were increased. The populations of three dominant cellulolytic bacteria were enhanced by BAFLOP supplementation, especially on high concentrate diet. BAFLOP supplementation did not influence the ammonia nitrogen (NH₃-N) concentration, while R:C did. In addition, the in vitro digestibility was improved by either R:C or BAFLOP supplementation. The BAFLOP supplementation showed an effect on gas production kinetics, except for the gas production rate constant for the insoluble fraction (c), while treatments with high concentrate ratio resulted in the highest values. In addition, BAFLOP tended to increase gas production. Based on this study, it could be concluded that R:C had an effect on rumen ecology both in buffalo and cattle rumen fluid and hence, BAFLOP could be used as a rumen buffering agent for enhancing rumen ecology fed on high concentrate diet. It is recommended that level of BAFLOP supplementation should be at 2 to 4% of total dry matter of substrate. However, in vivo trials should be subsequently conducted to investigate the effect of BAFLOP in high concentrate diets on rumen ecology as well as ruminant production.

Impact of rifaximin on the frequency and characteristics of spontaneous bacterial peritonitis in patients with liver cirrhosis and ascites

Background

Rifaximin is a non-absorbable antibiotic used to prevent relapses of hepatic encephalopathy which may also be a candidate for prophylaxis of spontaneous bacterial peritonitis (SBP).

Aim

To detect the impact of rifaximin on the occurrence and characteristics of SBP.

Methods

We prospectively studied all hospitalized patients that underwent a diagnostic paracentesis in our department from March 2012 to April 2013 for SBP and recorded all clinical data including type of SBP prophylaxis, prior use of rifaximin, concomitant complications of cirrhosis, as well as laboratory results and bacteriological findings. Patients were divided into the following three groups: no antibiotic prophylaxis, prophylaxis with rifaximin or with systemically absorbed antibiotic prophylaxis.

Results

Our study cohort comprised 152 patients with advanced liver cirrhosis, 32 of whom developed SBP during the study period. As expected, our study groups differed regarding a history of hepatic encephalopathy and SBP before inclusion into the study. None of the 17 patients on systemic antibiotic prophylaxis developed SBP while 8/27 patients on rifaximin and 24/108 without prophylaxis had SBP (p = 0.02 and p = 0.04 versus systemic antibiotics, respectively). In general, episodes of SBP were similar for patients treated with rifaximin and those without any prophylaxis. However, Escherichia coli and enterococci were dominant in the ascites of patients without any prophylaxis, while mostly klebsiella species were recovered from the ascites samples in the rifaximin group.

Conclusion

Rifaximin pretreatment did not lead to a reduction of SBP occurrence in hospitalized patients with advanced liver disease. However, the bacterial species causing SBP were changed by rifaximin.

Systemic anti-microbial agents used in periodontal therapy

Periodontitis is an infectious disease with marked inflammatory response, leading to destruction of underlying tissues. The aim of periodontal therapy is to eradicate the pathogens associated with the disease and attain periodontal health. This is achieved by non-surgical and surgical therapy; however, mechanical debridement and topical application of antiseptics may not be helpful in all cases. In such cases, adjunctive systemic antibiotic therapy remains the treatment of choice. It can reach micro-organisms at the base of the deep periodontal pockets and furcation areas via serum, and also affect organisms residing within gingival epithelium and connective tissue. Before advising any anti-microbial agent, it is necessary to have knowledge of that agent. The aim of this review article is to provide basic details of each systemic anti-microbial agent used in periodontal therapy. The points discussed are its mode of action, susceptible periodontal pathogens, dosage, its use in treatment of periodontal disease, and mechanism of bacterial resistance to each anti-microbial agent. It might be of some help while prescribing these drugs.

Pathogenicity of exopolysaccharide-producing Actinomyces oris isolated from an apical abscess lesion

Aim

To demonstrate a capacity for producing exopolysaccharides (EPSs) and an ability to form biofilm on abiotic materials of Actinomyces oris strain K20.

Methodology

The productivity of EPSs and the ability to form biofilm of strain K20 were evaluated by measuring viscosity of spent culture media and by scanning electron microscopy (SEM) and the biofilm assay on microtitre plates, respectively. High-performance liquid chromatography was used to determine the chemical composition of the viscous materials. To examine the role of the viscous materials attributable to the pathogenicity in this organism, the ability of strain K20 to induce abscess formation was compared in mice to that of ATCC 27044.

Results

The viscosity of the spent culture media of K20 was significantly higher than that of ATCC 27044. Strain K20 showed dense meshwork structures around the cells and formed biofilms on microtitre plates, whereas ATCC 27044 did not. Chemical analysis of the viscous materials revealed that they were mainly composed of neutral sugars with mannose constituting 77.5% of the polysaccharides. Strain K20 induced persistent abscesses in mice lasting at least 5 days at a concentration of 10⁸ cells mL⁻¹, whereas abscesses induced by ATCC 27044 healed and disappeared or decreased in size at day 5.

Conclusions

Strain K20 produced EPSs, mainly consisting of mannose, and formed biofilms. This phenotype might play an important role for A. oris to express virulence through the progression of apical periodontitis.

Bacteria-reactive immune response may induce RANKL-expressing T cells in the mouse periapical bone loss lesion

INTRODUCTION

The present study investigated whether bacteria infecting the root canal can activate any infiltrating T cells to produce receptor activator of nuclear factor kappa B (NF-κB) ligand (RANKL).

METHODS

Using a mouse model of periapical lesion induced by artificial dental pulp exposure, the presence of RANKL-positive T cells and osteoclasts in the periapical lesion was examined by an immunohistochemical approach. The bacteria colonizing the exposed root canal were identified by 16S ribosomal RNA (rRNA) sequence analysis. The isolated endodontic bacteria were further immunized to normal mice, and soluble activator of NF-κB ligand (sRANKL) production by the T cells isolated from the immunized mice was evaluated by ex vivo culture system.

RESULTS

RANKL-positive T cells along with TRAP+ osteoclasts were identified in periapical bone resorption lesions. The gram-negative bacterium Pasteurella pnumotropica, which was most frequently detected from the root canal of exposed pulp, showed remarkably elevated serum immunoglobulin G (IgG)-antibody response in pulp-exposed mice compared with control nontreated mice. Immunization of mice with P. pneumotropica induced not only serum IgG-antibody but also primed bacteria-reactive T cells that produced sRANKL in response to ex vivo exposure to P. pneumotropica.

CONCLUSIONS

T cells infiltrating the periapical region express RANKL, and the endodontic bacteria colonizing the root canal appear to induce RANKL expression from bacteria-reactive T cells, suggesting the possible pathogenic engagement of the immune response to endodontic bacteria in the context of developing bone resorptive periapical lesions.

Streptococcus cristatus modulates the Fusobacterium nucleatum-induced epithelial interleukin-8 response through the nuclear factor-kappa B pathway

BACKGROUND AND OBJECTIVE

We previously reported that the interleukin-8 (IL-8) response to Fusobacterum nucleatum was attenuated in the presence of Streptococcus cristatus. Here, we further examined the underlying mechanism(s) involved in the modulating effect of S. cristatus by looking specifically at its impact on the nuclear factor-kappa B (NF-κB) pathway under the toll-like receptor (TLR) signaling background.

MATERIAL AND METHODS

OKF6/TERT-2 and KB cells were co-cultured with F. nucleatum and S. cristatus, either alone or in combination. Secretion of IL-8 protein was measured by ELISA. The nuclear translocation of NF-κB was evaluated by confocal microscopy, while DNA-binding activity was quantified using TransAM™ ELISA kits. Western blot analysis was performed to determine whether the anti-inflammatory effect of S. cristatus is related to the modulation of the NF-κB inhibitory protein IκB-α.

RESULTS

Incubation with F. nucleatum significantly enhanced the nuclear translocation of NF-κB. Exposure to S. cristatus alone did not cause detectable NF-κB translocation and was able to inhibit the F. nucleatum-induced NF-κB nuclear translocation. The TransAM assay further confirmed that S. cristatus blocked the nuclear translocation of NF-κB in response to F. nucleatum stimulation. In contrast to the nearly complete degradation of IκB-α induced by F. nucleatum alone, the presence of S. cristatus stabilized IκB-α. Pre-incubation with TLR2 and TLR4 antibodies, however, did not affect the epithelial response to either species alone or in combination.

CONCLUSION

The mechanism by which S. cristatus attenuates F. nucleatum-induced proinflammatory responses in oral epithelial cells appears to involve blockade of NF-κB nuclear translocation at the level of IκB-α degradation.

Markedly different genome arrangements between serotype a strains and serotypes b or c strains of Aggregatibacter actinomycetemcomitans

BACKGROUND

Bacterial phenotype may be profoundly affected by the physical arrangement of their genes in the genome. The Gram-negative species Aggregatibacter actinomycetemcomitans is a major etiologic agent of human periodontitis. Individual clonal types of A. actinomycetemcomitans may exhibit variable virulence and different patterns of disease association. This study examined the genome arrangement of A. actinomycetemcomitans using the genome sequences of serotypes a-c strains. The genome alignment and rearrangement were analyzed by the MAUVE and the GRIMM algorithms. The distribution patterns of genes along the leading/lagging strands were investigated. The occurrence and the location of repeat sequences relative to the genome rearrangement breakpoints were also determined.

RESULTS

The genome arrangement of the serotype a strain D7S-1 is markedly different from the serotype b strain HK1651 or the serotype c strain D11S-1. Specific genome arrangements appear to be conserved among strains of the same serotypes. The reversal distance between D7S-1 and HK1651 by GRIMM analysis is also higher than the within-species comparisons of 7 randomly selected bacterial species. The locations of the orthologous genes are largely preserved between HK1651 and D11S-1 but not between D7S-1 and HK1651 (or D11S-1), irrespective of whether the genes are categorized as essential/nonessential or highly/nonhighly expressed. However, genome rearrangement did not disrupt the operons of the A. actinomycetemcomitans strains. A higher proportion of the genome in strain D7S-1 is occupied by repeat sequences than in strains HK1651 or D11S-1.

CONCLUSION

The results suggest a significant evolutionary divergence between serotype a strains and serotypes b/c strains of A. actinomycetemcomitans. The distinct patterns of genome arrangement may suggest phenotypic differences between serotype a and serotypes b/c strains.

Proteomic analysis of ampicillin-resistant oral Fusobacterium nucleatum

INTRODUCTION

Fusobacterium nucleatum represents one of the predominant anaerobic species in the oral microbiota. Penicillin-resistant F. nucleatum have been isolated from intra- and extraoral infections. This study aimed to assess ampicillin resistance in F. nucleatum by investigating the synthesis of resistance-associated proteins.

METHODS

Ampicillin-resistant and ampicillin-susceptible F. nucleatum isolates were obtained from 22 dental plaque samples. Two-dimensional gel electrophoresis and mass spectrometry were used to investigate bacterial protein synthesis. Proteins exhibiting statistically significant quantitative changes between sensitive and resistant isolates were identified using peptide mass mapping and matrix-assisted laser desorption/ionization - time of flight/time of flight (MALDI-TOF/TOF) mass spectrometry.

RESULTS

Twenty-three F. nucleatum isolates were recovered from plaque samples and their ampicillin minimum inhibitory concentrations ranged between 0.125 microg/ml and 256 microg/ml. Analysis of the bacterial cellular proteins by two-dimensional gel electrophoresis resolved 154-246 distinct protein spots (mean 212, n = 9). Between 32% and 83% of the protein spots were common for the F. nucleatum isolates. Comparisons of the protein profiles of sensitive and resistant isolates revealed the presence of a 29 kDa protein and significant increases in the synthesis of two proteins at 37 and 46 kDa in the ampicillin-resistant F. nucleatum isolates. These proteins were identified as a class D beta-lactamase, ATP-binding cassette (ABC) transporter ATP-binding protein and enolase, respectively.

CONCLUSION

Synthesis of a class D beta-lactamase by ampicillin-resistant F. nucleatum isolates could complicate antimicrobial treatment because these enzymes might confer resistance to many classes of beta-lactam antibiotics. The differences observed in protein synthesis between ampicillin-resistant and ampicillin-susceptible F. nucleatum may contribute to the antibiotic resistance and virulence of these bacteria.

Interspecies interactions within oral microbial communities

While reductionism has greatly advanced microbiology in the past 400 years, assembly of smaller pieces just could not explain the whole! Modern microbiologists are learning "system thinking" and "holism." Such an approach is changing our understanding of microbial physiology and our ability to diagnose/treat microbial infections. This review uses oral microbial communities as a focal point to describe this new trend. With the common name "dental plaque," oral microbial communities are some of the most complex microbial floras in the human body, consisting of more than 700 different bacterial species. For a very long time, oral microbiologists endeavored to use reductionism to identify the key genes or key pathogens responsible for oral microbial pathogenesis. The limitations of reductionism forced scientists to begin adopting new strategies using emerging concepts such as interspecies interaction, microbial community, biofilms, polymicrobial disease, etc. These new research directions indicate that the whole is much more than the simple sum of its parts, since the interactions between different parts resulted in many new physiological functions which cannot be observed with individual components. This review describes some of these interesting interspecies-interaction scenarios.

Prevention of infective endocarditis: guidelines from the American Heart Association: a guideline from the American Heart Association Rheumatic Fever, Endocarditis and Kawasaki Disease Committee, Council on Cardiovascular Disease in the Young, and the Council on Clinical Cardiology, Council on Cardiovascular Surgery and Anesthesia, and the Quality of Care and Outcomes Research Interdisciplinary Working Group

BACKGROUND

The purpose of this statement is to update the recommendations by the American Heart Association (AHA) for the prevention of infective endocarditis, which were last published in 1997.

METHODS AND RESULTS

A writing group appointed by the AHA for their expertise in prevention and treatment of infective endocarditis (IE) with liaison members representing the American Dental Association, the Infectious Diseases Society of America and the American Academy of Pediatrics. The writing group reviewed input from national and international experts on IE. The recommendations in this document reflect analyses of relevant literature regarding procedure-related bacteremia and IE; in vitro susceptibility data of the most common microorganisms, which cause IE; results of prophylactic studies in animal models of experimental endocarditis; and retrospective and prospective studies of prevention of IE. MEDLINE database searches from 1950 through 2006 were done for English language articles using the following search terms: endocarditis, infective endocarditis, prophylaxis, prevention, antibiotic, antimicrobial, pathogens, organisms, dental, gastrointestinal, genitourinary, streptococcus, enterococcus, staphylococcus, respiratory, dental surgery, pathogenesis, vaccine, immunization and bacteremia. The reference lists of the identified articles were also searched. The writing group also searched the AHA online library. The American College of Cardiology/AHA classification of recommendations and levels of evidence for practice guidelines were used. The article subsequently was reviewed by outside experts not affiliated with the writing group and by the AHA Science Advisory and Coordinating Committee.

CONCLUSIONS

The major changes in the updated recommendations include the following. (1) The committee concluded that only an extremely small number of cases of IE might be prevented by antibiotic prophylaxis for dental procedures even if such prophylactic therapy were 100 percent effective. (2) IE prophylaxis for dental procedures should be recommended only for patients with underlying cardiac conditions associated with the highest risk of adverse outcome from IE. (3) For patients with these underlying cardiac conditions, prophylaxis is recommended for all dental procedures that involve manipulation of gingival tissue or the periapical region of teeth or perforation of the oral mucosa. (4) Prophylaxis is not recommended based solely on an increased lifetime risk of acquisition of IE. (5) Administration of antibiotics solely to prevent endocarditis is not recommended for patients who undergo a genitourinary or gastrointestinal tract procedure. These changes are intended to define more clearly when IE prophylaxis is or is not recommended and to provide more uniform and consistent global recommendations.

Cross-reactive adaptive immune response to oral commensal bacteria results in an induction of receptor activator of nuclear factor-?B ligand (RANKL)-dependent periodontal bone resorption in a mouse model

INTRODUCTION

The present study examined whether induction of an adaptive immune response to orally colonizing non-pathogenic Pasteurella pneumotropica by immunization with the phylogenetically closely related bacterium, Actinobacillus actinomycetemcomitans, can result in periodontal bone loss in mice.

METHODS

BALB/c mice harboring P. pneumotropica (P. pneumotropica(+) mice) in the oral cavity or control P. pneumotropica-free mice were immunized with fixed A. actinomycetemcomitans. The animals were sacrificed on day 30, and the following measurements were carried out: (i) serum immunoglobulin G and gingival T-cell responses to A. actinomycetemcomitans and P. pneumotropica; (ii) periodontal bone loss; and (iii) identification of receptor activator of nuclear factor-kappaB ligand (RANKL) -positive T cells in gingival tissue.

RESULTS

Immunization with A. actinomycetemcomitans induced a significantly elevated serum immunoglobulin G response to the 29-kDa A. actinomycetemcomitans outer membrane protein (Omp29), which showed strong cross-reactivity with P. pneumotropica OmpA compared to results in the control non-immunized mice. The A. actinomycetemcomitans-immunized P. pneumotropica(+) mice developed remarkable periodontal bone loss in a RANKL-dependent manner, as determined by the abrogation of bone loss by treatment with osteoprotegerin-Fc. The T cells isolated from the gingival tissue of A. actinomycetemcomitans-immunized P. pneumotropica(+) mice showed an in vitro proliferative response to both A. actinomycetemcomitans and P. pneumotropica antigen presentation, as well as production of soluble(s)RANKL in the culture supernatant. Double-color confocal microscopy demonstrated that the frequency of RANKL(+) T cells in the gingival tissue of A. actinomycetemcomitans-immunized P. pneumotropica(+) mice was remarkably elevated compared to control mice.

CONCLUSION

The induction of an adaptive immune response to orally colonizing non-pathogenic P. pneumotropica results in RANKL-dependent periodontal bone loss in mice.

Prevention of infective endocarditis: guidelines from the American Heart Association: a guideline from the American Heart Association Rheumatic Fever, Endocarditis, and Kawasaki Disease Committee, Council on Cardiovascular Disease in the Young, and the Council on Clinical Cardiology, Council on Cardiovascular Surgery and Anesthesia, and the Quality of Care and Outcomes Research Interdisciplinary Working Group

BACKGROUND

The purpose of this statement is to update the recommendations by the American Heart Association (AHA) for the prevention of infective endocarditis that were last published in 1997.

METHODS AND RESULTS

A writing group was appointed by the AHA for their expertise in prevention and treatment of infective endocarditis, with liaison members representing the American Dental Association, the Infectious Diseases Society of America, and the American Academy of Pediatrics. The writing group reviewed input from national and international experts on infective endocarditis. The recommendations in this document reflect analyses of relevant literature regarding procedure-related bacteremia and infective endocarditis, in vitro susceptibility data of the most common microorganisms that cause infective endocarditis, results of prophylactic studies in animal models of experimental endocarditis, and retrospective and prospective studies of prevention of infective endocarditis. MEDLINE database searches from 1950 to 2006 were done for English-language papers using the following search terms: endocarditis, infective endocarditis, prophylaxis, prevention, antibiotic, antimicrobial, pathogens, organisms, dental, gastrointestinal, genitourinary, streptococcus, enterococcus, staphylococcus, respiratory, dental surgery, pathogenesis, vaccine, immunization, and bacteremia. The reference lists of the identified papers were also searched. We also searched the AHA online library. The American College of Cardiology/AHA classification of recommendations and levels of evidence for practice guidelines were used. The paper was subsequently reviewed by outside experts not affiliated with the writing group and by the AHA Science Advisory and Coordinating Committee.

CONCLUSIONS

The major changes in the updated recommendations include the following: (1) The Committee concluded that only an extremely small number of cases of infective endocarditis might be prevented by antibiotic prophylaxis for dental procedures even if such prophylactic therapy were 100% effective. (2) Infective endocarditis prophylaxis for dental procedures is reasonable only for patients with underlying cardiac conditions associated with the highest risk of adverse outcome from infective endocarditis. (3) For patients with these underlying cardiac conditions, prophylaxis is reasonable for all dental procedures that involve manipulation of gingival tissue or the periapical region of teeth or perforation of the oral mucosa. (4) Prophylaxis is not recommended based solely on an increased lifetime risk of acquisition of infective endocarditis. (5) Administration of antibiotics solely to prevent endocarditis is not recommended for patients who undergo a genitourinary or gastrointestinal tract procedure. These changes are intended to define more clearly when infective endocarditis prophylaxis is or is not recommended and to provide more uniform and consistent global recommendations.

Prevention of infective endocarditis: guidelines from the American Heart Association: a guideline from the American Heart Association Rheumatic Fever, Endocarditis, and Kawasaki Disease Committee, Council on Cardiovascular Disease in the Young, and the Council on Clinical Cardiology, Council on Cardiovascular Surgery and Anesthesia, and the Quality of Care and Outcomes Research Interdisciplinary Working Group

BACKGROUND

The purpose of this statement is to update the recommendations by the American Heart Association (AHA) for the prevention of infective endocarditis that were last published in 1997.

METHODS AND RESULTS

A writing group was appointed by the AHA for their expertise in prevention and treatment of infective endocarditis, with liaison members representing the American Dental Association, the Infectious Diseases Society of America, and the American Academy of Pediatrics. The writing group reviewed input from national and international experts on infective endocarditis. The recommendations in this document reflect analyses of relevant literature regarding procedure-related bacteremia and infective endocarditis, in vitro susceptibility data of the most common microorganisms that cause infective endocarditis, results of prophylactic studies in animal models of experimental endocarditis, and retrospective and prospective studies of prevention of infective endocarditis. MEDLINE database searches from 1950 to 2006 were done for English-language papers using the following search terms: endocarditis, infective endocarditis, prophylaxis, prevention, antibiotic, antimicrobial, pathogens, organisms, dental, gastrointestinal, genitourinary, streptococcus, enterococcus, staphylococcus, respiratory, dental surgery, pathogenesis, vaccine, immunization, and bacteremia. The reference lists of the identified papers were also searched. We also searched the AHA online library. The American College of Cardiology/AHA classification of recommendations and levels of evidence for practice guidelines were used. The paper was subsequently reviewed by outside experts not affiliated with the writing group and by the AHA Science Advisory and Coordinating Committee.

CONCLUSIONS

The major changes in the updated recommendations include the following: (1) The Committee concluded that only an extremely small number of cases of infective endocarditis might be prevented by antibiotic prophylaxis for dental procedures even if such prophylactic therapy were 100% effective. (2) Infective endocarditis prophylaxis for dental procedures is reasonable only for patients with underlying cardiac conditions associated with the highest risk of adverse outcome from infective endocarditis. (3) For patients with these underlying cardiac conditions, prophylaxis is reasonable for all dental procedures that involve manipulation of gingival tissue or the periapical region of teeth or perforation of the oral mucosa. (4) Prophylaxis is not recommended based solely on an increased lifetime risk of acquisition of infective endocarditis. (5) Administration of antibiotics solely to prevent endocarditis is not recommended for patients who undergo a genitourinary or gastrointestinal tract procedure. These changes are intended to define more clearly when infective endocarditis prophylaxis is or is not recommended and to provide more uniform and consistent global recommendations.

Rapid identification of Fusobacterium nucleatum and Fusobacterium necrophorum by fluorescence in situ hybridization

Identification of clinically relevant Fusobacterium spp. is hampered by their slow growth, their frequent occurrence in polymicrobial culture, and the low reliability of biochemical differentiation methods. A newly developed fluorescence in situ hybridization (FISH) assay allowed reliable and rapid identification of Fusobacterium necrophorum and Fusobacterium nucleatum from culture. Preliminary results show that the method offers the perspective for direct detection of these pathogens in blood cultures and abscess aspirates.

Determining the antibiotic resistance potential of the indigenous oral microbiota of humans using a metagenomic approach

Studies of the prevalence and identity of genes encoding resistance to antibiotics in a microbial community are usually carried out on only the cultivable members of the community. However, it is possible to include the as-yet-uncultivable organisms present by adopting a metagenomic approach to such studies. In this investigation, four metagenomic libraries of the oral microbiota were prepared from three groups of 20 adult humans and screened for antibiotic-resistant clones. Clones resistant to tetracycline and amoxycillin were present in all four libraries while gentamicin-resistant clones were found in three of the libraries. The genes encoding tetracycline resistance in the clones were identified and found to be tet(M), tet(O), tet(Q), tet(W), tet37 and tet(A). However, only the first three of these were detected in all three groups of individuals investigated.

Use of polymerase chain reaction techniques and sodium dodecyl sulfate-polyacrylamide gel electrophoresis for differentiation of oral Lactobacillus species

BACKGROUND/AIMS

The genus Lactobacillus has been associated with dental caries in humans, although it is seldom speciated due to lack of simple and nonlaborious identification methods. A considerable heterogeneity among Lactobacillus species has been demonstrated. The purpose of this study was to develop simple methods combining restriction fragment length polymorphism analysis of polymerase chain reaction (PCR)-amplified 16S rRNA (16S rRNA gene PCR-RFLP) and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) for the identification of 13 reference strains of Lactobacillus.

METHODS

The 16S rRNA gene sequences were amplified by PCR using universal primers and digestion of PCR products with the restriction endonucleases, HpaII and HaeIII. The 16S rRNA gene PCR-RFLP is reproducible and has been proved to be useful for differentiating Lactobacillus strains to species level. Seventy-seven Lactobacillus isolates from a Thai population were used to show the applicability of the identification test.

RESULTS

PCR-RFLP alone had limitations, because the RFLP patterns of Lactobacillus casei and Lactobacillus rhamnosus and of Lactobacillus acidophilus and Lactobacillus crispatus showed similar patterns; however, these could be differentiated by SDS-PAGE. Of the 77 isolates, 38 were identified as Lactobacillus fermentum, 25 as L. rhamnosus, 5 as Lactobacillus salivarius, 5 as L. casei, 3 as L. acidophilus and 1 as Lactobacillus plantarum.

CONCLUSION

16S rRNA gene PCR-RFLP, using HpaII and HaeIII, together with SDS-PAGE protein profiles could be an alternative method for the identification of oral Lactobacillus strains to species level, and may be applicable for large-scale studies on the association of Lactobacillus to dental caries.

Statistical analyses of complex denaturing gradient gel electrophoresis profiles

Studies using molecular techniques have demonstrated that a culture-based approach can severely underestimate the bacterial diversity in most environments. One of the molecular techniques that has been applied in microbial ecology is denaturing gradient gel electrophoresis (DGGE). The purpose of this study was to investigate differences in the microbiota of plaque, using a number of analysis techniques, from children without gingivitis (n = 30) and from those with gingivitis (n = 30). Extracted DNA from gingival margin plaque was subjected to PCR targeting the 16S rRNA gene using universal primers. DGGE profiles were analyzed in three ways. (i) Bacterial diversity was compared between cohorts by using the Shannon-Wiener index (also known as the Shannon-Weaver index). (ii) A hierarchical cluster analysis of the banding patterns was calculated and expressed as a dendrogram. (iii) Individual DGGE bands and their intensities for both cohorts were compared using a logistic regression analysis. The Shannon-Wiener indices demonstrated a greater bacterial diversity associated with no-gingivitis plaque (P = 0.009). Dendrograms demonstrated that seven clades associated with gingivitis and five clades associated with no gingivitis. The logistic regression demonstrated that one band was significantly associated with no gingivitis (P = 0.001), while two bands were significantly associated with gingivitis (P = 0.005 and P = 0.042). In conclusion, this study demonstrates that the development of gingivitis might be accompanied by a decrease in bacterial diversity. Furthermore, we have demonstrated that logistic regression is a good statistical method for analyzing and characterizing DGGE profiles.

Comparison of culture and real-time PCR for detection and quantification of five putative periodontopathogenic bacteria in subgingival plaque samples

OBJECTIVES

Bacterial cultivation is a well-established method for analyzing plaque samples. Real-time polymerase chain reaction (PCR) is a novel rapid method for the identification and quantification of periodontopathogenic bacteria that has been recently introduced. In this study, we compared real-time PCR with conventional anaerobic cultivation.

METHOD

A total of 78 subgingival plaque samples were harvested from pockets > or =5 mm in 22 patients with advanced chronic periodontitis and immediately transferred into transport medium. Aliquots were evaluated with species-specific probes by real-time PCR (meridol Perio Diagnostics, GABA) and anaerobic bacteria culture on selective media for the detection of Actinobacillus actinomycetemcomitans, Fusobacterium nucleatum, Porphyromonas gingivalis, Prevotella intermedia and Tannerella forsythensis. The analysis was performed by two separate, blinded examiners.

RESULTS

When real-time PCR was compared with the culture method (golden standard) for the detection of putative periodontopathogenic bacteria, the sensitivity and specificity for A. actinomycetemcomitans were 67% and 100%, respectively (kappa: 0.79); for F. nucleatum 73% and 53%, respectively (kappa: 0.21); for P. gingivalis 94% and 84%, respectively (kappa: 0.77); for P. intermedia 33% and 94%, respectively (kappa: 0.26) and for T. forsythensis 92% and 56%, respectively (kappa: 0.51). Spearman's correlation coefficients for the quantitative results of both methods were 0.82 for A. actinomycetemcomitans, 0.33 for F. nucleatum, 0.83 for P. gingivalis, 0.38 for P. intermedia and 0.67 for T. forsythensis.

CONCLUSION

Overall, the agreement between both test methods was excellent for A. actinomycetemcomitans and P. gingivalis, fair for T. forsythensis and poor for F. nucleatum and P. intermedia. The discrepancies in the results may be explained by the inability of cultivation methods to distinguish between close related taxa, and the problems of keeping periopathogenic bacteria viable, which is required for standard cultivation.

Pigmented-anaerobic bacteria associated with canine periodontitis

The etiology of human periodontal disease has been the focus of considerable research, yet relatively little is known about the causative agents of companion animal periodontitis. In humans, Porphyromonas gingivalis, a black-pigmented anaerobic bacteria (BPAB), has been implicated as the primary periopathogen. It has been demonstrated that BPAB are also found in companion animal periodontal pockets. While some animal BPAB have been individually identified, a study to identify the most frequently isolated subgingival BPAB has not been completed using genetic tools. The objective of this work was to identify the types and relative frequencies of pigmented anaerobic bacteria found in the periodontal pockets of dogs. Porphyromonas salivosa, Porphyromonas denticanis (a novel species) and Porphyromonas gulae were found to be the most frequently isolated BPAB associated with canine periodontitis.

Use of checkerboard DNA-DNA hybridization to study complex microbial ecosystems

It has been difficult to conduct large scale studies of microbiologically complex ecosystems using conventional microbiological techniques. Molecular identification techniques in new probe-target formats, such as checkerboard DNA-DNA hybridization, permit enumeration of large numbers of species in very large numbers of samples. Digoxigenin-labeled whole genomic probes to 40 common subgingival species were tested in a checkerboard hydridization format. Chemifluorescent signals resulting from the hybridization reactions were quantified using a Fluorimager and used to evaluate sensitivity and specificity of the probes. Sensitivity of the DNA probes was adjusted to detect 10(4) cells. In all, 93.5% of potential cross-reactions to 80 cultivable species exhibited signals <5% of that detected for the homologous probe signal. Competitive hybridization and probes prepared by subtraction hybridization and polymerase chain reaction were effective in minimizing cross-reactions for closely related taxa. To demonstrate utility, the technique was used to evaluate 8887 subgingival plaque samples from 79 periodontally healthy and 272 chronic periodontitis subjects and 8126 samples from 166 subjects taken prior to and after periodontal therapy. Significant differences were detected for many taxa for mean counts, proportion of total sample, and percentage of sites colonized between samples from periodontally healthy and periodontitis subjects. Further, significant reductions were observed post therapy for many subgingival species including periodontal pathogens. DNA probes used in the checkerboard DNA-DNA format provide a useful tool for the enumeration of bacterial species in microbiologically complex systems.

Simultaneous Detection of Dialister pneumosintes and Filifactor alocis in Endodontic Infections by 16S rDNA-directed Multiplex PCR

Dialister pneumosintes and Filifactor alocis have been recently considered as candidate endodontic pathogens. In this study, we devised a 16S rDNA-directed multiplex PCR protocol for simultaneous detection of these two bacterial species in endodontic infections. Samples were taken from infected root canals associated with asymptomatic periradicular lesions as well as from cases of acute periradicular abscesses. DNA extracted from the samples was used as template for simultaneous detection of D. pneumosintes and F. alocis through a multiplex PCR assay. Two fragments of the expected sizes, one specific for D. pneumosintes and the other for F. alocis, were simultaneously amplified from a mixture of reference genomic DNA containing DNA from both species. Clinical samples that were positive for the target species showed a single band of the predicted size for each species. D. pneumosintes was detected by multiplex PCR in 11 samples (7 asymptomatic and 4 abscesses) and F. alocis was identified in 9 cases (6 asymptomatic and 3 abscesses). Six samples (3 asymptomatic and 3 abscesses) shared the two species. Data from the present study confirmed that D. pneumosintes and F. alocis are common members of the microbiota present in primary endodontic infections and thereby may participate in the pathogenesis of periradicular lesions. The proposed multiplex PCR assay is a simple, rapid, and accurate method for the simultaneous detection of these two candidate endodontic pathogens.

Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics

Background

The phylogenetic position and evolutionary relationships of Fusobacteria remain uncertain. Especially intriguing is their relatedness to low G+C Gram positive bacteria (Firmicutes) by ribosomal molecular phylogenies, but their possession of a typical gram negative outer membrane. Taking advantage of the recent completion of the Fusobacterium nucleatum genome sequence we have examined the evolutionary relationships of Fusobacterium genes by phylogenetic analysis and comparative genomics tools.

Results

The data indicate that Fusobacterium has a core genome of a very different nature to other bacterial lineages, and branches out at the base of Firmicutes. However, depending on the method used, 35–56% of Fusobacterium genes appear to have a xenologous origin from bacteroidetes, proteobacteria, spirochaetes and the Firmicutes themselves. A high number of hypothetical ORFs with unusual codon usage and short lengths were found and hypothesized to be remnants of transferred genes that were discarded. Some proteins and operons are also hypothesized to be of mixed ancestry. A large portion of the Gram-negative cell wall-related genes seems to have been transferred from proteobacteria.

Conclusions

Many instances of similarity to other inhabitants of the dental plaque that have been sequenced were found. This suggests that the close physical contact found in this environment might facilitate horizontal gene transfer, supporting the idea of niche-specific gene pools. We hypothesize that at a point in time, probably associated to the rise of mammals, a strong selective pressure might have existed for a cell with a Clostridia-like metabolic apparatus but with the adhesive and immune camouflage features of Proteobacteria.

Identification of mutans streptococci by restriction fragment length polymorphism analysis of polymerase chain reaction-amplified 16S ribosomal RNA genes

Mutans streptococci are frequently isolated from dental plaque and carious lesions. These bacteria have been identified by conventional methods such as biochemical and serologic tests followed by the isolation of colonies on the mitis-salivarius agar, which are sometimes inconsistent. Recently, species-specific polymerase chain reaction (PCR) has been reported to rapidly identify Streptococcus mutans and Streptococcus sobrinus. However, in the case of identification and classification into several species, e.g. within the group of mutans streptococci consisting of seven species, the identification using species-specific PCR seems somewhat inefficient because of need for the development and preparation of specific primers for each species. Therefore, in this study we developed a simple method using restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal RNA genes (16S rRNA genes PCR-RFLP) for the identification of seven different species included in the group of mutans streptococci. We amplified 16S rRNA gene sequences from genomic DNA samples by PCR using universal primers and digested the PCR products with the restriction endonucleases, HpaII and HaeIII. HpaII produced six RFLP patterns for eight reference strains, since the patterns for S. sobrinus, Streptococcus downei and Streptococcus ferus were similar. RFLP patterns produced with HaeIII could separate these three species. Furthermore, the RFLP patterns predicted from the 16S rRNA gene sequences in the GenBank database agreed with the actual RFLP patterns produced in the present study. The 16S rRNA sequence comparisons can be used to identify oral mutans streptococci; however, the identification by sequencing is sometimes difficult in large-scale studies and for small laboratories. Therefore, 16S rRNA genes PCR-RFLP, using HpaII and HaeIII, could be an alternative method for the identification of mutans streptococci, and may be applicable for large-scale studies on the cariogenicity of mutans streptococci.

Nested PCR for detection of mutans streptococci in dental plaque

AIMS

Mutans streptococci such as Streptococcus mutans and Streptococcus sobrinus have been implicated in human dental caries. In an attempt to develop a rapid and sensitive method for detecting Strep. mutans and Strep. sobrinus in dental plaque, a nested PCR amplification based on the 16S rRNA gene was employed.

METHODS AND RESULTS

A universal set of PCR primers for bacterial 16S rRNA gene was introduced for the first PCR, and then two sets of primers specific for the 16S rRNA gene sequences of either Strep. mutans or Strep. sobrinus were used for the second PCR. Eighteen plaque samples were analyzed, and a nested PCR was shown to be more sensitive for detecting Strep. mutans and Strep. sobrinus than direct PCR.

CONCLUSIONS, SIGNIFICANCE AND IMPACT OF THE STUDY

The 16S rRNA gene-based nested PCR method is a rapid and sensitive method for the detection of mutans streptococci, and may also be suitable for carrying out large-scale studies on the cariogenicity of mutans streptococci.

Type IV pilus gene homologs pilABCD are required for natural transformation in Actinobacillus actinomycetemcomitans

Some clinical isolates of the gram-negative periodontal pathogen Actinobacillus actinomycetemcomitans are naturally competent for DNA uptake. In this study, we examined the sequence and the function of a type IV pilus-like pilABCD gene cluster and its downstream region in a naturally transformable A. actinomycetemcomitans strain D7S. Specific knockout mutants of pilABCD of strain D7S were constructed by replacing individual genes with an antibiotic resistance cassette. The transformation frequency of chromosome markers in the wildtype strain D7S was approximately 10(-3) per CFU. In contrast, the delta pilA, delta pilB, delta pilC, delta pilBC or delta pilD mutants were non-transformable (transformation frequency <10(-8)). Disruption of an ORF downstream of pilD had no apparent effect on the transformability of this bacterium. The pilA or pilBC deletion did not seem to affect fimbria expression or cell surface structure in either rough or smooth strains as determined by scanning and transmission electron microscopy examinations. RT-PCR analysis showed that pilA was expressed in strain D7S under a competence-inducing growth condition. The expression of pilA was barely detectable in strain D7S cultured under a non-competence-inducing condition or in the non-transformable strain JP-2. The results indicate that pilABCD are required for competence but are apparently not involved in fimbria expression of A. actinomycetemcomitans.

PCR methodology as a valuable tool for identification of endodontic pathogens

OBJECTIVES

This paper reviews the principles of polymerase chain reaction (PCR) methodology, its application in identification of endodontic pathogens and the perspectives regarding the knowledge to be reached with the use of this highly sensitive, specific and accurate methodology as a microbial identification test.

DATA SOURCES

Studies published in the medical, dental and biological literature.

STUDY SELECTION

Evaluation of published epidemiological studies examining the endodontic microbiota through PCR methodology.

CONCLUSIONS

PCR technology has enabled the detection of bacterial species that are difficult or even impossible to culture as well as cultivable bacterial strains showing a phenotypically divergent or convergent behaviour. Moreover, PCR is more rapid, much more sensitive, and more accurate when compared with culture. Its use in endodontics to investigate the microbiota associated with infected root canals has expanded the knowledge on the bacteria involved in the pathogenesis of periradicular diseases. For instance, Tannerella forsythensis (formerly Bacteroides forsythus), Treponema denticola, other Treponema species, Dialister pneumosintes, and Prevotella tannerae were detected in infected root canals for the first time and in high prevalence when using PCR analysis. The diversity of endodontic microbiota has been demonstrated by studies using PCR amplification, cloning and sequencing of the PCR products. Moreover, other fastidious bacterial species, such as Porphyromonas endodontalis, Porphyromonas gingivalis and some Eubacterium spp., have been reported in endodontic infections at a higher prevalence than those reported by culture procedures.

Intra-chromosomal heterogeneity between the four 16S rRNA gene copies in the genus Veillonella: implications for phylogeny and taxonomy

Among the seven species characterized within the genus Veillonella, three (Veillonella dispar, Veillonella parvula and Veillonella atypica) have so far been isolated from human flora and during infectious processes. Sequencing and analysis of 16S rDNA (rrs) has been described as the best method for identification of Veillonella strains at the species level since phenotypic characteristics are unable to differentiate between species. rrs sequencing for the three species isolated from humans showed more than 98 % identity between them. Four rrs copies were found in the reference strains and in all the clinical isolates studied. The sequences of each rrs were determined for the clinical strain ADV 360.1, and they showed a relatively high level of heterogeneity (1.43 %). In the majority of cases, polymorphic positions corresponded to nucleotides allowing differentiation between the three species isolated from humans. Moreover, variability observed between rrs copies was higher than that between 16S rDNA sequences of V. parvula and V. dispar. Phylogenetic analysis showed that polymorphism between rrs copies affected the position of strain ADV 360.1 in the tree. Variable positions occurred in stems and loops belonging to variable and hypervariable regions of the 16S rRNA secondary structure but did not change the overall structure of the 16S rRNA. PCR-RFLP experiments performed on 27 clinical isolates of Veillonella sp. suggested that inter-rrs heterogeneity occurs widely among the members of the genus VEILLONELLA: These results, together with the lack of phenotypic criteria for species differentiation, give preliminary arguments for unification of V. dispar and V. parvula.

Characterization of in vitro oral bacterial biofilms by traditional and molecular methods

The aim of this study was to compare culture-based bacterial isolation methods with direct amplification and cloning of 16S rRNA genes from oral biofilms grown in an in vitro model. The model used was a constant depth film fermentor which was inoculated with pooled human saliva. The use of culture techniques and cloning resulted in the identification of 36 different bacterial species from the saliva inoculum and from the biofilms. Of these, only five were detected solely by molecular methods. Three taxa were detected which, according to the databases, were unidentified. Using the molecular methods of detection, differences in the number of species observed were found using different 16S rRNA gene primers and numbers of PCR cycles. We have shown that microcosm supragingival plaque biofilms grown in a fermentor consisted of a community most of the members of which could be cultivated on laboratory media.

Genetic characterization of the oral Actinomyces

Actinomyces are difficult to identify using serological and biochemical methods but genotyping is an efficient and reliable means of bacterial characterization and can be used to determine clonal identity. The purpose here was to genotype 13 American type culture collection (ATCC) reference strains representing six different oral Actinomyces spp. by using chromosomal DNA fingerprinting (CDF), arbitrarily primed-polymerase chain reaction (AP-PCR) and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). In CDF analysis, BamHI, BstEII and SmaI yielded digestion patterns revealing characteristic differences among the known Actinomyces spp., with SmaI demonstrating optimal resolution. Amplicons generated by AP-PCR with primer OPB-07 displayed banding patterns that permitted discrimination of all Actinomyces strains tested. PCR-RFLP with MnlI digests generated fragment patterns that also characterized the reference strains. Collectively, genotypic profiles generated by CDF, AP-PCR and PCR-RFLP permitted differentiation of all 13 ATCC Actinomyces strains. SmaI CDF analysis of 18 clinical isolates of catalase-positive A. naeslundii genospecies 2 revealed extensive genetic diversity among these strains. These molecular approaches may be useful in determining genetic diversity within oral Actinomyces populations and fidelity of Actinomyces transmission between mother and child.

Direct amplification of rRNA gene sequences for identification of selected oral pathogens in root canal infections

AIM

The purpose of this study was to assess the prevalence of selected oral pathogens in root canal infections and their relationship with symptoms using a highly sensitive technique, the polymerase chain reaction.

METHODOLOGY

Samples were obtained from 91 infected teeth associated with periradicular lesions, including cases of acute periradicular abscesses. DNA was extracted from the samples and analysed for the presence of target microbial species using a PCR-based identification assay.

RESULTS

All samples were positive for the presence of bacteria. Streptococcus anginosus group was detected in 16.7%, Fusobacterium nucleatum in 14.3%, and Bacteroides forsythus in 7.1% of the abscess samples. No pus sample yielded Actinomyces israelii, Actinobacillus actinomycetemcomitans or fungal species. In general, B. forsythus was found in 20% of the cases (16 of 80), S. anginosus in 12% (6 of 50), F. nucleatum in 10% (6 of 60) and A. israelii in 5% (two of 40). A. actinomycetemcomitans was not detected in any case. Fungi were present in only one of 50 cases (2%). There was no correlation between the species and symptoms.

CONCLUSIONS

Direct molecular approaches appear to be a valuable tool for the rapid and reliable diagnosis of infectious diseases, as well as for research purposes. There was no correlation between target microbial species and symptoms.

A sensitive method for detecting Porphyromonas gingivalis by polymerase chain reaction and its possible clinical application

BACKGROUND

It is useful for the clinical diagnosis of periodontitis to monitor the colonization of periodontopathic bacteria in periodontal pockets. In this study, we attempted to establish and possibly identify the clinical application of a sensitive method to detect Porphyromonas gingivalis (P.g.), one of the putative periodontopathic bacteria related to chronic periodontitis.

METHODS

Genomic DNA extracted from cultured P.g. 381 and clinically isolated subgingival plaque samples were used as a template of polymerase chain reaction (PCR). We designed primers to amplify the genomic DNA coding 40 kDa outer membrane protein (OMP), one of the unique proteins to all strains of P.g. The efficiency and specificity of amplification were evaluated by agarose gel electrophoresis and subsequent Southern hybridization with a digoxygenin-labeled oligonucleotide probe.

RESULTS

Fewer than 100 P.g. bacterial cells in the specimen were reproducibly detected by PCR-hybridization assay. This PCR-hybridization assay was at least 100 times more sensitive than the conventional indirect immunofluorescence assay (IIF). Furthermore, the imaging analysis showed that there is a linear correlation between the strength of the signal and the cell number of P.g. from which the template DNA was extracted semiquantitatively. It is noteworthy that the PCR assay could also be applied to detect P.g. from clinical plaque samples and that it was approximately 100 times more sensitive than a conventional IIF assay.

CONCLUSION

The PCR assay established in this study can be a powerful tool to detect P.g. in periodontal pockets and monitor the colonization and/or recolonization of P.g. at the very early phase.

A microbiological study of Papillon-Lefévre syndrome in two patients

AIM

To analyse the microflora of subgingival plaque from patients with Papillon-Lefévre syndrome (PLS), which is a very rare disease characterised by palmar-plantar hyperkeratosis with precocious periodontal destruction.

METHODS

Bacterial isolates were identified using a combination of commercial identification kits, traditional laboratory tests, and gas liquid chromatography. Some isolates were also subjected to partial 16S rDNA sequencing. Plaque samples were also assayed for the presence of Porphyromonas gingivalis, Prevotella intermedia, and Actinobacillus actinomycetemcomitans in a quantitative enzyme linked immunosorbent assay (ELISA) using monoclonal antibodies.

RESULTS

The culture results showed that most isolates were capnophilic and facultatively anaerobic species-mainly Capnocytophaga spp and Streptococcus spp. The latter included S. constellatus, S. oralis, and S. sanguis. Other facultative bacteria belonged to the genera gemella, kingella, leuconostoc, and stomatococcus. The aerobic bacteria isolated were species of neisseria and bacillus. Anaerobic species included Prevotella intermedia, P. melaninogenica, and P. nigrescens, as well as Peptostreptococcus spp. ELISA detected P gingivalis in one patient in all sites sampled, whereas A. actinomycetemcomitans was detected in only one site from the other patient. Prevotella intermedia was present in low numbers.

CONCLUSIONS

Patients with PLS have a very complex subgingival flora including recognised periodontal pathogens. However, no particular periodontopathogen is invariably associated with PLS.

Oral microbial communities: biofilms, interactions, and genetic systems

Oral microbial-plaque communities are biofilms composed of numerous genetically distinct types of bacteria that live in close juxtaposition on host surfaces. These bacteria communicate through physical interactions called coaggregation and coadhesion, as well as other physiological and metabolic interactions. Streptococci and actinomyces are the major initial colonizers of the tooth surface, and the interactions between them and their substrata help establish the early biofilm community. Fusobacteria play a central role as physical bridges that mediate coaggregation of cells and as physiological bridges that promote anaerobic microenvironments which protect coaggregating strict anaerobes in an aerobic atmosphere. New technologies for investigating bacterial populations with 16S rDNA probes have uncovered previously uncultured bacteria and have offered an approach to in situ examination of the spatial arrangement of the participant cells in oral-plaque biofilms. Flow cells with saliva-coated surfaces are particularly useful for studies of biofilm formation and observation. The predicted sequential nature of colonization of the tooth surface by members of different genera can be investigated by using these new technologies and imaging the cells in situ with confocal scanning laser microscopy. Members of at least seven genera now can be subjected to genetic studies owing to the discovery of gene-transfer systems in these genera. Identification of contact-inducible genes in streptococci offers an avenue to explore bacterial responses to their environment and leads the way toward understanding communication among inhabitants of a multispecies biofilm.

Fluoroquinolones in the treatment of Actinobacillus actinomycetemcomitans-associated periodontitis

BACKGROUND

Periodontitis patients harboring Actinobacillus actinmycetemcomitans (Aa) are prime candidates for systemic antibiotic therapy. Besides tetracycline and the combination of metronidazole and amoxicillin the fluoroquinolones are also believed to have antibacterial activity against Aa. The aim of the present study was to evaluate systemic ofloxacin therapy as adjunct to flap surgery.

METHODS

Twenty-five adult periodontitis patients with subgingival detection of Aa were treated with 2x200 mg/d ofloxacin for 5 days as adjunct to open flap surgery (test). Another 10 patients received only flap surgery (control). Probing depth (PD) and clinical attachment level (CAL) was recorded and subgingival plaque samples were cultivated on TSBV agar for detection of Aa at baseline as well as 3 and 12 months following therapy.

RESULTS

At 3 and 12 months following therapy mean PD at monitored sites in the test group changed from 6.8 mm (+/-1.3) to 3.6 mm (+/-1.0), 3.8 mm (+/-1.1) and CAL from 7.5 mm (+/-1.4) to 5.4 mm (+/-1.4), 5.5 mm (+/-1.3). In the control group PD changed from 6.5 mm (+/-0.7) to 4.0 mm (+/-1.7), 4.1 mm (+/-1.6) and CAL from 7.5 mm (+/-1.0) to 6.3 mm (+/-1.7), 6.4 mm (+/-1.8). P was <0.05 for CAL between groups. Three and 12 months following adjunctive systemic ofloxacin therapy, Aa was suppressed below detectable levels in 22 of 22, test patients, whereas Aa could not be recovered in only 2 of the 10 controls. (P<0.0001).

CONCLUSIONS

Systemic ofloxacin as adjunct to open flap surgery is able to suppress A. actinomycetemcomitans below detectable level in patients harboring this organism at baseline.