Targeted antimicrobial therapy in the microbiome era

Antimicrobial photodynamic therapy against a dual-species cariogenic biofilm using a ruthenium-loaded resin-based dental material

BACKGROUND

Streptococcus mutans and Candida albicans are associated with caries recurrence. Therefore, this study evaluated the combination of a Ru(II)-loaded resin-based dental material (RDM) and antimicrobial photodynamic therapy (aPDT) against a dual-species biofilm of S. mutans and C. albicans.

METHODS

An aPDT protocol was established evaluating Ru(II)'s photocatalytic activity and antimicrobial potential under blue LED irradiation (440-460 nm, 22.55 mW/cm2) at different energy densities (0.00, 6.25, 20.25, 40.50 J/cm2). This evaluation involved singlet oxygen quantification and determination of minimum inhibitory concentration (MIC) and minimum bactericidal/fungicidal concentration (MBC/MFC). The biofilm was grown (72 h) on resin disks prepared with Ru(II)-doped RDM (0.00, 0.56, or 1.12 %) and samples were exposed to aPDT or dark conditions. The biofilm was then harvested to analyze cell viability (CFU counts) and formation of soluble and insoluble exopolysaccharides.

RESULTS

The photocatalytic activity of Ru(II) was concentration and energy density dependent (p < 0.05), and MIC/MBC values were reduced for the microorganisms after LED irradiation (40.5 J/cm2); therefor, this energy density was chosen for aPDT. Although incorporation of Ru(II) into RDM reduced the biofilm growth compared to Ru(II)-free RDM for both species in dark conditions (p < 0.05), aPDT combined with an Ru(II)-loaded RDM (0.56 or 1.12 %) potentialized CFU reductions (p < 0.05). Conversely, only 1.12 % Ru(II) with LED irradiation showed lower levels of both soluble and insoluble exopolysaccharides compared to Ru(II)-free samples in dark conditions (p < 0.05).

CONCLUSIONS

When the Ru(II)-loaded RDM was associated with blue LED, aPDT reduced cell viability and lower soluble and insoluble exopolysaccharides were found in the cariogenic dual-species biofilm.

Non-traditional approaches for control of antibiotic resistance

INTRODUCTION

The drying up of antibiotic pipeline has necessitated the development of alternative therapeutic strategies to control the problem of antimicrobial resistance (AMR) that is expected to kill 10-million people annually by 2050. Newer therapeutic approaches address the shortcomings of traditional small-molecule antibiotics - the lack of specificity, evolvability, and susceptibility to mutation-based resistance. These 'non-traditional' molecules are biologicals having a complex structure and mode(s) of action that makes them resilient to resistance.

AREAS COVERED

This review aims to provide information about the non-traditional drug development approaches to tackle the problem of antimicrobial resistance, from the pre-antibiotic era to the latest developments. We have covered the molecules under development in the clinic with literature sourced from reviewed scholarly articles, official company websites involved in innovation of concerned therapeutics, press releases from the regulatory bodies, and clinical trial databases.

EXPERT OPINION

Formal introduction of non-traditional therapies in general practice can be quick and feasible only if supported with companion diagnostics and used in conjunction with established therapies. Owing to relatively higher development costs, non-traditional therapeutics require more funding as well as well as clarity in regulatory and clinical path. We are hopeful these issues are adequately addressed before AMR develops into a pandemic.

Streptococcus mutans dexA affects exopolysaccharides production and biofilm homeostasis

OBJECTIVES

The study aimed to evaluate the role of Streptococcus mutans (S. mutans) dexA gene on biofilm structure and microecological distribution in multispecies biofilms.

MATERIALS AND METHODS

A multispecies biofilm model consisting of S. mutans and its dexA mutants, Streptococcus gordonii (S. gordonii) and Streptococcus sanguinis (S. sanguinis) was constructed, and bacterial growth, biofilm architecture and microbiota composition were determined to study the effect of the S. mutans dexA on multispecies biofilms.

RESULTS

Our results showed that either deletion or overexpression of S. mutans dexA had no effect on the planktonic growth of bacterium, while S. mutans dominated in the multispecies biofilms to form cariogenic biofilms. Furthermore, we revealed that the SmudexA+ group showed structural abnormality in the form of more fractures and blank areas. The morphology of the SmudexA group was sparser and more porous, with reduced and less agglomerated exopolysaccharides scaffold. Interestingly, the microbiota composition analysis provided new insights that the inhibition of S. gordonii and S. sanguinis was alleviated in the SmudexA group compared to the significantly suppressed condition in the other groups.

CONCLUSION

In conclusion, deletion of S. mutans dexA gene re-modules biofilm structure and microbiota composition, thereby leading to decreased cariogenicity. Thus, the S. mutans dexA may be an important target for regulating the cariogenicity of dental plaque biofilms, expecting to be a probiotic for caries control.

Effect of a Short-Term Intervention with Lactobacillus salivarius Probiotic on Early Childhood Caries-An Open Label Randomized Controlled Trial

ECC is a significant therapeutic and social problem and a global burden on public health. The aim of this clinical trial was to test whether a 2-week daily consumption of chewing tablets containing thermally inactivated L. salivarius reduces the 12-month caries increment compared to the control group. The investigation was a single-center, randomized, controlled open-label, blinded end-point evaluation trial in two parallel groups. At baseline, 140 generally healthy children between 3 and 6 years of age with or without ECC were randomly assigned to the probiotic test group (n = 70) or to the treatment as the usual control group (n = 70). The primary outcome measure was the 1-year increment in caries incidence and prevalence. Secondary endpoints assessed were the initial, cavitated and obvious dentinal caries increment as well as the measurement of dental plaque accumulation, as an indicator of the ECC risk. Data were collected through the clinical assessment of the children's caries (dmft and ICDAS II) and oral hygiene status (DI-S of OHI-S index). Caries incidence and prevalence were statistically significantly lower in the probiotic group versus the control group (p < 0.001 and p = 0.0075). The initial and final mean OHI-S scores in the probiotic group did not show any significant differences. In conclusion, the regular short-term intake of probiotics may reduce caries development. Our findings suggest that self-administered probiotic therapy may provide a good complement to increase the effectiveness of individual preventive home care in preschool children. This is the first clinical study evaluating the effect of a short-term probiotic intervention on reducing early childhood caries with 12 months of follow-up.

The Current Strategies in Controlling Oral Diseases by Herbal and Chemical Materials

Dental plaque is a biofilm composed of complex microbial communities. It is the main cause of major dental diseases such as caries and periodontal diseases. In a healthy state, there is a delicate balance between the dental biofilm and host tissues. Nevertheless, due to the oral cavity changes, this biofilm can become pathogenic. The pathogenic biofilm shifts the balance from demineralization-remineralization to demineralization and results in dental caries. Dentists should consider caries as a result of biological processes of dental plaque and seek treatments for the etiologic factors, not merely look for the treatment of the outcome caused by biofilm, i.e., dental caries. Caries prevention strategies can be classified into three groups based on the role and responsibility of the individuals doing them: (1) community-based strategy, (2) dental professionals-based strategy, and (3) individual-based strategy. The community-based methods include fluoridation of water, salt, and milk. The dental professionals-based methods include professional tooth cleaning and use of varnish, fluoride gel and foam, fissure sealant, and antimicrobial agents. The individual-based (self-care) methods include the use of fluoride toothpaste, fluoride supplements, fluoride mouthwashes, fluoride gels, chlorhexidine gels and mouthwashes, slow-release fluoride devices, oral hygiene, diet control, and noncariogenic sweeteners such as xylitol. This study aimed to study the research in the recent five years (2015–2020) to identify the characteristics of dental biofilm and its role in dental caries and explore the employed approaches to prevent the related infections.

Recent Innovations in Bacterial Infection Detection and Treatment

Bacterial infections are a major threat to human health, exacerbated by increasing antibiotic resistance. These infections can result in tremendous morbidity and mortality, emphasizing the need to identify and treat pathogenic bacteria quickly and effectively. Recent developments in detection methods have focused on electrochemical, optical, and mass-based biosensors. Advances in these systems include implementing multifunctional materials, microfluidic sampling, and portable data-processing to improve sensitivity, specificity, and ease of operation. Concurrently, advances in antibacterial treatment have largely focused on targeted and responsive delivery for both antibiotics and antibiotic alternatives. Antibiotic alternatives described here include repurposed drugs, antimicrobial peptides and polymers, nucleic acids, small molecules, living systems, and bacteriophages. Finally, closed-loop therapies are combining advances in the fields of both detection and treatment. This review provides a comprehensive summary of the current trends in detection and treatment systems for bacterial infections.

Genome-wide identification of Streptococcus sanguinis fitness genes in human serum and discovery of potential selective drug targets

Streptococcus sanguinis is a primary colonizer of teeth and is associated with oral health. When it enters the bloodstream, however, this bacterium may cause the serious illness infective endocarditis. The genes required for survival and proliferation in blood have not been identified. The products of these genes could provide a rich source of targets for endocarditis-specific antibiotics possessing greater efficacy for endocarditis, and also little or no activity against those bacteria that remain in the mouth. We previously created a comprehensive library of S. sanguinis mutants lacking every nonessential gene. We have now screened each member of this library for growth in human serum and discovered 178 mutants with significant abundance changes. The main biological functions disrupted in these mutants, including purine metabolism, were highlighted via network analysis. The components of an ECF-family transporter were required for growth in serum and were shown for the first time in any bacterium to be essential for endocarditis virulence. We also identified two mutants whose growth was reduced in serum but not in saliva. This strategy promises to enable selective targeting of bacteria based on their location in the body, in this instance, treating or preventing endocarditis while leaving the oral microbiome intact.

Metagenomic sequencing provides new insights into the subgingival bacteriome and aetiopathology of periodontitis

"Open-ended" molecular techniques such as 16S rRNA sequencing have revealed that the oral bacteriome of subgingival plaque is more diverse than originally thought. 16S rRNA analysis has demonstrated that constituents of the overall bacterial community are qualitatively similar in health and disease, differing mainly in their relative proportions with respect to each other. Species in low abundance can also act as critical species, leading to the concept of global community dysbiosis which relates to shifts in community structure, rather than shifts in membership. Correlation analysis suggests that coordinated interactions in the community are essential for incipient dysbiosis and disease pathogenesis. The subgingival bacteriome also provides biomarkers that are useful for disease detection and management. Combined with clinical and biological parameters, these may assist clinicians in developing and implementing effective treatment strategies to restore microbial homeostasis and monitor disease. Identification of higher risk groups or poor responders to treatment using unique subgingival bacteriome signatures may also lead to early intervention.

Non-Surgical Periodontal Therapy with Adjunctive Amoxicillin/Metronidazole or Metronidazole When No Aggregatibacter actinomycetemcomitans Is Detected—A Randomized Clinical Trial

Background: The aim was to compare two different systemic antibiotics regimens adjunctive to non-surgical periodontal therapy when Aggregatibacter actinomycetemcomitans was not detected in the subgingival biofilm. Methods: A total of 58 patients with periodontitis and with no A. actinomycetemcomitans in the subgingival biofilm were treated with full-mouth subgingival instrumentation and either metronidazole (MET; n = 29) or amoxicillin/metronidazole (AMX/MET; n = 29). Probing depth (PD), clinical attachment level (CAL) and bleeding on probing (BOP) were recorded at baseline, as well as after three and six months. Subgingival biofilm and gingival crevicular fluid were collected and analyzed for major periodontopathogens and biomarkers. Results: PD, CAL and BOP improved at 3 and 6 months (each p < 0.001 vs. baseline) with no difference between the groups. Sites with initial PD ≥ 6 mm also improved in both groups after 3 and 6 months (p < 0.001) with a higher reduction of PD in the AMX/MET group (p < 0.05). T. forsythia was lower in the AMX/MET group after 3 months (p < 0.05). MMP-8 and IL-1β were without significant changes and differences between the groups. Conclusion: When A. actinomycetemcomitans was not detected in the subgingival biofilm, the adjunctive systemic use of amoxicillin/metronidazole results in better clinical and microbiological outcomes of non-surgical periodontal therapy when the application of systemic antibiotics is scheduled.

Targeted and Intracellular Antibacterial Activity against S. agalactiae of the Chimeric Peptides Based on Pheromone and Cell-Penetrating Peptides

The significance of the complex bacterial ecosystem in the human body and the impediment of the mammalian membrane against many antibiotics together emphasize the necessity to develop antimicrobial agents with precise antimicrobial and cell-penetrating activities. A simple and feasible method for generating dual-function antimicrobial peptides inspired by highly hydrophobic peptide pheromone and cationic cell-penetrating peptides is presented. Furthermore, the extension of the peptide candidate library is achieved by modifying the charged domain. The bacteria-selective peptides L1, L2, L10, and L11 kill Streptococcus agalactiae by disrupting the membrane structure, and the targeted mechanism is suggested where the peptides offset the entrapment of S. agalactiae rather than of other bacteria. Moreover, L2 and L10 possess intracellular antibacterial activity and carrier property, which is mainly dependent on endocytosis. Given their suitable biocompatibility, high tolerance, no drug resistance, and effective antimicrobial capacity in a mouse mastitis model, L2 and L10 can be powerful weapons against S. agalactiae pathogen infection.

Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus

Human microbiome studies are increasingly incorporating macroecological approaches, such as community assembly, network analysis and functional redundancy to more fully characterize the microbiome. Such analyses have not been applied to ancient human microbiomes, preventing insights into human microbiome evolution. We address this issue by analysing published ancient microbiome datasets: coprolites from Rio Zape (n = 7; 700 CE Mexico) and historic dental calculus (n = 44; 1770–1855 CE, UK), as well as two novel dental calculus datasets: Maya (n = 7; 170 BCE-885 CE, Belize) and Nuragic Sardinians (n = 11; 1400–850 BCE, Italy). Periodontitis-associated bacteria (Treponema denticola, Fusobacterium nucleatum and Eubacterium saphenum) were identified as keystone taxa in the dental calculus datasets. Coprolite keystone taxa included known short-chain fatty acid producers (Eubacterium biforme, Phascolarctobacterium succinatutens) and potentially disease-associated bacteria (Escherichia, Brachyspira). Overlap in ecological profiles between ancient and modern microbiomes was indicated by similarity in functional response diversity profiles between contemporary hunter–gatherers and ancient coprolites, as well as parallels between ancient Maya, historic UK, and modern Spanish dental calculus; however, the ancient Nuragic dental calculus shows a distinct ecological structure. We detected key ecological signatures from ancient microbiome data, paving the way to expand understanding of human microbiome evolution.

This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.

Salivary parameters and oral health status amongst adolescents in Mexico

Background

In the last years an increased interest in the use of salivary parameters in connection with caries experience and caries prediction has been shown. In schoolchildren investigations are known, where the relationship between caries prevalence and salivary parameters has been assessed, but in the adolescent population studies are scarce. The aim of the study was evaluate of the association among salivary parameters, oral health status and caries experience in adolescents in Mexico.

Methods

A cross-sectional study was conducted on 256 (DMFT≥5) and 165 (DMFT< 5) 12-to- 14-year-old adolescents. From all the adolescents, unstimulated mid-morning saliva samples were collected, after which the salivary flow rate was calculated, and the salivary pH and buffer capacity was measured. The caries was evaluated via the application of the DMFT score. Clinical variables such as oral hygiene and dental calculus were examined in the adolescent’s oral cavity. The adolescents provided data on their personal characteristics by completing a questionnaire, while socioeconomic data were collected from their parents. Descriptive, bivariate and logistic regression model analyses were performed.

Results

The prevalence of caries was 61.1% (DMFT≥5) in permanent dentition, with 72.7% of subjects presenting poor oral hygiene. The mean levels of salivary flow rate, pH, and buffer capacity was significantly lower (p < 0.05) in adolescents with caries score of DMFT≥5 than in those with caries score of DMFT < 5. Salivary flow and buffer capacity were higher in boys than in girls. The logistic regression model applied showed that adolescents with a salivary flow rate < 1 ml per min were more likely to present caries [OR = 1.58 (CI95% 1.04–2.40); p = 0.033] than adolescents with a flow rate ≥ 1 ml per-min, and that, for each unit of increased pH, the probability of presenting caries reduced by 76% [OR = 0.24 (CI95% 0.10–0.55); p = 0.001].

Conclusion

Significant association was found in salivary flow rate, pH and buffer capacity in adolescents with caries (DMFT≥5). In addition to differences of these parameters by sex, the results suggest saliva parameters may act as indicators of caries in adolescents.

Candidal carriage in saliva and subgingival plaque among smokers and non-smokers with chronic periodontitis-a cross-sectional study

Background and Objectives

Studies of gum or periodontal disease have focused mainly on bacterial pathogens. However, information related to fungal species in the saliva and subgingival mileu is particularly lacking in smokers with periodontitis. This cross-sectional study compared the prevalence of various Candida species in saliva and subgingival plaque samples of smokers and non-smokers with periodontal disease.

Methodology

Study subjects were recruited into three group-Group 1: Smokers with chronic periodontitis (N = 30), Group 2: Non-smokers with chronic periodontitis (N = 30) and Group 3: Healthy controls (N = 30). Clinical parameters recorded included plaque index (PI), gingival index (GI), periodontal probing depth (PPD) and clinical attachment loss (CAL). Saliva and subgingival plaque samples were collected from subjects from the above groups. The collected samples were processed for isolation and identification of various Candida species using CHROMagar chromogenic media. Additionally, antifungal susceptibility tests were performed for the isolated Candida species in order to assess antifungal drug resistance to fluconazole and voriconazole.

Results

Prevalence of Candida species in saliva samples was quantified as 76.6% in Group 1, 73.3% in Group 2 and 36.6% in Group 3 and statistically significant differences were observed between groups 1 & 3. Prevalence of Candida species in subgingival plaque samples was quantified as 73.3% in Group 1, 66.6% in Group 2 and 60% in Group 3 and no statistically significant differences were observed between groups. Candida albicans was the most frequently isolated species followed by Candida krusei and Candida tropicalis. A positive correlation was observed for smoking exposure, pack years and Candida colonization. A marginally significant positive correlation was observed between Candida colonization and increasing pocket depth and attachment loss. Antifungal drug resistance was mainly observed for Candida krusei in both saliva and subgingival plaque samples.

Conclusion

Based on the results we can conclude that oral candidal carriage is significantly increased in smokers with periodontal disease. Mechanistic studies are needed to understand the importance of Candida species in periodontal disease.

ePath: an online database towards comprehensive essential gene annotation for prokaryotes

Experimental techniques for identification of essential genes (EGs) in prokaryotes are usually expensive, time-consuming and sometimes unrealistic. Emerging in silico methods provide alternative methods for EG prediction, but often possess limitations including heavy computational requirements and lack of biological explanation. Here we propose a new computational algorithm for EG prediction in prokaryotes with an online database (ePath) for quick access to the EG prediction results of over 4,000 prokaryotes ( https://www.pubapps.vcu.edu/epath/ ). In ePath, gene essentiality is linked to biological functions annotated by KEGG Ortholog (KO). Two new scoring systems, namely, E_score and P_score, are proposed for each KO as the EG evaluation criteria. E_score represents appearance and essentiality of a given KO in existing experimental results of gene essentiality, while P_score denotes gene essentiality based on the principle that a gene is essential if it plays a role in genetic information processing, cell envelope maintenance or energy production. The new EG prediction algorithm shows prediction accuracy ranging from 75% to 91% based on validation from five new experimental studies on EG identification. Our overall goal with ePath is to provide a comprehensive and reliable reference for gene essentiality annotation, facilitating the study of those prokaryotes without experimentally derived gene essentiality information.

Prevention of dental caries as a non-communicable disease

Today, dental caries is regarded as a preventable non-communicable disease (NCD) that affects a majority of the population across their lifespan. As such, it shares a number of behavioural, socio-economic, and lifestyle factors with other NCDs, such as overweight and diabetes, and should be subjected to a similar model of chronic disease management. Caries prevention has traditionally relied on fluoride exposure, diet control, thorough oral hygiene, and antibacterial measures. Prevention of caries as an NCD does certainly not disqualify these methods, but brings them into a new context. This conference paper provides a brief review on how common preventive measures can interfere with the drivers of dysbiosis and promote the growth of health-associated clusters in the oral microbiome. Besides the established routines of regular toothbrushing with fluoride products, there is an opportunity for additional technologies, based on ecological principles, to address and modify the oral biofilm. Methods to reduce dietary sugar intake, slow down plaque metabolism, and support saliva functions should be further developed and investigated in terms of efficacy, compliance, and cost-effectiveness. Furthermore, biofilm engineering through pre- and probiotics early in life to support microbial diversity seem promising in order to obtain a sustained caries-preventive effect.

A built-in adjuvant-engineered mucosal vaccine against dysbiotic periodontal diseases

Periodontitis is associated with a dysbiotic shift in the oral microbiome. Vaccine approaches to prevent microbial shifts from healthy to diseased state in oral biofilms would provide a fundamental therapeutic strategy against periodontitis. Since dental plaque formation is a polymicrobial and multilayered process, vaccines targeting single bacterial species would have limited efficacy in clinical applications. In this study, we developed a divalent mucosal vaccine consisting of a mixture of FlaB-tFomA and Hgp44-FlaB fusion proteins targeting virulence factors of inflammophilic bacteria Fusobacterium nucleatum and Porphyromonas gingivalis, respectively. Introduction of peptide linkers between FlaB and antigen improved the stability and immunogenicity of engineered vaccine antigens. The intranasal immunization of divalent vaccine induced protective immune responses inhibiting alveolar bone loss elicited by F. nucleatum and P. gingivalis infection. The built-in flagellin adjuvant fused to protective antigens enhanced antigen-specific antibody responses and class switch recombination. The divalent vaccine antisera recognized natural forms of surface antigens and reacted with diverse clinical isolates of Fusobacterium subspecies and P. gingivalis. The antisera inhibited F. nucleatum-mediated biofilm formation, co-aggregation of P. gingivalis and Treponema denticola, and P. gingivalis-host cell interactions. Taken together, the built-in adjuvant-engineered mucosal vaccine provides a technological platform for multivalent periodontitis vaccines targeting dysbiotic microbiome.

Narrow-Spectrum Antibacterial Agents

While broad spectrum antibiotics play an invaluable role in the treatment of bacterial infections, there are some drawbacks to their use, namely selection for and spread of resistance across multiple bacterial species, and the detrimental effect they can have upon the host microbiome. If the causitive agent of the infection is known, the use of narrow-spectrum antibacterial agents has the potential to mitigate some of these issues. This review outlines the advantages and challenges of narrow-spectrum antibacterial agents, discusses the progress that has been made toward developing diagnostics to enable their use, and describes some of the narrow-spectrum antibacterial agents currently being investigated against some of the most clinically important bacteria including Clostridium difficile, Mycobacterium tuberculosis and several ESKAPE pathogens.

Targeted antimicrobial therapy in the microbiome era

Even though the oral microbiome is one of the most complex sites on the body it is an excellent model for narrow‐spectrum antimicrobial therapy. Current research indicates that disruption of the microbiome leads to a dysbiotic environment allowing for the overgrowth of pathogenic species and the onset of oral diseases. The gram‐negative colonizer, Porphyromonas gingivalis has long been considered a key player in the initiation of periodontitis and Streptococcus mutans has been linked to dental caries. With antibiotic research still on the decline, new strategies are greatly needed to combat infectious diseases. By targeting key pathogens, it may be possible to treat oral infections while allowing for the recolonization of the beneficial, healthy flora. In this review, we examine unique strategies to specifically target periodontal pathogens and address what is needed for the success of these approaches in the microbiome era.