Rapid detection of the cariogenic pathogens Streptococcus mutans and Streptococcus sobrinus using loop-mediated isothermal amplification

Spontaneous droplet generation via surface wetting

A surface wetting-driven droplet generation microfluidic chip was developed, and could produce droplets spontaneously once adding a drop of oil and an aqueous sample on the chip without any power source and equipment. The chip is simply composed of three drilled holes connected by a single microchannel. The aqueous sample dropped in the middle hole could be converged and segmented into monodispersed droplets spontaneously by preloading oil in the side hole, and then flow into the other side hole through the microchannel. To address the high throughput and stability in practical applications, a siphon pump was further integrated into the microfluidic chip by simply connecting oil-filled tubing also acting as a collector. In this way, droplets can be generated spontaneously with a high uniformity (CV < 3.5%) and adjustable size (30-80 μm). Higher throughput (280 Hz) and multi-sample emulsification are achieved by parallel integration of a multi-channel structure. Based on that, the microfluidic chip was used as the droplet generator for the ddPCR to absolutely quantify S. mutans DNA. This is the first time that the feasibility of droplet generation driven only by oil wettability on hydrophobic surfaces is demonstrated. It offers great opportunity for self-sufficient and portable W/O droplet generation in biomedical samples, thus holding the potential for point-of-care testing (POCT).

Antibacterial quaternary ammonium compounds in dental materials: A systematic review

OBJECTIVE

Quaternary ammonium compounds (QACs) represent one of the most effective classes of disinfectant agents in dental materials and resin nanocomposites. This reviews aims to give a wide overview on the research in the field of antibacterial QACs in dental materials and nanocomposites.

METHOD

An introduction to dental materials components as well as the microorganisms and methods of evaluation for the antimicrobial assays are presented. Then, the properties and synthesis route of QACs, as monomer and filler, are shown. Finally, antimicrobial monomers and fillers, specifically those contain quaternary ammonium salts (QASs), in dental materials are reviewed.

RESULTS

QACs have been used as monomer and micro/nanofiller in restorative dentistry. They possess one or more methacrylate functional groups to participate in polymerization reactions. QACs with multiple methacrylate groups can also be used as crosslinking agents. Furthermore, QACs with chain length from ∼12 to 16 have higher antimicrobial activity in cured dental resins. In general, increasing the chain length leads to a threshold value (critical point) and then it causes decrease in the antimicrobial activity.

SIGNIFICANCE

The current state of the art of dental materials and resin nanocomposites includes a wide variety of antimicrobial materials. Among them, QACs presents low cytotoxicity and excellent long-term antimicrobial activity without leaching out over time.

Five-year longitudinal study of dental caries risk associated with Streptococcus mutans and Streptococcus sobrinus in individuals with intellectual disabilities

Streptococcus mutans (S. mutans) and Streptococcus sobrinus (S. sobrinus) are important etiologic agents in human dental caries. Using quantitative real-time polymerase chain reaction assays for the presence of those strains, we examined 145 outpatients with intellectual disability (ID), calculated the proportion of each of these strains to total bacteria, and compared dental caries incidence over 5 years. Plaque samples were collected from all erupted tooth sites, and dental examinations were performed annually to determine numbers of decayed, missing, and filled teeth (DMFT score; World Health Organization caries diagnostic criteria). Elevated DMFT scores were calculated as ∆DMFT, and sites of newly affected caries (∆SNAC) were identified. Sixty-six patients had both strains. The proportion of S. mutans to total bacteria was moderately correlated with DMFT in year 2, ∆DMFT in years 2 and 5, and ∆SNAC in years 2 and 5 (correlation coefficient = 0.470, P < 0.001), while the proportion of S. sobrinus to total bacteria was moderately correlated with DMFT in years 2 and 5, ∆DMFT in years 1, 2, and 5, and ∆SNAC in years 2 and 5 (correlation coefficient = 0.695, P < 0.001). Individuals with ID who harbored both bacterial strains had a higher risk of dental caries and a significantly higher proportion of S. sobrinus to total bacteria.

Monitoring the prevalence of viable and dead cariogenic bacteria in oral specimens and in vitro biofilms by qPCR combined with propidium monoazide

Background

Streptococcus mutans and Streptococcus sobrinus are associated with the development of dental caries in humans. However, previous diagnostic systems are unsuitable for monitoring viable cell numbers in oral specimens. Assessing the relationship between the numbers of viable and dead bacterial cells and oral status is important for understanding oral infectious diseases. Propidium monoazide (PMA) has been reported to penetrate dead cells following membrane damage and to cross-link DNA, thereby inhibiting DNA amplification. In the present study, we established an assay for selective analysis of two viable human cariogenic pathogens, S. mutans and S. sobrinus, using PMA combined with real-time PCR (PMA-qPCR).

Results

We designed species-specific primer sets for S. mutans and S. sobrinus, generated standard curves for measuring cell numbers, and evaluated the dynamic range of the assay. To determine the effectiveness of the assay, PMA was added to viable and autoclave-killed cell mixtures. PMA treatment effectively prevented DNA amplification from dead cells. No amplification of DNA from dead cells was observed in these organisms. In addition, we applied this assay to analyze viable cell numbers in oral specimens. A significant correlation was found between the number of viable S. mutans cells in saliva and that in plaque among caries-free patients, whereas no correlation was observed between saliva and carious dentin. The total and viable cell numbers in caries-positive saliva were significantly higher than those in caries-free saliva. Finally, we analyzed the usefulness of this assay for in vitro oral biofilm analysis. We applied PMA-qPCR for monitoring viable S. mutans cell numbers in vitro in planktonic cells and oral biofilm treated with hydrogen peroxide (H₂O₂). In planktonic cells, the number of viable cells decreased significantly with increasing H₂O₂ concentration, whereas only a small decrease was observed in biofilm cell numbers.

Conclusions

PMA-qPCR is potentially useful for quantifying viable cariogenic pathogens in oral specimens and is applicable to oral biofilm experiments. This assay will help to elucidate the relationship between the number of viable cells in oral specimens and the oral status.

Development and evaluation of a loop-mediated isothermal amplification method for rapid detection and differentiation of two genotypes of porcine circovirus type 2

BACKGROUND

Porcine circovirus type 2 (PCV2) is one of the major swine viral diseases and has caused significant economic loss to pig producers. PCV2 has been divided into two major genotypes: PCV2a, PCV2b. A loop-mediated isothermal amplification (LAMP) method was developed for the detection and differentiation of PCV2a and PCV2b in clinical samples.

METHODS

LAMP-specific primer sets were designed based on six PCV2a and six PCV2b reference isolates. To determine the analytical specificity of LAMP, DNA samples extracted from 36 porcine virus isolates were tested by LAMP, including eight PCV2a, 11 PCV2b, four PCV type 1, two porcine parvovirus, three pseudorabies virus, and eight porcine reproductive and respiratory virus. To evaluate the analytical sensitivity of the assay, 10-fold serial dilutions of PCV2a and PCV2b recombinant plasmids were performed to prepare the dilutions at concentration from 10(6) to 1 copy(ies)/μL, and each dilution was tested by both LAMP and nested polymerase chain reaction (nested PCR). A total of 168 clinical samples were analyzed by both LAMP and nested PCR, and the relative sensitivity and specificity of LAMP compared to nested PCR were calculated.

RESULTS

Using different primer sets of LAMP, LAMP could be completed within 50 minutes. This method was found to be highly analytically specific for PCV2a and PCV2b; only the target gene was detected without cross-reaction. The analytical sensitivity of LAMP for PCV2a and PCV2b were 10 copies/μL, demonstrating analytical sensitivity comparable to that obtained using nested PCR. In addition, the sensitivity and specificity of LAMP relative to those of nested PCR were 97.7% and 100.0%, respectively. The percentage of observed agreement was 98.2%, and the κ statistic was 0.949.

CONCLUSION

LAMP is a rapid, specific, and sensitive diagnostic method for the detection and differentiation of PCV2a and PCV2b in clinical samples.

Visual detection of Potato Leafroll virus by loop-mediated isothermal amplification of DNA with the GeneFinder™ dye

The most common virus affecting potatoes in the field worldwide is Potato Leafroll virus (PLRV), belonging to the family Luteoviridae, genius Plerovirus. There are several molecular methods to detect PLRV including polymerase chain reaction (PCR), Multiplex AmpliDet RNA and double antibody sandwich ELISA (DAS-ELISA). But these techniques take a long time for 3h to two days, requiring sophisticated tools. The aim of this study was to reduce the time required to detect PLRV, using a newly designed loop-mediated isothermal amplification (LAMP) technique requiring only an ordinary water bath or thermoblock. PLRV RNA was extracted from overall 80 infected naturally potato leaves. A set of six novel primers for the LAMP reaction was designed according to the highly conserved sequence of the viral coat protein (CP) gene. LAMP was carried out under isothermal conditions, applying the Bst DNA polymerase enzyme; the LAMP products were detected visually using the GeneFinder™ florescence dye. A positive result using the GeneFinder™ dye was a color change from the original orange to green. Results confirmed LAMP with GeneFinder™ provides a rapid and safe assay for detection of PLRV. Since with other molecular methods, equipping laboratories with a thermocycler or expensive detector systems is unavoidable, this assay was found to be a simple, cost-effective molecular method that has the potential to replace other diagnostic methods in primary laboratories without the need for expensive equipment or specialized techniques. It can also be considered as a reliable alternative viral detection system in further investigations.

Real-time quantitative polymerase chain reaction for enumeration of Streptococcus mutans from oral samples

This study compared SYBR Green real-time quantitative PCR (qPCR) with standard plate counting for the enumeration of Streptococcus mutans in oral samples. Oral samples (n = 710) were collected from high-caries-risk children for quantification of S. mutans by qPCR using primer pairs. The S. mutans copy number was calculated with reference to a qPCR quantification cycle (Cq) standard curve and compared with the absorbance value at 600 nm of a standard suspension of S. mutans UA159. The S. mutans copy number results were evaluated in relation to standard plate count (SPC) results obtained from each sample following culture on Petri plates containing S. mutans selective media and reported as colony-forming units (CFUs). The mean S. mutans copy number calculated from qPCR was higher than the SPC CFUs (1.3 × 10(6) and 1.5 × 10(5) CFUs, respectively). The qPCR values were usually higher in individual samples and qPCR detected the presence of S. mutans 84% (231/276) of the time that the SPC did not, compared with 33% (4/12) of the time when qPCR failed to detect S. mutans and the SPC did. The qPCR technique was found to be more sensitive for detection of S. mutans from oral samples, a method that is not dependent on the viability of the sample taken and therefore is proposed as a more reliable and efficient means of quantification of S. mutans.

Detection of porcine circovirus type 1 in commercial porcine vaccines by loop-mediated isothermal amplification

A loop-mediated isothermal amplification (LAMP) method with a real-time monitoring system was developed for the detection of porcine circovirus type 1 (PCV1) in commercial swine vaccines. This method was highly specific for PCV1. No cross-reaction to porcine circovirus type 2, porcine parvovirus, pseudorabies virus, classical swine fever virus, and porcine reproductive and respiratory syndrome virus was observed. The analytical sensitivity of the LAMP for PCV1 DNA was 10 copies/μl in the case of positive recombinant plasmid comparable to that obtained from the nested polymerase chain reaction (nested PCR). Furthermore, 25 commercial swine vaccines were tested by both the LAMP and the nested PCR, and three of them were tested positive for PCV1 DNA. These results indicate that PCV1 DNA can be real-time detected by the LAMP; the method was highly specific, sensitive, and rapid for the detection of PCV1 DNA, particularly in commercial swine vaccines.

Development of loop-mediated isothermal amplification method for rapid detection of Streptococcus iniae, the causative agent of streptococcicosis in fish

Streptococcus iniae is a major pathogen that causes sever economic losses in tilapia aquaculture. A set of four specific primers was designed by targeting lctO gene. With Bst DNA polymerase, the target DNA can be clearly amplified for 60 min at 64 °C in a simple water bath. The sensitivity of the LAMP assay for the detection of S. iniae is about 12.4 cells per reaction in both of pure cultures and added fish tissues cultures. LAMP products could be judged with agar gel or naked eye after addition of SYBR Green I. There were no cross-reactions with other bacterial strains indicating high specificity of the LAMP. The LAMP method was also applied to detect S. iniae-infected tilapia tissues effectively. The LAMP assay reported here indicates the potential usefulness of the technique as a valuable simple, rapid alternative procedure for the detection of S. iniae during streptococcicosis monitoring of cultured fish.

A simple identification method of saliva by detecting Streptococcus salivarius using loop-mediated isothermal amplification

We previously reported that detection of Streptococcus salivarius is feasible for proving the presence of saliva in a forensic sample. Here, a simple and rapid method for the detection of S. salivarius in forensic samples was developed that uses loop-mediated isothermal amplification (LAMP). The LAMP primer set was designed using S. salivarius-specific sequences of glucosyltransferase K. To simplify the procedure, the sample was prepared by boiling and mutanolysin treatment only, and the entire analytical process was completed within 2.5 h. The cut-off value was set at 0.1 absorbance units, measured at 660 nm, upon termination of the reaction. S. salivarius was identified in all saliva samples, but was not detected in other body fluids or on the skin surface. Using this method, S. salivarius was successfully detected in various mock forensic samples. We therefore suggest that this approach is useful for the identification of saliva in forensic practice.