Loop-mediated isothermal amplification method for rapid detection of the periodontopathic bacteria Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola

A method for Porphyromonas gingivalis based on recombinase polymerase amplification and lateral flow strip technology

OBJECTIVE

A practical visual detection method was established to detect Porphyromonas gingivalis (P. gingivalis) by employing a combination of recombinase polymerase amplification and lateral flow strips (RPA-LF) assay, designed for conducting point-of-care testing in clinical settings.

METHODS

Primers and probes targeting the P. gingivalis pepO gene were designed. The RPA-LF assay was established by optimising reaction temperature and time, determining the limit of detection (LOD). The specificity of the method was determined by assessing its cross-reactivity with deoxyribonucleic acid from 23 pathogenic bacteria. Finally, the clinical samples from healthy controls (n = 30) and individuals with periodontitis (n = 31) were analysed. The results were compared with those obtained using real-time polymerase chain reaction (PCR).

RESULTS

The optimal reaction temperature and time were 39 °C and 12 min. The method exhibited a LOD at 6.40 × 10-4 μg/mL and demonstrated high specificity and sensitivity during cross-reactivity assessment. The RPA-LF assay achieved a P. gingivalis detection rate of 84 % in individuals with periodontitis and 3 % in healthy controls. The results were consistent with those obtained through real-time PCR.

CONCLUSION

An RPA-LF assay was developed for detecting P. gingivalis, characterised by its high sensitivity, high specificity, simple operational procedure, and rapid reaction time.

Enhancing leptospirosis control with nanosensing technology: A critical analysis

Leptospirosis is a serious health problem in tropical areas; thus, animals shed leptospires in the environment. Humans are accidental hosts infected through exposure to contaminating bacteria in the environment. One health strategy can be applied to protect and eliminate leptospirosis because this cooperates and coordinates activities between doctors, veterinarians, and ecologists. However, conventional methods still have limitations. Therefore, the main challenges of leptospirosis control are the high sensing of detection methods to screen and control the pathogens. Interestingly, nano sensing combined with a leptospirosis detection approach can increase the sensitivity and eliminate some limitations. This article reviews nanomaterial development for an advanced leptospirosis detection method, e.g., latex beads-based agglutination test, magnetic nanoparticles enrichment, and gold-nanoparticles-based immunochromatographic assay. Thus, nanomaterials can be functionalized with biomolecules or sensing molecules utilized in various mechanisms such as biosensors. Over the last decade, many biosensors have been developed for Leptospira spp. pathogen and others. The evolution of biosensors for leptospirosis detection was designed for high efficiency and might be an alternative tool. In addition, the high-sensing fabrications are useful for leptospires screening in very low levels, for example, soil or water from the environment.

A point-of-care platform for hair loss-related single nucleotide polymorphism genotyping

Rapid genotyping of single nucleotide polymorphism (SNP) is crucial for prognostics and disease management, enabling more rapid therapy selection and treatment determination. Here, we introduce a point-of-care platform for hair loss-related SNP genotyping based on allele-specific loop-mediated isothermal amplification (AS-LAMP) combined with naked-eye visualization. The specificity of the AS-LAMP assay was significantly enhanced by using mismatched allele-specific primers. AS-LAMP reaction and Schiff's reagent-based colorimetric detection were successfully performed using a thermoplastic genotyping chip. This strategy also showed potential for determining homozygotes and heterozygotes in a target sample. To assess SNP genotyping capacity, the genotyping chip was fabricated to visually detect rs6152 polymorphism of an androgen receptor gene associated with genetically induced hair loss. The genotyping platform rapidly identified the SNP within 40 min, and the detection limit was as low as 1 pg/μL of the target DNA contained in human serum. The introduced strategy showed high specificity and stability in discriminating low-abundance mutations, making it suitable as a portable and affordable point-of-care platform for rapid and accurate SNP discrimination applicable for bedside detection.

The application of the loop-mediated isothermal amplification method for rapid detection of methicillin-resistant Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) is an important problem associated with significant mortality and morbidity and well known as a predominant bacterial pathogen. The aim of this study was to identify MRSA strains. In this study (June 2018 to June 2019) isolates of S. aureus were obtained from patients referred to teaching hospitals of Ahvaz, Iran. All isolates were confirmed by conventional microbiological methods. In following, antimicrobial susceptibility testing (AST), MRSA screening, PCR detection of MRSA and LAMP assay were performed. Out of a total of 156 staphylococcal isolates, 126 isolates were identified as MRSA. Seventy-two (57.1%) MRSA isolates were recovered from wound. All MRSA isolates were sensitive to vancomycin, linezolid, teicoplanin, quinupristin-dalfopristin, and tigecycline. The results of LAMP showed 100% agreement with PCR. Sensitivity and specificity of the LAMP assays for the mecA genes were 100% and 100%, respectively. The LAMP assay is a rapid and simple method for the identifications of MRSA. Because of its performance without the need for specific instrumentation, this method can be easily employed in medical centers for the detection of mecA.

Loop-Mediated Isothermal Amplification (LAMP): The Better Sibling of PCR?

In 1998, when the PCR technique was already popular, a Japanese company called Eiken Chemical Co., Ltd. designed a method known as the loop-mediated isothermal amplification of DNA (LAMP). The method can produce up to 109 copies of the amplified DNA within less than an hour. It is also highly specific due to the use of two to three pairs of primers (internal, external, and loop), which recognise up to eight specific locations on the DNA or RNA targets. Furthermore, the Bst DNA polymerase most used in LAMP shows a high strand displacement activity, which eliminates the DNA denaturation stage. One of the most significant advantages of LAMP is that it can be conducted at a stable temperature, for instance, in a dry block heater or an incubator. The products of LAMP can be detected much faster than in standard techniques, sometimes only requiring analysis with the naked eye. The following overview highlights the usefulness of LAMP and its effectiveness in various fields; it also considers the superiority of LAMP over PCR and presents RT-LAMP as a rapid diagnostic tool for SARS-CoV-2.

Selective and easy detection of the Porphyromonas gingivalis fimA type II and IV genes by loop-mediated isothermal amplification

Porphyromonas gingivalis fimbrillin (fimA) type II and IV, the definitive factors for periodontitis, are also found to be associated with systemic diseases. To detect the fimA type II and IV genes easily and rapidly, we used the loop-mediated isothermal amplification (LAMP) method. The LAMP method showed high specificity as DNA from the P. gingivalis HW24D1 strain could only be amplified by the type II-specific primers and that from the W83 strain could only be amplified by the type IV-specific primers. Pathogens, namely, Streptococcus sobrinus, S. mutans, and Candida species, lack the type II and IV genes, and hence, were not detected by the LAMP reaction. Both bacterial cells and purified DNA could be used in the LAMP reaction. The LAMP reaction was highly sensitive and both type II and type IV genes could be detected in 1000 DNA molecules. In the bacterial suspensions of HW24D1 and W83 strains, type II and type IV genes, respectively, could be detected in 100 bacterial cells. We examined the type II and type IV genes in the dental plaques from 22 P. gingivalis-positive patients using the LAMP method. Only one person was found to be positive for the type II gene (4.5%). For the type IV gene, 3 positive cases (13.6%) were identified. Moreover, type II and type IV genes could be detected simultaneously using a multiplex amplification primer of fimA type II and type IV, under visible light. Thus, we established a selective and easy method to detect P. gingivalis fimA type II and IV genes using LAMP.

The Loop-Mediated Isothermal Amplification Technique in Periodontal Diagnostics: A Systematic Review

The course of periodontal disease is affected by many factors; however, the most significant are the dysbiotic microflora, showing different pathogenicity levels. Rapid colonization in the subgingival environment can radically change the clinical state of the periodontium. This systematic review aims to present an innovative technique of loop-mediated isothermal amplification for rapid panel identification of bacteria in periodontal diseases. The decisive advantage of the loop-mediated isothermal amplification (LAMP) technique in relation to molecular methods based on the identification of nucleic acids (such as polymerase chain reaction (PCR or qPCR) is the ability to determine more pathogens simultaneously, as well as with higher sensitivity. In comparison with classical microbiological seeding techniques, the use of the LAMP method shortens a few days waiting time to a few minutes, reducing the time necessary to identify the species and determine the number of microorganisms. The LAMP technology requires only a small hardware base; hence it is possible to use it in outpatient settings. The developed technique provides the possibility of almost immediate assessment of periodontal status and, above all, risk assessment of complications during the treatment (uncontrolled spread of inflammation), which can certainly be of key importance in clinical work.

Adjunctive Antiseptic Irrigation of Periodontal Pockets: Effects on Microbial and Cytokine Profiles

To evaluate the effect of adjunctive antiseptic irrigation of periodontal pockets on microbial and cytokine profiles. Fifty-nine patients with severe periodontitis were allocated to one of three groups for scaling and root planing facilitated with different adjunctive antiseptics: 1% polyhexamethyleneguanidine phosphate (PHMG-P) (n = 19), 0.2% chlorhexidine (CHX) (n = 21) or distilled water (n = 19). Gingival crevicular fluid and subgingival bacterial samples were collected at baseline, and at 2 weeks, and 1 and 4 months. The levels of interleukin (IL)-1β, IL-8, IL-10, and IL-17A, matrix metalloproteinase (MMP)-8, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Fusobacterium nucleatum,Aggregatibacter actinomycetemcomitans, and Prevotella intermedia were determined. There were no intergroup differences in cytokine concentrations and bacterial counts at any follow-up, however, varying patterns were observed. In the PHMG-P and water groups IL-1β expression peaked at 2 weeks and then gradually declined. In all three groups, the dynamics of MMP-8 concentration were non-linear, increasing by 2 weeks and then declining to below baseline (p > 0.05). P. gingivalis and T. forsythia declined within the first month and increased thereafter, not regaining the baseline level. Adjunctive antiseptic treatment was associated with changes in biomarkers and bacterial counts in the course of the study. The effects of adjunctive antiseptic irrigation were limited in the applied protocol.

The Development of Highly Specific and Sensitive Primers for the Detection of Potentially Allergenic Soybean (Glycine max) Using Loop-Mediated Isothermal Amplification Combined with Lateral Flow Dipstick (LAMP-LFD)

The soybean (Glycine max) has been recognized as a frequent elicitor of food allergy worldwide. A lack of causative immunotherapy of soybean allergy makes soybean avoidance essential. Therefore, sensitive and specific methods for soybean detection are needed to allow for soybean verification in foods. Loop-mediated isothermal amplification (LAMP) represents a rapid and simple DNA-based detection method principally suitable for field-like applications or on-site analytical screening for allergens during the manufacturing of foods. This work describes the systematic development and selection of suitable LAMP primers based on soybean multicopy genes. The chemistry applied allows for a versatile detection of amplified DNA, using either gel electrophoresis, fluorescence recording, or a simple Lateral Flow Dipstick (LFD). LAMP based on the ORF160b gene was highly specific for the soybean and may allow for a detection level equivalent to approximately 10 mg soy per kg food. Various soybean cultivars were detectable at a comparable level of sensitivity. LAMP combined with LFD-like detection facilitates a simple, highly specific and sensitive detection of the soybean without the need for expensive analytical equipment. In contrast to the majority of antibody-based methods for soybean detection, all identified primer sequences and optimized protocols are disclosed and broadly available to the community.

Rapid bacterial detection and antibiotic susceptibility testing in whole blood using one-step, high throughput blood digital PCR

Sepsis due to antimicrobial resistant pathogens is a major health problem worldwide. The inability to rapidly detect and thus treat bacteria with appropriate agents in the early stages of infections leads to excess morbidity, mortality, and healthcare costs. Here we report a rapid diagnostic platform that integrates a novel one-step blood droplet digital PCR assay and a high throughput 3D particle counter system with potential to perform bacterial identification and antibiotic susceptibility profiling directly from whole blood specimens, without requiring culture and sample processing steps. Using CTX-M-9 family ESBLs as a model system, we demonstrated that our technology can simultaneously achieve unprecedented high sensitivity (10 CFU per ml) and rapid sample-to-answer assay time (one hour). In head-to-head studies, by contrast, real time PCR and BioRad ddPCR only exhibited a limit of detection of 1000 CFU per ml and 50-100 CFU per ml, respectively. In a blinded test inoculating clinical isolates into whole blood, we demonstrated 100% sensitivity and specificity in identifying pathogens carrying a particular resistance gene. We further demonstrated that our technology can be broadly applicable for targeted detection of a wide range of antibiotic resistant genes found in both Gram-positive (vanA, nuc, and mecA) and Gram-negative bacteria, including ESBLs (bla_CTX-M-1 and bla_CTX-M-2 families) and CREs (bla_OXA-48 and bla_KPC), as well as bacterial speciation (E. coli and Klebsiella spp.) and pan-bacterial detection, without requiring blood culture or sample processing. Our rapid diagnostic technology holds great potential in directing early, appropriate therapy and improved antibiotic stewardship in combating bloodstream infections and antibiotic resistance.

Utilizing multiplex fluor LAMPs to illuminate multiple gene expressions in situ

In situ gene expression detection is the best way to determine temporal and spatial differences in gene expression. However, in situ hybridization procedures are inherently difficult to execute and typically suffer from degradation of sample tissues, limited sensitivity to genes with low expression, high background, and limitation to single gene detections. We propose to utilize an isothermal gene amplification technique, LAMP (Loop-Mediated Isothermal Amplification), to solve these problems in a novel way. LAMP greatly amplifies the signal of expressed genes and can use multiple sets of primers and different fluorescent-labeled probes to produce multiplex gene detection. LAMP is a rapid, isothermal reaction that reduces the handling and degradation of tissue by cutting down on the washing steps required by other methods. Using this technique, we have successfully amplified 3 target genes, have produced positive fluorescent in situ results simultaneously for two genes. We have also demonstrated that LAMP can be used to exploit standard NBT/BCIP (nitro-blue tetrazolium chloride/5-bromo-4-chloro-3'-indolyphosphate p-toluidine salt) detection of single expression. In situ LAMP is a robust and applicable method that can be exploited for detection of gene expression in plant species, as well as in animals and bacteria.

Modern Approach to Medical Diagnostics - the Use of Separation Techniques in Microorganisms Detection

Background:

Analytical chemistry and biotechnology as an interdisciplinary fields of science have been developed during many years and are experiencing significant growth, to cover a wide range of microorganisms separation techniques and methods, utilized for medical therapeutic and diagnostic purposes. Currently scientific reports contribute by introducing electrophoretical and immunological methods and formation of devices applied in food protection (avoiding epidemiological diseases) and healthcare (safety ensuring in hospitals).

Methods:

Electrophoretic as well as nucleic-acid-based or specific immunological methods have contributed tremendously to the advance of analyses in recent three decades, particularly in relation to bacteria, viruses and fungi identifications, especially in medical in vitro diagnostics, as well as in environmental or food protection.

Results:

The paper presents the pathogen detection competitiveness of these methods against conventional ones, which are still too time consuming and also labor intensive. The review is presented in several parts following the current trends in improved pathogens separation and detection methods and their subsequent use in medical diagnosis.

Discussion:

Part one, consists of elemental knowledge about microorganisms as an introduction to their characterization: descriptions of divisions, sizes, membranes (cells) components. Second section includes the development, new technological and practical solution descriptions used in electrophoretical procedures during microbes analyses, with special attention paid to bio-samples analyses like blood, urine, lymph or wastewater. Third part covers biomolecular areas that have created a basis needed to identify the progress, limitations and challenges of nucleic-acid-based and immunological techniques discussed to emphasize the advantages of new separative techniques in selective fractionating of microorganisms.

Methods for the detection of Cryptosporidium and Giardia: From microscopy to nucleic acid based tools in clinical and environmental regimes

The detection and characterization of genotypes and sub genotypes of Cryptosporidium and Giardia is essential for their enumeration, surveillance, prevention, and control. Different diagnostic methods are available for the analysis of Cryptosporidium and Giardia including conventional phenotypic tools that face major limitations in the specific diagnosis of these protozoan parasites. The substantial advancement in the development of genetic signature based molecular tools for the quantification, diagnosis and genetic variation analysis has increased the understanding of the epidemiology and preventive measures of related infections. The conventional methods such as microscopy, antibody and enzyme based approaches, offer better detection results when combined with advanced molecular methods. Gene based approaches increase the precision of identification, for example, many signatures detected in environmental matrices represent species/genotype that are not infectious to humans. This review summarizes the available methods and the advantages and limitations of advance detection techniques like nucleic acid-based approaches for the detection of viable oocysts and cysts of Cryptosporidium and Giardia along with the conventional and widely accepted detection techniques like microscopy, antibody and enzyme based ones. This technical article also encourages the wide application of molecular methods in genetic characterization of distinct species of Cryptosporidium and Giardia, to adopt necessary preventive measures with reliable identification and mapping the source of contamination.

Gene target selection for loop-mediated isothermal amplification for rapid discrimination of Treponema pallidum subspecies

We show proof of concept for gene targets (polA, tprL, and TP_0619) that can be used in loop-mediated isothermal amplification (LAMP) assays to rapidly differentiate infection with any of the three Treponema pallidum subspecies (pallidum (TPA), pertenue (TPE), and endemicum (TEN)) and which are known to infect humans and nonhuman primates (NHPs). Four TPA, six human, and two NHP TPE strains, as well as two human TEN strains were used to establish and validate the LAMP assays. All three LAMP assays were highly specific for the target DNA. Amplification was rapid (5-15 min) and within a range of 10E+6 to 10E+2 of target DNA molecules. Performance in NHP clinical samples was similar to the one seen in human TPE strains. The newly designed LAMP assays provide proof of concept for a diagnostic tool that enhances yaws clinical diagnosis. It is highly specific for the target DNA and does not require expensive laboratory equipment. Test results can potentially be interpreted with the naked eye, which makes it suitable for the use in remote clinical settings.

Detection of contaminants in water supply: A review on state-of-the-art monitoring technologies and their applications

Water monitoring technologies are widely used for contaminants detection in wide variety of water ecology applications such as water treatment plant and water distribution system. A tremendous amount of research has been conducted over the past decades to develop robust and efficient techniques of contaminants detection with minimum operating cost and energy. Recent developments in spectroscopic techniques and biosensor approach have improved the detection sensitivities, quantitatively and qualitatively. The availability of in-situ measurements and multiple detection analyses has expanded the water monitoring applications in various advanced techniques including successful establishment in hand-held sensing devices which improves portability in real-time basis for the detection of contaminant, such as microorganisms, pesticides, heavy metal ions, inorganic and organic components. This paper intends to review the developments in water quality monitoring technologies for the detection of biological and chemical contaminants in accordance with instrumental limitations. Particularly, this review focuses on the most recently developed techniques for water contaminant detection applications. Several recommendations and prospective views on the developments in water quality assessments will also be included.

A Guide to Using STITCHER for Overlapping Assembly PCR Applications

Overlapping PCR is commonly used in many molecular applications that include stitching PCR fragments together, generating fluorescent transcriptional and translational fusions, inserting mutations, making deletions, and PCR cloning. Overlapping PCR is also used for genotyping and in detection experiments using techniques such as loop-mediated isothermal amplification (LAMP). STITCHER is a web tool providing a central resource for researchers conducting all types of overlapping assembly PCR experiments with an intuitive interface for automated primer design that's fast, easy to use, and freely available online.

Genotypic detection of the blaCTX-M-1 gene among extended-spectrum β-lactamase-producing Enterobacteriaceae

OBJECTIVES

Extended-spectrum β-lactamases (ESBLs), a group of β-lactamase enzymes produced by bacteria in the family Enterobacteriaceae, are becoming a major problem in the healthcare community worldwide. Although many attempts have been made in the detection of ESBL-producing bacteria, the cost and speed of detection remains an important challenge. Therefore, this study aimed to develop a rapid, effective and affordable method for detection of the bla_CTX-M-1 ESBL gene by a loop-mediated isothermal amplification (LAMP) technique.

METHODS

Clinical ESBL-producing Enterobacteriaceae, including Escherichia coli and Klebsiella pneumoniae, were isolated and were used as representative strains. The double-disk synergy method was performed to detect ESBL-producing Enterobacteriaceae. Performance of the LAMP method in the detection of bla_CTX-M-1 was compared with conventional PCR in terms of sensitivity and specificity.

RESULTS

The developed LAMP method efficiently identified the presence of the bla_CTX-M-1 gene in ESBL-producing Enterobacteriaceae. It provided similar results to conventional PCR, but the LAMP technique required only 20min of testing time. The accuracy of the LAMP method was confirmed by restriction digestion, which showed the predicted size of the bla_CTX-M-1 gene. In addition, the developed method was comparable with PCR that amplified only the target bla_CTX-M-1 gene in terms of specificity, but LAMP was ca. 1000-fold more sensitive than PCR.

CONCLUSIONS

A rapid assay to detect ESBL-producing Enterobacteriaceae by a LAMP technique was developed in this study. The developed method is sensitive and suitable for rapid screening of bla_CTX-M-1 in routine laboratories with limited resources.

Flower-like ZnO nanostructure assisted loop-mediated isothermal amplification assay for detection of Japanese encephalitis virus

In this study, we described a novel and effective flower-like ZnO nanostructure assisted Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) method to detect Japanese Encephalitis Virus (JEV). The effects of different concentrations of ZnO nanoflower on the RT-LAMP reaction were investigated. With the increase of concentration of ZnO nanoflower, RT-LAMP reaction obtained optimization, until the concentration exceeded 1.5nM, RT-LAMP reaction was inhibited. Made 1nM as optimum concentration of ZnO nanoflower, we found that optimum RT-LAMP reaction temperature and time were 60°C and 30min, respectively. The optimization might be connected with good adsorption to DNA and thermal conductivity of ZnO nanoflower, but mechanism of the RT-LAMP reaction affected by ZnO nanoflower needs to be explored further.

Visualized detection of single-base difference in multiplexed loop-mediated isothermal amplification amplicons by invasive reaction coupled with oligonucleotide probe-modified gold nanoparticles

Loop-mediated isothermal amplification (LAMP) is a well-developed DNA amplification method with an ultra-high sensitivity, but it is difficult to recognize a single-base difference (like genotyping) in target-specific amplicons by conventional detection ways, such as the intercalation of dyes into dsDNA amplicons or the increase of solution turbidity along with the polymerization process. To allow genotyping based on LAMP suitable for POCT (point-of-care testing) or on-site testing, here we proposed a highly specific and cost-effective method for detecting a single-base difference in LAMP amplicons. The method includes three key steps, sequence amplifier to amplify multiple fragments containing the single nucleotide polymorphisms (SNPs) of interest, allele identifier to recognize a targeted base in the amplicons by invasive reaction, and signal generator to yield signals by hybridization-induced assembly of oligonucleotide probe-modified gold nanoparticles. Because the allele identifier is sensitive to one base difference, it is possible to use multiplexed LAMP (mLAMP) to generate amplicon mixtures for multiple SNP typing. Genotyping of 3 different SNPs (CYP2C19*2, CYP2C19*3 and MDR1-C3435T) for guiding the dosage of clopidogrel is successfully carried out in a 3-plex LAMP on real clinical samples. As our method relies on the naked-eye detection and constant-temperature reaction, no expensive instrument is required for both target amplification and sequence identification, thus much suitable for inexpensive gene-guided personalized medicine in source-limited regions.

Development of a loop-mediated isothermal amplification method for the rapid diagnosis of Ascochyta rabiei L. in chickpeas

Ascochyta blight (AB) is a devastating fungal disease of chickpeas that has spread to nearly all of the chickpea cultivating regions of the world. The rapid diagnosis of Ascochyta rabiei L. (A. rabiei), the pathogen that causes AB, plays an important role in A. rabiei epidemic tracking and AB management. In this study, a group of loop-mediated isothermal amplification (LAMP) primers was designed to detect A. rabiei in chickpea plants and seeds via a LAMP method and a conventional PCR method based on an internal transcribed spacer (ITS) sequence analysis of A. rabiei. Compared with the conventional PCR method, the LAMP method not only exhibited greater sensitivity and specificity in the detection of A. rabiei but also used simpler equipment and required less operational time. The minimum detectable concentration of the A. rabiei genomic DNA solution with the LAMP method was 6.01 × 10(-6 )ng/μl, which was 100 times lower than that of the conventional PCR method with the same outer primers. The greatest advantage of the LAMP method is that results can be observed via the visualization of color changes in SYBR Green I dye with the naked eye, and it does not require expensive instruments, also with less time consumption.

Loop-mediated isothermal amplification assay targeting the blaCTX-M9 gene for detection of extended spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae

Extended-spectrum β-lactamases (ESBLs) produced by Enterobacteriaceae are one of the resistance mechanisms to most β-lactam antibiotics. ESBLs are currently a major problem in both hospitals and community settings worldwide. Rapid and reliable means of detecting ESBL-producing bacteria is necessary for identification, prevention and treatment. Loop-mediated isothermal amplification (LAMP) is a technique that rapidly amplifies DNA with high specificity and sensitivity under isothermal conditions. This study was aimed to develop a convenient, accurate and inexpensive method for detecting ESBL-producing bacteria by a LAMP technique. ESBLs-producing Escherichia coli and Klebsiella pneumoniae were isolated from a tertiary hospital in Bangkok, Thailand and reconfirmed by double-disk synergy test. A set of four specific oligonucleotide primers of LAMP for detection of bla(CTX-M9) gene was designed based on bla(CTX-M9) from E. coli (GenBank Accession No. AJ416345). The LAMP reaction was amplified under isothermal temperature at 63°C for 60 min. Ladder-like patterns of band sizes from 226 bp of the bla(CTX-M9) DNA target was observed. The LAMP product was further analyzed by restriction digestion with MboI and TaqI endonucleases. The fragments generated were approximately 168, 177 and 250 bp in size for MboI digestion and 165, 193, 229, 281 and 314 bp for TaqI digestion, which is in agreement with the predicted sizes. The sensitivity of the LAMP technique to bla(CTX-M9) was greater than that of the PCR method by at least 10,000-fold. These results showed that the LAMP primers specifically amplified only the bla(CTX-M9) gene. Moreover, the presence of LAMP amplicon was simply determined by adding SYBR Green I in the reaction. In conclusion, this technique for detection of ESBLs is convenient, reliable and easy to perform routinely in hospitals or laboratory units in developing countries.

Improved tagmentation-based whole-genome bisulfite sequencing for input DNA from less than 100 mammalian cells

AIM

To develop a whole-genome methylation sequencing method that fulfills the needs for studies using ultra-low-input DNA.

MATERIALS & METHODS

The tagmentation-based whole-genome bisulfite sequencing (T-WGBS) technology is modified, enabling stable library construction with complexity from minimally 0.5 ng of initial genomic DNA, which equals less than 100 mammalian cells.

RESULTS

We thoroughly assessed the performance of this T-WGBS method by sequencing the methylomes of a rice strain and pre-implantation embryos of rhesus monkey and compare to traditional WGBS approach, thereby demonstrating the efficacy of this new approach.

CONCLUSION

This new approach is highly attractive for the complete methylome analysis of very few cells, for example, mammalian pre-implantation embryos, or tiny human biopsy specimens.

STITCHER: A web resource for high-throughput design of primers for overlapping PCR applications

Overlapping PCR is routinely used in a wide number of molecular applications. These include stitching PCR fragments together, generating fluorescent transcriptional and translational fusions, inserting mutations, making deletions, and PCR cloning. Overlapping PCR is also used for genotyping by traditional PCR techniques and in detection experiments using techniques such as loop-mediated isothermal amplification (LAMP). STITCHER is a web tool providing a central resource for researchers conducting all types of overlapping PCR experiments with an intuitive interface for automated primer design that's fast, easy to use, and freely available online (http://ohalloranlab.net/STITCHER.html). STITCHER can handle both single sequence and multi-sequence input, and specific features facilitate numerous other PCR applications, including assembly PCR, adapter PCR, and primer walking. Field PCR, and in particular, LAMP, offers promise as an on site tool for pathogen detection in underdeveloped areas, and STITCHER includes off-target detection features for pathogens commonly targeted using LAMP technology.

Three Tests Used to Identify Non-Culturable Form of Helicobacter pylori in Water Samples

Background:

Helicobacter pylori, causing the most common chronic bacterial infection, exist in two forms; bacilli and coccoid. The coccoid form is identified as viable but non-culturable bacteria.

Objectives:

The current study aimed to conduct culture, polymerase chain reaction (PCR), and loop-mediated isothermal amplification (LAMP) tests to identify coccoid forms of H. pylori.

Materials and Methods:

The PCR and LAMP tests were optimized using specific primers for glmM gene. The sensitivity and specificity of the tests were determined. The current experimental study was conducted on 10 different strains isolated from clinical cases (H1-H10). The isolates were added to tap water and incubated at three different temperatures for one and two months intervals. After pure-culturing of the bacteria, DNAs were extracted and PCR and LAMP were performed.

Results:

Ten copies of targeted DNA were required for PCR detection whereas only five copies gave a positive reaction by LAMP assay, with 100% specificity. Of the 10 isolates inoculated in water for one and two months at three different temperatures 4, 22, and 37°C, only three cases (5%) were found positive in the first month; 13 (21.6%) and 29 cases (48.3%) were also positive by PCR and LAMP tests in the first and second months.

Conclusions:

Results of the current study confirmed that molecular methods such as PCR and LAMP were much more sensitive, rapid, and specific than culturing to identify non-culturable coccoid forms of H. pylori in water.

Development of Loop-Mediated Isothermal Amplification (LAMP) assay for rapid detection of Fusarium oxysporum f. sp. ciceris - wilt pathogen of chickpea

Background

Fusarium oxysporum f. sp. ciceris (Foc), the causal agent of Fusarium wilt is a devastating pathogen of chickpea. In chickpea, various soil borne pathogens produce (s) similar symptoms, therefore cannot be distinguished easily at field level. There is real need for a rapid, inexpensive, and easy to operate and maintain genotyping tool to facilitate accurate disease diagnosis and surveillance for better management of Fusarium wilt outbreaks.

Results

In this study, we developed a loop-mediated isothermal amplification (LAMP) assay targeting the elongation factor 1 alpha gene sequence for visual detection of Foc. The LAMP reaction was optimal at 63°C for 60 min. When hydroxynaphthol blue (HNB) was added before amplification, samples with Foc DNA developed a characteristic sky blue colour but those without DNA or with the DNA of six other plant pathogenic fungi did not. Results obtained with LAMP and HNB were confirmed when LAMP products were subjected to gel electrophoresis. The detection limit of this LAMP assay for Foc was 10 fg of genomic DNA per reaction, while that of conventional PCR was 100 pg.

Conclusions

In conclusion, it was found that a LAMP assay combined with HNB is simple, rapid, sensitive, and specific. The LAMP assay does not require specialized equipment, hence can be used in the field for the rapid detection of Foc. This is the first report of the use of LAMP assay for the detection of Foc. The presented LAMP method provides a specific, sensitive and rapid diagnostic tool for the distinction of Foc, with the potential to be standardized as a detection method for Foc in endemic areas and will be very useful for monitoring the disease complex in the field further suggesting the management strategies.

Electronic supplementary material

The online version of this article (doi:10.1186/s13104-015-0997-z) contains supplementary material, which is available to authorized users.

Isothermal amplification methods for the detection of nucleic acids in microfluidic devices

Diagnostic tools for biomolecular detection need to fulfill specific requirements in terms of sensitivity, selectivity and high-throughput in order to widen their applicability and to minimize the cost of the assay. The nucleic acid amplification is a key step in DNA detection assays. It contributes to improving the assay sensitivity by enabling the detection of a limited number of target molecules. The use of microfluidic devices to miniaturize amplification protocols reduces the required sample volume and the analysis times and offers new possibilities for the process automation and integration in one single device. The vast majority of miniaturized systems for nucleic acid analysis exploit the polymerase chain reaction (PCR) amplification method, which requires repeated cycles of three or two temperature-dependent steps during the amplification of the nucleic acid target sequence. In contrast, low temperature isothermal amplification methods have no need for thermal cycling thus requiring simplified microfluidic device features. Here, the use of miniaturized analysis systems using isothermal amplification reactions for the nucleic acid amplification will be discussed.

The oral microflora in obesity and type-2 diabetes

Background

Type 2 diabetes mellitus (T2DM) is prevalent in people with obesity. It has been proposed that these conditions are related to specific features of the microflora of the mouth and lower gastrointestinal (GI) tract. Hyperglycemia often resolves quickly after Roux-en-Y gastric bypass (RYGB) but the role of the GI microflora cannot be examined easily because of reduced intestinal mobility. We propose that the study of microorganisms present in the mouth of patients undergoing RYGB will contribute to our understanding of the role of bacteria in the pathogenesis of T2DM.

Objective

To conduct a feasibility study to examine differences in oral microbes in obese patients with and without T2DM and to determine whether it is feasible to measure changes after gastric bypass surgery.

Methods

Individuals with morbid obesity (n=29), of whom 13 had T2DM, were studied. Oral rinses, stool samples, and blood samples were obtained before RYGB, and oral rinses and blood samples were obtained at 2 and 12 weeks postsurgery.

Results

Prior to surgery, participants with T2DM had slightly higher total levels of oral bacteria than those without diabetes. Those with HbA1c > 6.5% had rather lower levels of Bifidobacteria in the mouth and stool. At 2 weeks post-RYGB, patients with T2DM were able to reduce or discontinue their hypoglycemic medications. Stool samples could not be obtained but oral rinses were readily available. The levels of oral Bifidobacteria had increased tenfold and levels of circulating endotoxin and tumor necrosis factor-alpha had decreased.

Conclusions

The study of oral bacteria before and after RYGB is feasible and should be tested in larger patient populations to increase our understanding of the role of microorganisms in the pathogenesis of obesity and T2DM.

Development of a loop-mediated isothermal amplification assay for detection of Cronobacter spp. (Enterobacter sakazakii)

Contamination of Cronobacter spp. (Enterobacter sakazakii) in infant formulas and other food products is a severe problem. Here a loop-mediated isothermal amplification (LAMP) assay was developed for rapidly detecting Cronobacter spp. in powdered infant formula. Sequences of 16S/23S rDNA internal intergenic spacer of Cronobacter spp. were used as the target template to design LAMP primers. The detection outcome can be evaluated by the white precipitate or the fluorescence intensity under ultraviolet irradiation, both visible to naked eyes. The sensitivity and specificity of the LAMP assay was further analyzed in comparison with that of regular PCR and real time quantitative PCR. The results showed that all of Cronobacter spp. strains display positive reaction to the detections while all of the non-Cronobacter spp. strains were negative, and that the LAMP assay exhibits a high sensitivity of 9.1 fg/μL (The sensitivity of regular PCR and real time quantitative PCR is 91 and 9.1 pg/μL, respectively.). The amplified reaction could be accomplished in about 1 h, with the results visible to naked eyes. Hence, the LAMP assay developed by this study can provide a rapid and simple approach for the detection of Cronobacter spp. in infant formula.

Development of loop-mediated isothermal amplification (LAMP) assays for rapid detection of Ehrlichia ruminantium

Background

The rickettsial bacterium Ehrlichia ruminantium is the causative agent of heartwater, a potential zoonotic disease of ruminants transmitted by ticks of the genus Amblyomma. The disease is distributed in nearly all of sub-Saharan Africa and some islands of the Caribbean, from where it threatens the American mainland. This report describes the development of two different loop-mediated isothermal amplification (LAMP) assays for sensitive and specific detection of E. ruminantium.

Results

Two sets of LAMP primers were designed from the pCS20 and sodB genes. The detection limits for each assay were 10 copies for pCS20 and 5 copies for sodB, which is at least 10 times higher than that of the conventional pCS20 PCR assay. DNA amplification was completed within 60 min. The assays detected 16 different isolates of E. ruminantium from geographically distinct countries as well as two attenuated vaccine isolates. No cross-reaction was observed with genetically related Rickettsiales, including zoonotic Ehrlichia species from the USA. LAMP detected more positive samples than conventional PCR but less than real-time PCR, when tested with field samples collected in sub-Saharan countries.

Conclusions

Due to its simplicity and specificity, LAMP has the potential for use in resource-poor settings and also for active screening of E. ruminantium in both heartwater-endemic areas and regions that are at risk of contracting the disease.

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.

Development and evaluation of loop-mediated isothermal amplification (LAMP) for the rapid diagnosis of Penicillium marneffei in archived tissue samples

Penicillium marneffei is the etiologic agent of a severe systemic disease in immunocompromised hosts in Southeast Asia. In the present study, a novel method, known as loop-mediated isothermal amplification (LAMP), is described for the rapid and specific detection of the species, using a primer set derived from the internal transcribed spacer (ITS) region of the rRNA gene. Amplification products can be detected macroscopically by visual inspection in vials using SYBR Green I as well as by electrophoresis on agarose gel. The LAMP assay resulted in specific amplification of P. marneffei ITS using pure cultures after a 1-h reaction at 65 degrees C in a water bath; no cross-reactivity with other fungi including other biverticillate penicillia was observed. The detectable DNA limit was two copies. In addition, specific amplification was achieved using paraffin wax-embedded tissue samples from patients with penicilliosis marneffei and tissue samples from bamboo rats. The method provides a powerful tool for rapid diagnostics in the clinical lab, and has potential for use in ecological studies.

Development and evaluation of loop-mediated isothermal amplification (LAMP) for the rapid diagnosis of Penicillium marneffei in archived tissue samples

Penicillium marneffei is the etiologic agent of a severe systemic disease in immunocompromised hosts in Southeast Asia. In the present study, a novel method, known as loop-mediated isothermal amplification (LAMP), is described for the rapid and specific detection of the species, using a primer set derived from the internal transcribed spacer (ITS) region of the rRNA gene. Amplification products can be detected macroscopically by visual inspection in vials using SYBR Green I as well as by electrophoresis on agarose gel. The LAMP assay resulted in specific amplification of P. marneffei ITS using pure cultures after a 1-h reaction at 65 degrees C in a water bath; no cross-reactivity with other fungi including other biverticillate penicillia was observed. The detectable DNA limit was two copies. In addition, specific amplification was achieved using paraffin wax-embedded tissue samples from patients with penicilliosis marneffei and tissue samples from bamboo rats. The method provides a powerful tool for rapid diagnostics in the clinical lab, and has potential for use in ecological studies.

Rapid detection of pathogenic fungi using loop-mediated isothermal amplification, exemplified by Fonsecaea agents of chromoblastomycosis

Loop-mediated isothermal amplification (LAMP) was developed for rapid detection of pathogenic or allergenic fungal in the environment. Primers applied were derived from the rDNA Internal Transcribed Spacer and the 5.8S rRNA gene. The assay enabled amplification of target fungi at the level of genus or closely related species using pure cultures after 1h reaction at 65 degrees C in a water bath. No cross-reactivity to related species was observed. The DNA detection limit was 0.2fg. The method also proved to work well with fungi on non-sterile adhesive tape. Amplification products were detected by visual inspection using SYBR Green I as well as by electrophoresis on agarose gels. As a model organism we selected Fonsecaea, a fungal genus containing etiologic agents of chromoblastomycosis, a widely distributed tropical and subtropical skin disease in otherwise healthy patients and supposed to be acquired by environmental inoculation. It is suggested that LAMP can also be used for rapid clinical diagnosis, for environmental detection, and for retrospective studies in archived clinical samples.

Rapid quantification of periodontitis-related bacteria using a novel modification of Invader PLUS technologies

The Invader PLUS technology is a sensitive, rapid method for the detection and quantification of nucleic acid. While the original technology is based on the amplification by polymerase chain reaction (PCR) of the target sequence followed by its detection using the Invader technology, the current modification allows simultaneous PCR amplification and Invader reaction. The PCR primers and the Invader probes are designed to operate at the same temperature. This allows simpler design and faster results. This technology has been applied for the quantification of six periodontitis-related bacteria (Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Toreponema denticola, Tannerella forsythensis and Fusobacterium nucleatum). Direct comparison of this modified Invader PLUS with real-time PCR demonstrated similar linear range. Furthermore, testing of 64 volunteers showed a good correlation between both technologies with correlation factors r2 spanning between 0.827 and 0.987. We demonstrated here that the proposed improvement of the Invader PLUS allows the detection and quantification of DNA sequences using a simple design and protocol that can be implemented in clinical testing.

Site-specific development of periodontal disease is associated with increased levels of Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia in subgingival plaque

BACKGROUND

Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia (previously T. forsythensis), which are regarded as the principal periodontopathogenic bacteria, exist as a consortium in subgingival biofilms. We aimed to examine quantitative relationships between P. gingivalis, T. denticola, and T. forsythia in subgingival biofilms and the relationship between the quantity and prevalence of these three bacteria and site-specific periodontal health.

METHODS

This study was cross-sectional. The study population consisted of 35 adult subjects who visited the Kyushu Dental College Hospital. Plaque samples were collected from 105 periodontal pocket sites. Quantitative analyses of each of the three periodontopathogenic bacteria were performed using real-time polymerase chain reaction with species-specific primers and hybridization probes.

RESULTS

The plaque samples were divided into four groups based on the presence or absence of a periodontal pocket (probing depth [PD] > or =4 mm) and bleeding on probing (BOP), regardless of attachment loss. The proportions of all three target bacteria detected in samples from sites of periodontal disease (with PD and BOP) were markedly higher than those in the other sample groups. Cell numbers of P. gingivalis, T. denticola, and T. forsythia in the subgingival plaque of each sampling site were significantly mutually correlated and were increased in the plaque of sites of periodontal disease with PD > or =4 mm and BOP.

CONCLUSION

The symbiotic effects of P. gingivalis, T. denticola, and T. forsythia, which coaggregate and exist concomitantly in subgingival biofilms, may be associated with the local development of periodontitis.

Rapid and simple detection of eight major periodontal pathogens by the loop-mediated isothermal amplification method

Loop-mediated isothermal amplification (LAMP) was applied to develop a rapid and simple detection system for eight periodontal pathogens: Aggregatibacter (Actinobacillus) actinomycetemcomitans, Campylobacter rectus, Eikenella corrodens, Fusobacterium nucleatum, Porphyromonas gingivalis, Prevotella intermedia, Treponema denticola and Tannerella forsythia. Primers were designed from the 16S ribosomal RNA gene for each pathogen, and the LAMP amplified the targets specifically and efficiently under isothermal condition at 64 degrees C. To simplify the manipulation of LAMP examination, boiled cells and intact cells suspended in phosphate-buffered saline (PBS) were tested as templates besides extracted DNA template. The detection limits were 1-10 cells per tube using extracted DNA template. However, LAMP methods using boiled cells and intact cells required 10-100 and 100-1000 cells per tube, respectively. LAMPs for A. actinomycetemcomitans, P. gingivalis and P. intermedia were then applied to clinical plaque samples, and the method demonstrated equal or higher sensitivity compared with the conventional real-time PCR method. These findings suggest the usefulness of the LAMP method for the rapid and simple microbiological diagnosis of periodontitis, and the possibility of LAMP examination without the DNA extraction step.

African trypanosomiasis: sensitive and rapid detection of the sub-genus Trypanozoon by loop-mediated isothermal amplification (LAMP) of parasite DNA

Control of human African trypanosomiasis (HAT) is dependent on accurate diagnosis and treatment of infected patients. However, sensitivities of tests in routine use are unsatisfactory, due to the characteristically low parasitaemias in naturally infected individuals. We have identified a conserved sequence in the repetitive insertion mobile element (RIME) of the sub-genus Trypanozoon and used it to design primers for a highly specific loop-mediated isothermal amplification (LAMP) test. The test was used to analyse Trypanozoon isolates and clinical samples from HAT patients. The RIME LAMP assay was performed at 62 degrees C using real-time PCR and a water bath. DNA amplification was detectable within 25min. All positive samples detected by gel electrophoresis or in real-time using SYTO-9 fluorescence dye could also be detected visually by addition of SYBR Green I to the product. The amplicon was unequivocally confirmed through restriction enzyme NdeI digestion, analysis of melt curves and sequencing. The analytical sensitivity of the RIME LAMP assay was equivalent to 0.001 trypanosomes/ml while that of classical PCR tests ranged from 0.1 to 1000 trypanosomes/ml. LAMP detected all 75 Trypanozoon isolates while TBR1 and two primers (specific for sub-genus Trypanozoon) showed a sensitivity of 86.9%. The SRA gene PCR detected 21 out of 40 Trypanosoma brucei rhodesiense isolates while Trypanosoma gambiense-specific glycoprotein primers (TgsGP) detected 11 out of 13 T. b. gambiense isolates. Using clinical samples, the LAMP test detected parasite DNA in 18 out of 20 samples which included using supernatant prepared from boiled blood, CSF and direct native serum. The sensitivity and reproducibility of the LAMP assay coupled with the ability to detect the results visually without the need for sophisticated equipment indicate that the technique has strong potential for detection of HAT in clinical settings. Since the LAMP test shows a high tolerance to different biological substances, determination of the appropriate protocols for processing the template to make it a user-friendly technique, prior to large scale evaluation, is needed.

Loop-mediated isothermal amplification (LAMP) method for rapid detection of Trypanosoma brucei rhodesiense

Loop-mediated isothermal amplification (LAMP) of DNA is a novel technique that rapidly amplifies target DNA under isothermal conditions. In the present study, a LAMP test was designed from the serum resistance-associated (SRA) gene of Trypanosoma brucei rhodesiense, the cause of the acute form of African sleeping sickness, and used to detect parasite DNA from processed and heat-treated infected blood samples. The SRA gene is specific to T. b. rhodesiense and has been shown to confer resistance to lysis by normal human serum. The assay was performed at 62 degrees C for 1 h, using six primers that recognised eight targets. The template was varying concentrations of trypanosome DNA and supernatant from heat-treated infected blood samples. The resulting amplicons were detected using SYTO-9 fluorescence dye in a real-time thermocycler, visual observation after the addition of SYBR Green I, and gel electrophoresis. DNA amplification was detected within 35 min. The SRA LAMP test had an unequivocal detection limit of one pg of purified DNA (equivalent to 10 trypanosomes/ml) and 0.1 pg (1 trypanosome/ml) using heat-treated buffy coat, while the detection limit for conventional SRA PCR was approximately 1,000 trypanosomes/ml. The expected LAMP amplicon was confirmed through restriction enzyme RsaI digestion, identical melt curves, and sequence analysis. The reproducibility of the SRA LAMP assay using water bath and heat-processed template, and the ease in results readout show great potential for the diagnosis of T. b. rhodesiense in endemic regions.

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

INTRODUCTION

Streptococcus mutans and Streptococcus sobrinus are associated with the development of dental caries in humans. In this study, we developed a rapid, sensitive method for detecting these major cariogenic pathogens using loop-mediated isothermal amplification (LAMP). The assay procedure is quite simple: the amplification is carried out in a single tube under isothermal conditions at 63 degrees C, and the result can be obtained in less than 1 h.

METHODS

Initially, a set of six primers was designed by targeting S. mutans-specific and S. sobrinus-specific regions, identified using the genomic subtractive hybridization technique. We evaluated the specificities and sensitivities of these assays. Furthermore, we detected and quantified these bacteria in saliva and carious dentin from eight children.

RESULTS

The sensitivities of the S. mutans-specific and S. sobrinus-specific LAMP methods, examined using agarose gel electrophoresis, were each one cell for a 30-min reaction. The detection limits using real-time turbidimetry analysis were 1 to 10(7) cells (3.28 x 10(1) to 3.28 x 10(8) fg S. mutans template DNA) per reaction tube and 1 to 10(5) cells (2.72 x 10(3) to 2.72 x 10(8) fg S. sobrinus template DNA) per reaction tube. Using these assays, we detected and quantified these cariogenic bacteria for evaluation of the LAMP assay for clinical diagnosis.

CONCLUSIONS

Our results suggest that the LAMP-based assay in combination with subtractive hybridization is valuable for preparing species-specific primers for closely related species. Furthermore, the LAMP-based assay will be a useful tool for the rapid and sensitive prediction of dental caries.

Rapid detection of Actinobacillus actinomycetemcomitans using a loop-mediated isothermal amplification method

INTRODUCTION

Actinobacillus actinomycetemcomitans has been implicated in the etiology of aggressive periodontitis. In this study, we applied a novel nucleic acid amplification method, called loop-mediated isothermal amplification (LAMP), which amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions, allowing the rapid detection of A. actinomycetemcomitans.

METHODS

We designed the primers for detecting A. actinomycetemcomitans and evaluated the specificity and sensitivity of the assay.

RESULTS

The LAMP primers used in this study successfully amplified serotypes a-e of A. actinomycetemcomitans, while other oral bacteria were not amplified. By measuring the precipitation of magnesium pyrophosphate, we could quantify the chromosomal DNA of A. actinomycetemcomitans. The detection limits using the real-time turbidimetry analysis were 5.8 x 10(2)-5.8 x 10(7) copies of A. actinomycetemcomitans template DNA per reaction tube. In addition, the LAMP assay was used for the rapid detection of A. actinomycetemcomitans in clinical specimens from eight individuals. The results with the LAMP method were similar to those using conventional polymerase chain reaction.

CONCLUSION

Our results suggest that the LAMP-based assay is very useful for the rapid detection of A. actinomycetemcomitans.

Loop-mediated isothermal amplification method for the rapid detection of Enterococcus faecalis in infected root canals

INTRODUCTION

Enterococcus faecalis is a major pathogen in the etiology of apical periodontitis after root canal treatment. A loop-mediated isothermal amplification method, which amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions using a set of four specially designed primers and a DNA polymerase with strand-displacement activity, was developed for the rapid detection of E. faecalis in clinical specimens from root canals.

METHODS

Primers for detecting E. faecalis from the azoA gene were designed. The specificity of this assay was evaluated using various oral bacteria and the sensitivity was evaluated using serially diluted E. faecalis chromosomal DNA. In addition, loop-mediated isothermal amplification assays were applied to the rapid detection of E. faecalis from endodontic samples.

RESULTS

The loop-mediated isothermal amplification products amplified with the primer set were specific for E. faecalis. To confirm the specificity of the amplicon, the amplified products were digested with the restriction endonuclease Sau3AI. The lower detection limit of the E. faecalis primer set without the loop primer set was 10 microg/tube for a 50-min loop-mediated isothermal amplification reaction. Using loop primers increased the detection sensitivity by several orders of magnitude. Furthermore, E. faecalis was detected with the loop-mediated isothermal amplification assay in four root canals from 18 individuals and the detection results were consistent with those of conventional polymerase chain reactions.

CONCLUSION

These results indicate that the loop-mediated isothermal amplification assay is very useful for rapid detection of E. faecalis and diagnosis of endodontic infection.

Use of a combination of brushing technique and the loop-mediated isothermal amplification method as a novel, rapid, and safe system for detection of Helicobacter pylori

Gastric mucosal biopsy is widely used in the detection of Helicobacter pylori but is associated with a number of problems, including false-negative results due to sampling error and massive bleeding after biopsy. Given the extended period required to culture H. pylori, detection would be further improved by the use of rapid detection methods such as PCR. Here, we developed a rapid, safe, and convenient method for collecting H. pylori which combines endoscopic brushing with the loop-mediated isothermal amplification (LAMP) method. The specificity and sensitivity of LAMP were examined using nine urease-generating non-H. pylori bacterial species, Escherichia coli, Clostridium perfringens, Campylobacter jejuni, Helicobacter hepaticus, and 51 H. pylori strains. Results showed that H. pylori-specific LAMP primers amplified H. pylori DNA only and that the lowest detection limit of the LAMP reaction was 10(2) CFU. Brushing and biopsy samples taken from 200 patients with peptic ulcer at Nagoya University Hospital and a regional health care center were subjected to both LAMP and culturing. No adverse effects such as severe bleeding or penetration occurred during the procedure. By LAMP assay, 123 patients were confirmed as H. pylori positive when brushing technique samples were assayed, whereas only 100 were positive when biopsy samples were assayed. Culture assay detected H. pylori in 117 patients when it was combined with the brushing technique and in 96 when it was combined with biopsy. Combination of the endoscopic brushing technique with LAMP is considered a useful and safe system for identifying H. pylori infection.

Prevalence of periodontopathic bacteria on the tongue dorsum of elderly people

OBJECTIVES

The aim of this study was to analyse the prevalence of oral bacteria on the dorsum of the tongue. In addition, the relationship between the number of teeth and the microflora present on the coating of the tongue in a population of 85-year-old people was assessed.

SUBJECTS AND METHODS

Two hundred and five individuals (89 males, 116 females) from the same geographical area who were 85 years of age were examined. Five periodontopathic bacteria (Porphyromonas gingivalis, Tannerella forsythia, Actinobacillus actinomycetemcomitans, Fusobacterium nucleatum, and Treponema denticola) and one cariogenic bacterium (Streptococcus mutans) were analysed using a polymerase chain reaction assay of tongue samples from the population.

RESULTS

Periodontal bacteria-positive individuals have more teeth than that of periodontal bacteria-negative people. Between the periodontal bacteria-positive and -negative individuals, there were significant differences in the mean number of teeth for P. gingivalis (p<0.0001), T. denticola (p<0.001), F. nucleatum (p=0.002), and T. forsythia (p=0.005), while there were no significant differences for A. actinomycetemcomitans (p=0.998) or S. mutans (p=0.147).

CONCLUSIONS

A wide range of species, including anaerobes, was detected in 85-year-old subjects. It was found that the detection of periodontal bacteria on the tongue coating increased with the number of teeth. There was a positive relationship between the tooth number and periodontopathic bacteria, except for A. actinomycetemcomitans. These results suggest that tongue care is essential for preventing oral disease and needs to be part of any oral care programme in elderly people.