One-tube loop-mediated isothermal amplification combined with restriction endonuclease digestion and ELISA for colorimetric detection of resistance to isoniazid, ethambutol and streptomycin in Mycobacterium tuberculosis isolates

Identification of Antibiotic Resistance in ESKAPE Pathogens through Plasmonic Nanosensors and Machine Learning

Antibiotic-resistant ESKAPE pathogens cause nosocomial infections that lead to huge morbidity and mortality worldwide. Rapid identification of antibiotic resistance is vital for the prevention and control of nosocomial infections. However, current techniques like genotype identification and antibiotic susceptibility testing are generally time-consuming and require large-scale equipment. Herein, we develop a rapid, facile, and sensitive technique to determine the antibiotic resistance phenotype among ESKAPE pathogens through plasmonic nanosensors and machine learning. Key to this technique is the plasmonic sensor array that contains gold nanoparticles functionalized with peptides differing in hydrophobicity and surface charge. The plasmonic nanosensors can interact with pathogens to generate bacterial fingerprints that alter the surface plasmon resonance (SPR) spectra of nanoparticles. In combination with machine learning, it enables the identification of antibiotic resistance among 12 ESKAPE pathogens in less than 20 min with an overall accuracy of 89.74%. This machine-learning-based approach allows for the identification of antibiotic-resistant pathogens from patients and holds great promise as a clinical tool for biomedical diagnosis.

Loop-Mediated Isothermal Amplification for Detection of Plant Pathogens in Wheat (Triticum aestivum)

Wheat plants can be infected by a variety of pathogen species, with some of them causing similar symptoms. For example, Zymoseptoria tritici and Parastagonospora nodorum often occur together and form the Septoria leaf blotch complex. Accurate detection of wheat pathogens is essential in applying the most appropriate disease management strategy. Loop-mediated isothermal amplification (LAMP) is a recent molecular technique that was rapidly adopted for detection of plant pathogens and can be implemented easily for detection in field conditions. The specificity, sensitivity, and facility to conduct the reaction at a constant temperature are the main advantages of LAMP over immunological and alternative nucleic acid-based methods. In plant pathogen detection studies, LAMP was able to differentiate related fungal species and non-target strains of virulent species with lower detection limits than those obtained with PCR. In this review, we explain the amplification process and elements of the LAMP reaction, and the variety of techniques for visualization of the amplified products, along with their advantages and disadvantages compared with alternative isothermal approaches. Then, a compilation of analyses that show the application of LAMP for detection of fungal pathogens and viruses in wheat is presented. We also describe the modifications included in real-time and multiplex LAMP that reduce common errors from post-amplification detection in traditional LAMP assays and allow discrimination of targets in multi-sample analyses. Finally, we discuss the utility of LAMP for detection of pathogens in wheat, its limitations, and current challenges of this technique. We provide prospects for application of real-time LAMP and multiplex LAMP in the field, using portable devices that measure fluorescence and turbidity, or facilitate colorimetric detection. New technologies for detection of plant pathogen are discussed that can be integrated with LAMP to obtain elevated analytical sensitivity of detection.

Loop-mediated isothermal amplification (LAMP): a versatile technique for detection of micro-organisms

Loop‐mediated isothermal amplification (LAMP) amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions by using a DNA polymerase with high displacement strand activity and a set of specifically designed primers to amplify targeted DNA strands. Following its first discovery by Notomi et al. (2000Nucleic Acids Res 28: E63), LAMP was further developed over the years which involved the combination of this technique with other molecular approaches, such as reverse transcription and multiplex amplification for the detection of infectious diseases caused by micro‐organisms in humans, livestock and plants. In this review, available types of LAMP techniques will be discussed together with their applications in detection of various micro‐organisms. Up to date, there are varieties of LAMP detection methods available including colorimetric and fluorescent detection, real‐time monitoring using turbidity metre and detection using lateral flow device which will also be highlighted in this review. Apart from that, commercialization of LAMP technique had also been reported such as lyophilized form of LAMP reagents kit and LAMP primer sets for detection of pathogenic micro‐organisms. On top of that, advantages and limitations of this molecular detection method are also described together with its future potential as a diagnostic method for infectious disease.

Simple Identification of Human Taenia Species by Multiplex Loop-Mediated Isothermal Amplification in Combination with Dot Enzyme-Linked Immunosorbent Assay

For differential detection of Taenia solium, Taenia saginata, and Taenia asiatica, loop-mediated isothermal amplification (LAMP) assay targeting the cytochrome c oxidase subunit 1 gene has been recently developed and shown to be sensitive, specific, and effective. However, to achieve differential identification, one specimen requires three reaction mixtures containing a primer set of each Taenia species separately, which is complex and time consuming and increases the risk of cross-contamination. In this study, we developed a simple differential identification of human Taenia species using multiplex LAMP (mLAMP) in combination with dot enzyme-linked immunosorbent assay (dot-ELISA). Forward inner primers of T. solium, T. saginata, and T. asiatica labeled with fluorescein isothiocyanate (FITC), digoxigenin (DIG), and tetramethylrhodamine (TAMRA), respectively, and biotin-labeled backward inner primers were used in mLAMP. The mLAMP assay succeeded in specific amplification of each respective target gene in a single tube. Furthermore, the mLAMP product from each species was easily distinguished by dot-ELISA with an antibody specific for FITC, DIG, or TAMRA. The mLAMP assay in combination with dot-ELISA will make identification of human Taenia species simpler, easier, and more practical.

Fighting an old disease with modern tools: characteristics and molecular detection methods of drug-resistant Mycobacterium tuberculosis

Tuberculosis (TB) is an ancient disease, but not a disease of the past. The increasing prevalence of drug-resistant strains of Mycobacterium tuberculosis, the causative agent of TB, demands new measures to combat the situation. Rapid and accurate detection of the pathogen, and its drug susceptibility pattern, is essential for timely initiation of treatment, and ultimately, control of the disease. Molecular-based methods offer a great chance to improve detection of drug-resistant TB; however, their development and usage should be accompanied with a profound understanding of drug resistance mechanisms and circulating M. tuberculosis strains in specific settings, as otherwise, the usefulness of such tests may be limited. This review gives an overview of the history of TB treatment and drug resistance, drug resistance mechanisms for the most commonly used drugs and molecular methods designed to detect drug-resistant strains.

Classical and new assays for detecting drug resistance in tuberculosis

Tuberculosis is a public health concern worldwide. Particularly worrying is the emergence of severe forms of drug resistance, such as extensively drug resistant and totally drug resistant tuberculosis, with few treatment options for the afflicted patients. To avoid further spread of drug resistance, its early detection is extremely important. Conventional phenotypic procedures to detect drug resistance depended on the in vitro slow growth of the bacteria. More recent molecular approaches such as reverse-hybridization assays and real-time PCR tests have been introduced. Newer options proposed include, faster culture-based methods and whole-genome sequencing and nanotechnology. Not yet available is a real point-of-care test, applied directly in clinical samples and reliable enough for guiding a treatment option.

Molecular analysis of the rpsL gene for rapid detection of streptomycin-resistant Mycobacterium tuberculosis: a meta-analysis

BACKGROUND

Drug-resistant Mycobacterium tuberculosis (MTB) is a major threat to tuberculosis (TB) control programs and public health. Most conventional methods of drug susceptibility testing (DST) are precise but time-consuming. Molecular analysis of the rpsL gene has been used widely in diagnosing streptomycin-resistant MTB since it is rapid and specific. The aim of the present study was to perform a meta-analysis to assess the accuracy of molecular assay of the rpsL gene for the rapid detection of streptomycin-resistant MTB.

METHODS

We searched PubMed, Web of Science, and EBSCO databases for studies that applied a molecular assay of the rpsL gene to detect streptomycin-resistant MTB with a conventional method as the reference. The sensitivity and specificity were pooled by a random effect model using Meta-DiSc software. A summary receiver operating characteristic curve (SROC) was applied to summarize the diagnostic accuracy.

RESULTS

A total of 22 studies involving 2618 specimens with 1372 streptomycin-resistant and 1246 streptomycin-susceptible specimens met our inclusion criteria. The overall sensitivity and specificity estimates were 0.64 (95% confidence interval (CI) 0.61-0.66) and 1.00 (95% CI 0.99-1.00), respectively. The area under the SROC curve was 0.9069 and the Cochrane (Q*) index was 0.8387.

CONCLUSIONS

This meta-analysis reveals that molecular assay of the rpsL gene is a reliable and useful method for the detection of streptomycin-resistant MTB.

G-quadruplex-generating polymerase chain reaction for visual colorimetric detection of amplicons

We have developed a self-reporting polymerase chain reaction (PCR) system for visual colorimetric gene detection and distinction of single nucleotide polymorphisms (SNPs). Amplification is performed using target-specific primers modified with a 5'-end tail that is complementary to a G-quadruplex deoxyribozyme-forming sequence. At end-point, G-quadruplexes are forced to fold from PCR-generated duplex DNA and then are used to colorimetrically report the successful occurrence of PCR by assaying their peroxidase activity using a chromogenic substrate. Furthermore, primer design considerations for the G-quadruplex-generating PCR system have allowed us to visually distinguish SNPs associated with Mycobacterium tuberculosis drug resistance alleles.

Design and Proof-of-Concept Use of a Circular PMMA Platform with 16-Well Sample Capacity for Microwave-Accelerated Bioassays

We demonstrate the design and the proof-of-concept use of a new, circular poly(methyl methacrylate)-based bioassay platform (PMMA platform), which affords for the rapid processing of 16 samples at once. The circular PMMA platform (5 cm in diameter) was coated with a silver nanoparticle film to accelerate the bioassay steps by microwave heating. A model colorimetric bioassay for biotinylated albumin (using streptavidin-labeled horse radish peroxidase) was performed on the PMMA platform coated with and without silver nanoparticles (a control experiment), and at room temperature and using microwave heating. It was shown that the simulated temperature profile of the PMMA platform during microwave heating were comparable to the real-time temperature profile during actual microwave heating of the constructed PMMA platform in a commercial microwave oven. The model colorimetric bioassay for biotinylated albumin was successfully completed in ~2 min (total assay time) using microwave heating, as compared to 90 min at room temperature (total assay time), which indicates a ~45-fold decrease in assay time. Our PMMA platform design afforded for significant reduction in non-specific interactions and low background signal as compared to non-silvered PMMA surfaces when employed in a microwave-accelerated bioassay carried out in a conventional microwave cavity.

Gene-Z: a device for point of care genetic testing using a smartphone

By 2012, point of care (POC) testing will constitute roughly one third of the $59 billion in vitro diagnostics market. The ability to carry out multiplexed genetic testing and wireless connectivity are emerging as key attributes of future POC devices. In this study, an inexpensive, user-friendly and compact device (termed Gene-Z) is presented for rapid quantitative detection of multiple genetic markers with high sensitivity and specificity. Using a disposable valve-less polymer microfluidic chip containing four arrays of 15 reaction wells each with dehydrated primers for isothermal amplification, the Gene-Z enables simultaneous analysis of four samples, each for multiple genetic markers in parallel, requiring only a single pipetting step per sample for dispensing. To drastically reduce the cost and size of the real-time detector necessary for quantification, loop-mediated isothermal amplification (LAMP) was performed with a high concentration of SYTO-81, a non-inhibiting fluorescent DNA binding dye. The Gene-Z is operated using an iPod Touch, which also receives data and carries out automated analysis and reporting via a WiFi interface. This study presents data pertaining to performance of the device including sensitivity and reproducibility using genomic DNA from Escherichia coli and Staphylococcus aureus. Overall, the Gene-Z represents a significant step toward truly inexpensive and compact tools for POC genetic testing.