Novel helix loop-mediated isothermal amplification (HAMP) assay for colorimetric detection of Staphylococcus aureus in milk

Staphylococcus aureus is an important and leading cause of foodborne diseases worldwide. Prompt detection and recall of contaminated foods are crucial to prevent untoward health consequences caused by S. aureus. Helix loop-mediated isothermal amplification (HAMP) is an exciting recent addition to the array of available isothermal-based nucleic acid amplification techniques. This study aimed to develop and evaluate a HAMP assay for detecting S. aureus in milk and milk products. The assay is completed in 75 minutes of isothermal temperature incubation (64 ˚C) and dye-based visual interpretation of results based on colour change. The specificity of the developed assay was ascertained using 27 S. aureus and 17 non S. aureus bacterial strains. The analytical sensitivity of the developed HAMP assay was 9.7 fg/µL of pure S. aureus DNA. The detection limit of the HAMP assay in milk (86 CFU/mL) was 1000x greater than the routinely used endpoint PCR (86 × 103 CFU/mL). The practicality of applying the HAMP assay was also assessed by analysing milk and milk product samples (n = 95) obtained from different dairy farms and retail outlets. The developed test is a more rapid, sensitive, and user-friendly method for the high-throughput screening of S. aureus in food samples and may therefore be suitable for field laboratories. To our knowledge, this is the first study to develop and evaluate the HAMP platform for detecting S. aureus.

Enzyme-free amplified detection of circulating microRNA by making use of DNA circuits, a DNAzyme, and a catalytic hairpin assembly

A homogeneous and enzyme-free fluorometric assay is described for the determination of microRNA-182. It is based on the use of DNA circuits and DNAzyme. The DNA circuits warrant strong signal amplification by virtue of catalytic hairpin assembly, a system that consists of two hairpin substrates. A part of the DNAzyme sequence is programmed to sequester into one of the two hairpin substrates. In the presence of target microRNA-182, the two hairpin substrates undergo catalytic assembling. This results in the formation of a DNA duplex and the release of the DNAzyme from the hairpin structure. Upon cyclic amplification, one target catalyzes the formation of Mg (II)-dependent DNAzymes. These bind to, and hydrolyze, the fluorescently labeled substrates for signal amplification and transduction. Based on nucleic acid programmability, this engineered assay has a limit of detection as low as 6.8 f. and a dynamic range that covers the 10 f. to10 nM microRNA-182 concentration range. Detection can be performed within 60 min. The assay is simple, rapid, homogenous, cost-effective, and enzyme-free. These features make the method an attractive tool in routine microRNA diagnosis and, conceivably, in point of care uses. Graphical abstract Schematic of a homogeneous and enzyme-free fluorometric assay for the determination of microRNA-182. It is based on the use of DNA circuits and DNAzymes. The DNA circuits warrant strong signal amplification by virtue of catalytic hairpin assembly that uses two hairpin substrates. The method represents an attractive tool for routine microRNA diagnosis and, conceivably, point of care uses.

Isothermal diagnostic assays for the detection of soil-transmitted helminths based on the SmartAmp2 method

Background

Diagnosis of soil-transmitted helminths (STHs) has traditionally relied on stool microscopy, which has a number of critical deficiencies. Molecular diagnostics are powerful tools to identify closely related species, but the requirement for costly equipment makes their implementation difficult in low-resource or field settings. Rapid, sensitive and cost-effective diagnostic tools are crucial for accurate estimation of STH infection intensity in MDA programmes in which the goal is to reduce morbidity following repeated rounds of chemotherapy.

Results

In this study, colourimetric isothermal assays were developed using SmartAmp2 primer sets and reagents in loop-mediated amplification (LAMP) assays. Species-specific primer sets, designed on a specific target sequence in the β-tubulin gene, were used to identify Necator americanus, Trichuris trichiura and Ascaris lumbricoides. After initial optimization on control plasmids and genomic DNA from adult worms, assays were evaluated on field samples. Assays showed high sensitivity and demonstrated high tolerance to inhibitors in spiked faecal samples. Rapid and sensitive colourimetric assays were successfully developed to identify the STHs in field samples using hydroxy napthol blue (HNB) dye.

Conclusions

Rapid and simple colourimetric diagnostic assays, using the SmartAmp2 method, were developed, with the potential to be applied in the field for detection of STH infections and the estimation of response to treatment. However, further validation on large numbers of field samples is needed.

Electronic supplementary material

The online version of this article (10.1186/s13071-017-2420-1) contains supplementary material, which is available to authorized users.