Basic Rules in Nucleic Acid-Mediated Amplification and Hybridization Methods in Food Safety Detection: A Review

BACKGROUND : Biosensing techniques have been the subject of exponentially increasing interest due to their performance advantages such as high selectivity and sensitivity, easy operation, low cost, short analysis time, simple sample preparation, and real-time detection. Biosensors have been developed by integrating the unique specificity of biological reactions and the high sensitivity of physical sensors. Therefore, there has been a broad scope of applications for biosensing techniques, and nowadays, they are ubiquitous in different areas of environmental, healthcare, and food safety. Biosensors have been used for environmental studies, detecting and quantifying pollutants in water, air, and soil. Biosensors also showed great potential for developing analytical tools with countless applications in diagnosing, preventing, and treating diseases, mainly by detecting biomarkers. Biosensors as a medical device can identify nucleic acids, proteins, peptides, metabolites, etc.; these analytes may be biomarkers associated with the disease status. Bacterial food contamination is considered a worldwide public health issue; biosensor-based analytical techniques can identify the presence or absence of pathogenic agents in food. OBJECTIVES: The present review aims to establish state-of-the-art, comprising the recent advances in the use of nucleic acid-based biosensors and their novel application for the detection of nucleic acids. Emphasis will be given to the performance characteristics, advantages, and challenges. Additionally, food safety applications of nucleic acid-based biosensors will be discussed. METHODS: Recent research articles related to nucleic acid-based biosensors, biosensors for detecting nucleic acids, biosensors and food safety, and biosensors in environmental monitoring were reviewed. Also, biosensing platforms associated with the clinical diagnosis and food industry were included. RESULTS: It is possible to appreciate that multiple applications of nucleic acid-based biosensors have been reported in the diagnosis, prevention, and treatment of diseases, as well as to identify foodborne pathogenic bacteria. The use of PNA and aptamers opens the possibility of developing new biometric tools with better analytical properties. CONCLUSIONS: Biosensors could be considered the most important tool for preventing, treating, and monitoring diseases that significantly impact human health. The aptamers have advantages as biorecognition elements due to the structural conformation, hybridization capacity, robustness, stability, and lower costs. It is necessary to implement biosensors in situ to identify analytes with high selectivity and lower detection limits.

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RAPID LISTERIA MONOCYTOGENES ASSAY BASED ON HELICASE DEPENDENT AMPLIFICATION (HDA) AND NUCLEIC ACID HYBRIDIZATION IN BLUE SILVER NANOPLATES

International Journal of Research -GRANTHAALAYAH ◽

10.29121/granthaalayah.v5.i10.2017.2308 ◽

2017 ◽

Vol 5 (10) ◽

pp. 322-335

Author(s):

Kankanit Pisamayarom ◽

Piyasak Chaumpluk

Keyword(s):

Listeria Monocytogenes ◽

Food Safety ◽

Nucleic Acid ◽

Foodborne Pathogen ◽

Health And Safety ◽

Nucleic Acid Hybridization ◽

Blue Color ◽

Monitoring Method ◽

Silver Nanoplates ◽

Laboratory Facilities

Listeria monocytogenes, a foodborne pathogen, is considered as one of the major problems in food safety. With strong safety regulations, a monitoring measure is essential for protecting the health and safety of consumers. Thus, a reliable monitoring method is required. In this study, a rapid assay based on a combination of helicase dependent amplification (HDA) and DNA signal detection via nucleic acid hybridization in blue silver nanoplates (AgNPls) was established. The assay started directly after short term enrichment in terrific broth using cotton ball swapping technique on seafood surface. A HDA amplification of hly gene of L. monocytogenes at 65 °C allowed DNA signals to be increased, whereas the rendered DNA products were detected via nucleic acid hybridization with an oligonucleotide probe in AgNPls solution. The positive specimens induced blue silver nanoplates’ aggregation resulting in pale gray change to colorless, while the negative specimens showed the blue color of non-aggregated nanoplates. The method had a detection limit at 100 copies of L. monocytogenes DNA per 50 g of sample. This method was rapid, simple, did not require laboratory facilities and was suitable for field food safety monitoring

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Functional Nucleic Acid Based Biosensors for Food Safety Detection

Functional Nucleic Acid Based Biosensors for Food Safety Detection ◽

10.1007/978-981-10-8219-1_1 ◽

2018 ◽

pp. 1-14 ◽

Cited By ~ 1

Author(s):

Yunbo Luo

Keyword(s):

Food Safety ◽

Nucleic Acid

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Barcoded microbial system for high-resolution object provenance

Science ◽

10.1126/science.aba5584 ◽

2020 ◽

Vol 368 (6495) ◽

pp. 1135-1140 ◽

Cited By ~ 4

Author(s):

Jason Qian ◽

Zhi-xiang Lu ◽

Christopher P. Mancuso ◽

Han-Ying Jhuang ◽

Rocío del Carmen Barajas-Ornelas ◽

...

Keyword(s):

Food Safety ◽

Nucleic Acid ◽

High Resolution ◽

Human Health ◽

Nucleic Acid Detection ◽

Single Spore ◽

Detection Assay ◽

Wide Range ◽

Fundamental Challenge ◽

Microbial System

Determining where an object has been is a fundamental challenge for human health, commerce, and food safety. Location-specific microbes in principle offer a cheap and sensitive way to determine object provenance. We created a synthetic, scalable microbial spore system that identifies object provenance in under 1 hour at meter-scale resolution and near single-spore sensitivity and can be safely introduced into and recovered from the environment. This system solves the key challenges in object provenance: persistence in the environment, scalability, rapid and facile decoding, and biocontainment. Our system is compatible with SHERLOCK, a Cas13a RNA-guided nucleic acid detection assay, facilitating its implementation in a wide range of applications.

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RPA-Cas12a-FS: A frontline nucleic acid rapid detection system for food safety based on CRISPR-Cas12a combined with recombinase polymerase amplification

Food Chemistry ◽

10.1016/j.foodchem.2020.127608 ◽

2021 ◽

Vol 334 ◽

pp. 127608

Author(s):

Hua Liu ◽

Jinbin Wang ◽

Haijuan Zeng ◽

Xiaofeng Liu ◽

Wei Jiang ◽

...

Keyword(s):

Food Safety ◽

Nucleic Acid ◽

Rapid Detection ◽

Detection System ◽

Recombinase Polymerase Amplification

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DNA extraction and host depletion methods significantly impact and potentially bias bacterial detection in a biological fluid

10.1101/2020.08.21.262337 ◽

2020 ◽

Author(s):

Erika Ganda ◽

Kristen L. Beck ◽

Niina Haiminen ◽

Ban Kawas ◽

Brittany Cronk ◽

...

Keyword(s):

Food Safety ◽

Nucleic Acid ◽

Nucleic Acids ◽

Biological Fluid ◽

Genetic Material ◽

Bovine Milk ◽

Extraction Methods ◽

Acid Extraction ◽

Primary Material ◽

The Impact

ABSTRACTAbstractUntargeted sequencing of nucleic acids present in food can inform the detection of food safety and origin, as well as product tampering and mislabeling issues. The application of such technologies to food analysis could reveal valuable insights that are simply unobtainable by targeted testing, leading to the efforts of applying such technologies in the food industry. However, before these approaches can be applied, it is imperative to verify that the most appropriate methods are used at every step of the process: gathering primary material, laboratory methods, data analysis, and interpretation.The focus of this study is in gathering the primary material, in this case, DNA. We used bovine milk as a model to 1) evaluate commercially available kits for their ability to extract nucleic acids from inoculated bovine milk; 2) evaluate host DNA depletion methods for use with milk, and 3) develop and evaluate a selective lysis-PMA based protocol for host DNA depletion in milk.Our results suggest that magnetic-based nucleic acid extraction methods are best for nucleic acid isolation of bovine milk. Removal of host DNA remains a challenge for untargeted sequencing of milk, highlighting that the individual matrix characteristics should always be considered in food testing. Some reported methods introduce bias against specific types of microbes, which may be particularly problematic in food safety where the detection of Gram-negative pathogens and indicators is essential. Continuous efforts are needed to develop and validate new approaches for untargeted metagenomics in samples with large amounts of DNA from a single host.ImportanceTracking the bacterial communities present in our food has the potential to inform food safety and product origin. To do so, the entire genetic material present in a sample is extracted using chemical methods or commercially available kits and sequenced using next-generation platforms to provide a snapshot of what the relative composition looks like. Because the genetic material of higher organisms present in food (e.g., cow in milk or beef, wheat in flour) is around one thousand times larger than the bacterial content, challenges exist in gathering the information of interest. Additionally, specific bacterial characteristics can make them easier or harder to detect, adding another layer of complexity to this issue. In this study, we demonstrate the impact of using different methods in the ability of detecting specific bacteria and highlight the need to ensure that the most appropriate methods are being used for each particular sample.

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Padlock Probe-based Rolling Circle Amplification Lateral Flow Assay for Point-of-Need Nucleic Acid Detection

The Analyst ◽

10.1039/d1an00399b ◽

2021 ◽

Author(s):

Sidhartha Jain ◽

David S. Dandy ◽

Brian Geiss ◽

Charles Henry

Keyword(s):

Food Safety ◽

Nucleic Acid ◽

Environmental Monitoring ◽

Rolling Circle Amplification ◽

Cost Effective ◽

Clinical Diagnostics ◽

Nucleic Acid Amplification ◽

Nucleic Acid Detection ◽

Padlock Probe ◽

Rolling Circle

Sensitive, reliable and cost-effective detection of pathogens has wide ranging applications in clinical diagnostics and therapeutics, water and food safety, environmental monitoring, biosafety and epidemiology. Nucleic acid amplification tests (NAATs)...

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