Application of Nanopore Sequencing in the Detection of Foodborne Microorganisms

Nanopore-based glycan sequencing: state of the art and future prospects

Sequencing of biomacromolecules is a crucial cornerstone in life sciences. Glycans, one of the fundamental biomolecules, derive their physiological and pathological functions from their structures. Glycan sequencing faces challenges due to its structural complexity and current detection technology limitations. As a highly sensitive sensor, nanopores can directly convert nucleic acid sequence information into electrical signals, spearheading the revolution of third-generation nucleic acid sequencing technologies. However, their potential for deciphering complex glycans remains untapped. Initial attempts demonstrated the significant sensitivity of nanopores in glycan sensing, which provided the theoretical basis and insights for the realization of nanopore-based glycan sequencing. Here, we present three potential technical routes to employ nanopore technology in glycan sequencing for the first time. The three novel technical routes include: strand sequencing, capturing glycan chains as they translocate through nanopores; sequential hydrolysis sequencing, capturing released monosaccharides one by one; splicing sequencing, mapping signals from hydrolyzed glycan fragments to an oligosaccharide database/library. Designing suitable nanopores, enzymes, and motors, and extracting characteristic signals pose major challenges, potentially aided by artificial intelligence. It would be highly desirable to design an all-in-one high-throughput glycan sequencer instrument by integrating a sample processing unit, nanopore array, and signal acquisition system into a microfluidic device. The nanopore sequencer invention calls for intensive multidisciplinary cooperation including electrochemistry, glycochemistry, engineering, materials, enzymology, etc. Advancing glycan sequencing will promote the development of basic research and facilitate the discovery of glycan-based drugs and disease markers, fostering progress in glycoscience and even life sciences.

Rapid and sensitive detection of Salmonella in agro-Food and environmental samples: A review of advances in rapid tests and biosensors

Salmonella is as an intracellular bacterium, causing many human fatalities when the host-specific serotypes reach the host gastrointestinal tract. Nontyphoidal Salmonella are responsible for numerous foodborne outbreaks and product recalls worldwide whereas typhoidal Salmonella are responsible for Typhoid fever cases in developing countries. Yet, Salmonella-related foodborne disease outbreaks through its food and water contaminations have urged the advancement of rapid and sensitive Salmonella-detecting methods for public health protection. While conventional detection methods are time-consuming and ineffective for monitoring foodstuffs with short shelf lives, advances in microbiology, molecular biology and biosensor methods have hastened the detection. Here, the review discusses Salmonella pathogenic mechanisms and its detection technology advancements (fundamental concepts, features, implementations, efficiency, benefits, limitations and prospects). The time-efficiency of each rapid test method is discussed in relation to their limit of detections (LODs) and time required from sample enrichment to final data analysis. Importantly, the matrix effects (LODs and sample enrichments) were compared within the methods to potentially speculate Salmonella detection from environmental, clinical or food matrices using certain techniques. Although biotechnological advancements have led to various time-efficient Salmonella-detecting techniques, one should consider the usage of sophisticated equipment to run the analysis by moderately to highly trained personnel. Ultimately, a fast, accurate Salmonella screening that is readily executed by untrained personnels from various matrices, is desired for public health procurement.

Nanopore sequencing technology and its applications

Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third-generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID-19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus-2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID-19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID-19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.

Unlocking the Power of Nanopores: Recent Advances in Biosensing Applications and Analog Front-End

The biomedical field has always fostered innovation and the development of various new technologies. Beginning in the last century, demand for picoampere-level current detection in biomedicine has increased, leading to continuous breakthroughs in biosensor technology. Among emerging biomedical sensing technologies, nanopore sensing has shown great potential. This paper reviews nanopore sensing applications, such as chiral molecules, DNA sequencing, and protein sequencing. However, the ionic current for different molecules differs significantly, and the detection bandwidths vary as well. Therefore, this article focuses on current sensing circuits, and introduces the latest design schemes and circuit structures of different feedback components of transimpedance amplifiers mainly used in nanopore DNA sequencing.

Recent Progress in Nanotechnology-Based Approaches for Food Monitoring

Throughout the food supply chain, including production, storage, and distribution, food can be contaminated by harmful chemicals and microorganisms, resulting in a severe threat to human health. In recent years, the rapid advancement and development of nanotechnology proposed revolutionary solutions to solve several problems in scientific and industrial areas, including food monitoring. Nanotechnology can be incorporated into chemical and biological sensors to improve analytical performance, such as response time, sensitivity, selectivity, reliability, and accuracy. Based on the characteristics of the contaminants and the detection methods, nanotechnology can be applied in different ways in order to improve conventional techniques. Nanomaterials such as nanoparticles, nanorods, nanosheets, nanocomposites, nanotubes, and nanowires provide various functions for the immobilization and labeling of contaminants in electrochemical and optical detection. This review summarizes the recent advances in nanotechnology for detecting chemical and biological contaminations in the food supply chain.

CRISPR-Cas systems mediated biosensing and applications in food safety detection

Food safety, closely related to economic development of food industry and public health, has become a global concern and gained increasing attention worldwide. Effective detection technology is of great importance to guarantee food safety. Although several classical detection methods have been developed, they have some limitations in portability, selectivity, and sensitivity. The emerging CRISPR-Cas systems, uniquely integrating target recognition specificity, signal transduction, and efficient signal amplification abilities, possess superior specificity and sensitivity, showing huge potential to address aforementioned challenges and develop next-generation techniques for food safety detection. In this review, we focus on recent progress of CRISPR-Cas mediated biosensing and their applications in food safety monitoring. The properties and principles of commonly used CRISPR-Cas systems are highlighted. Notably, the frequently coupled nucleic acid amplification strategies to enhance their selectivity and sensitivity, especially isothermal amplification methods, as well as various signal output modes are also systematically summarized. Meanwhile, the application of CRISPR-Cas systems-based biosensors in food safety detection including foodborne virus, foodborne bacteria, food fraud, genetically modified organisms (GMOs), toxins, heavy metal ions, antibiotic residues, and pesticide residues is comprehensively described. Furthermore, the current challenges and future prospects in this field are tentatively discussed.