Development and evaluation of a novel nucleic acid sequence-based amplification method using one specific primer and one degenerate primer for simultaneous detection of Salmonella Enteritidis and Salmonella Typhimurium

A review on nanomaterial-based SERS substrates for sustainable agriculture

The agricultural sector plays a pivotal role in driving the economy of many developing countries. Any dent in this economical structure may have a severe impact on a country's population. With rising climate change and increasing pollution, the agricultural sector is experiencing significant damage. Over time this cumulative damage will affect the integrity of food crops and create food security issues around the world. Therefore, an early warning system is needed to detect possible stress on food crops. Here we present a review of the recent developments in nanomaterial-based Surface Enhanced Raman Spectroscopy (SERS) substrates which could be utilized to monitor agricultural crop responses to natural and anthropogenic stress. Initially, our review delves into diverse and cost-effective strategies for fabricating SERS substrates, emphasizing their intelligent utilization across various agricultural scenarios. In the second phase of our review, we spotlight the specific application of SERS in addressing critical food security issues. By detecting nutrients, hormones, and effector molecules in plants, SERS provides valuable insights into plant health. Furthermore, our exploration extends to the detection of contaminants, chemicals, and foodborne pathogens within plants, showcasing the versatility of SERS in ensuring food safety. The cumulative knowledge derived from these discussions illustrates the transformative potential of SERS in bolstering the agricultural economy. By enhancing precision in nutrient management, monitoring plant health, and enabling rapid detection of harmful substances, SERS emerges as a pivotal tool in promoting sustainable and secure agricultural practices. Its integration into agricultural processes not only augments productivity but also establishes a robust defence against potential threats to crop yield and food quality. As SERS continues to evolve, its role in shaping the future of agriculture becomes increasingly pronounced, promising a paradigm shift in how we approach and address challenges in food production and safety.

Advances in microbial analysis: based on volatile organic compounds of microorganisms in food

In recent years, microbial volatile organic compounds (mVOCs) produced by microbial metabolism have attracted more and more attention because they can be used to detect food early contamination and flaws. So far, many analytical methods have been reported for the determination of mVOCs in food, but few integrated review articles discussing these methods are published. Consequently, mVOCs as indicators of food microbiological contamination and their generation mechanism including carbohydrate, amino acid, and fatty acid metabolism are introduced. Meanwhile, a detailed summary of the mVOCs sampling methods such as headspace, purge trap, solid phase microextraction, and needle trap is presented, and a systematic and critical review of the analytical methods (ion mobility spectrometry, electronic nose, biosensor, and so on) of mVOCs and their application in the detection of food microbial contamination is highlighted. Finally, the future concepts that can help improve the detection of food mVOCs are prospected.

Antimicrobial peptides: Promising alternatives over conventional capture ligands for biosensor-based detection of pathogenic bacteria

The detection of pathogenic bacteria using biosensing techniques could be a potential alternative to traditional culture based methods. However, the low specificity and sensitivity of conventional biosensors, critically related to the choice of bio-recognition elements, limit their practical applicability. Mammalian antibodies have been widely investigated as biorecognition ligands due to high specificity and technological advancement in antibody production. However, antibody-based biosensors are not considered as an efficient approach due to the batch-to-batch inconsistencies as well as low stability. In recent years, antimicrobial peptides (AMPs) have been increasingly investigated as ligands as they have demonstrated high stability and possessed multiple sites for capturing bacteria. The conjugation of chemo-selective groups with AMPs has allowed effective immobilization of peptides on biosensor surface. However, the specificity of AMPs is a major concern for consideration as an efficient ligand. In this article, we have reviewed the advances and concerns, particularly the selectivity of AMPs for specific detection of pathogenic bacteria. This review also focuses the state-of-the-art mechanisms, challenges and prospects for designing potential AMP conjugated biosensors. The application of AMP in different biosensing transducers such as electrochemical, optical and piezoelectric varieties has been widely discussed. We argue that this review would provide insights to design and construct AMP conjugated biosensors for the pathogenic bacteria detection.

Development of one-pot single specific primer-LAMP (SSP-LAMP) for identification of Shigella genus using 16S rDNA

Ribosomal RNA gene as a high-copy number nucleo-biomarker is extremely conserved among bacteria which limits its application to the discriminative detection approaches. We have developed a colorimetric isothermal amplification method called "single specific primer-LAMP (SSP-LAMP)" requiring only one specific primer for the amplification of the target and applied to the identification of the 16S rRNA gene in the Shigella genus. A region with high sequence homology in the genus and low homology with other bacteria was considered as the most appropriate. In that regard, a 23 bp sequence in the 16S rRNA gene of the genus was targeted based on the alignment of the gene with fifty-three closely related bacterial species, and a single specific primer along with five degenerate primers were designed. Using hydroxy-naphthol blue (HNB) as an indicator and gel electrophoresis, the proposed approach of SSP-LAMP was able to detect S. boydii, S. sonnei, S. flexneri and S. dysenteriae specifically while other species remained unidentified. The SSP-LAMP method could provide a rapid one-pot point-of-care method for molecular diagnostics of pathogens in many circumstances mainly samples with high genetic homogeneity.

The mechanism and improvements to the isothermal amplification of nucleic acids, at a glance

A comparative review of the most common isothermal methods is provided. In the last two decades, the challenge of using isothermal amplification systems as an alternate to the most extensive and long-standing nucleic acids-amplifying method-the polymerase chain reaction-has arisen. The main advantage of isothermal amplification is no requirement for expensive laboratory equipment for thermal cycling. Considerable efforts have been made to improve the current techniques of nucleic acid amplification and the development of new approaches based on the main drawbacks of each method. The most important and challenging goal was to achieve a low-cost, straightforward system that is rapid, specific, accurate, and sensitive.

COVID-19 Pandemic: Review of Contemporary and Forthcoming Detection Tools

Recent severe acute respiratory syndrome 2 (SARS-CoV-2) known as COVID-19, presents a deadly challenge to the global healthcare system of developing and developed countries, exposing the limitations of health facilities preparedness for emerging infectious disease pandemic. Opportune detection, confinement, and early treatment of infected cases present the first step in combating COVID-19. In this review, we elaborate on various COVID-19 diagnostic tools that are available or under investigation. Consequently, cell culture, followed by an indirect fluorescent antibody, is one of the most accurate methods for detecting SARS-CoV-2 infection. However, restrictions imposed by the regulatory authorities prevented its general use and implementation. Diagnosis via radiologic imaging and reverse transcriptase PCR assay is frequently employed, considered as standard procedures, whereas isothermal amplification methods are currently on the verge of clinical introduction. Notably, techniques such as CRISPR-Cas and microfluidics have added new dimensions to the SARS-CoV-2 diagnosis. Furthermore, commonly used immunoassays such as enzyme-linked immunosorbent assay (ELISA), lateral flow immunoassay (LFIA), neutralization assay, and the chemiluminescent assay can also be used for early detection and surveillance of SARS-CoV-2 infection. Finally, advancement in the next generation sequencing (NGS) and metagenomic analysis are smoothing the viral detection further in this global challenge.

Power of Scanning Electron Microscopy and Energy Dispersive X-Ray Analysis in Rapid Microbial Detection and Identification at the Single Cell Level

The demand for rapid, consistent and easy-to-use techniques for detecting and identifying pathogens in various areas, such as clinical diagnosis, the pharmaceutical industry, environmental science and food inspection, is very important. In this study, the reference strains of six food-borne pathogens, namely, Escherichia coli 0157: H7 ATCC 43890, Cronobacter sakazakii ATCC 29004, Salmonella Typhimurium ATCC 43971, Staphylococcus aureus KCCM 40050, Bacillus subtilis ATCC 14579, and Listeria monocytogenes ATCC 19115, were chosen for scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) analysis. In our study, the time-consuming sample preparation step for the microbial analysis under SEM was avoided, which makes this detection process notably rapid. Samples were loaded onto a 0.01-µm-thick silver (Ag) foil surface to avoid any charging effect. Two different excitation voltages, 10 kV and 5 kV, were used to determine the elemental information. Information obtained from SEM-EDX can distinguish individual single cells and detect viable and nonviable microorganisms. This work demonstrates that the combination of morphological and elemental information obtained from SEM-EDX analysis with the help of principal component analysis (PCA) enables the rapid identification of single microbial cells without following time-consuming microbiological cultivation methods.

Conjugated Oligo- and Polymers for Bacterial Sensing

Fast and accurate detection of bacteria and differentiation between pathogenic and commensal colonization are important keys in preventing the emergence and spread of bacterial resistance toward antibiotics. As bacteria undergo major lifestyle changes during colonization, bacterial sensing needs to be achieved on different levels. In this review, we describe how conjugated oligo- and polymers are used to detect bacterial colonization. We summarize how oligothiophene derivatives have been tailor-made for detection of biopolymers produced by a wide range of bacteria upon entering the biofilm lifestyle. We further describe how these findings are translated into diagnostic approaches for biofilm-related infections. Collectively, this provides an overview on how synthetic biorecognition elements can be used to produce fast and easy diagnostic tools and new methods for infection control.

Microdevice-based solid-phase polymerase chain reaction for rapid detection of pathogenic microorganisms

We demonstrate the integration of DNA amplification and detection functionalities developed on a lab-on-a-chip microdevice utilizing solid-phase polymerase chain reaction (SP-PCR) for point-of-need (PON) DNA analyses. First, the polycarbonate microdevice was fabricated by thermal bonding  to contain microchambers as reservoirs for performing SP-PCR. Next, the microchambers were subsequently modified with polyethyleneimine and glutaraldehyde for immobilizing amine-modified forward primers. During SP-PCR, the immobilized forward primers and freely diffusing fluorescence-labeled reverse primers cooperated to generate target amplicons, which remained covalently attached to the microchambers for the fluorescence detection. The SP-PCR microdevice was used for the direct identifications of two widely detected foodborne pathogens, namely Salmonella spp. and Staphylococcus aureus, and an alga causing harmful algal blooms annually in South Korea, Cochlodinium polykrikoides. The SP-PCR microdevice would be versatilely applied in PON testing as a universal platform for the fast identification of foodborne pathogens and environmentally threatening biogenic targets.

Advanced molecular diagnostic techniques for detection of food-borne pathogens: Current applications and future challenges

The elimination of disease-causing microbes from the food supply is a primary goal and this review deals with the overall techniques available for detection of food-borne pathogens. Now-a-days conventional methods are replaced by advanced methods like Biosensors, Nucleic Acid-based Tests (NAT), and different PCR-based techniques used in molecular biology to identify specific pathogens. Bacillus cereus, Staphylococcus aureus, Proteus vulgaris, Escherichia coli, Campylobacter, Listeria monocytogenes, Salmonella spp., Aspergillus spp., Fusarium spp., Penicillium spp., and pathogens are detected in contaminated food items that cause always diseases in human in any one or the other way. Identification of food-borne pathogens in a short period of time is still a challenge to the scientific field in general and food technology in particular. The low level of food contamination by major pathogens requires specific sensitive detection platforms and the present area of hot research looking forward to new nanomolecular techniques for nanomaterials, make them suitable for the development of assays with high sensitivity, response time, and portability. With the sound of these, we attempt to highlight a comprehensive overview about food-borne pathogen detection by rapid, sensitive, accurate, and cost affordable in situ analytical methods from conventional methods to recent molecular approaches for advanced food and microbiology research.

From research lab to standard environmental analysis tool: Will NASBA make the leap?

Nucleic acid sequence-based amplification (NASBA) is a sensitive and efficient molecular tool for amplification of RNA and has been widely adopted in clinical diagnostics. Monitoring of water and other environmental samples demands sensitive techniques, as potential pathogens may be in low concentrations and require only a few infectious units to infect their host. NASBA has qualities that should be advantageous for analysis of environmental samples, such as short reaction times, high sensitivity, and not readily affected by inhibitory substances that are often abundant in environmental samples. NASBA is well suited for incorporation into lab-on-a-chip (LOC) devices, as part of analysis systems that can be taken into the field for on-site screening. In this review, we explore advantages and drawbacks of NASBA as a tool for environmental analyses, and try to answer the question of whether it will be a recognised technique in the same manner as in clinical diagnostics.

Development and evaluation of enzyme-linked immunosorbent assay of nucleic acid sequence-based amplification for diagnosis of invasive aspergillosis

Invasive aspergillosis (IA) is a life-threatening infection in immunocompromised patients, rapid and sensitive detection of Aspergillus from clinical samples has been a major challenge in the early diagnosis of IA. An enzyme-linked immunosorbent assay of nucleic acid sequence-based amplification (NASBA-ELISA) was developed to fulfil the need for the efficient diagnosis of these infections. The primers targeting 18S rRNA were selected for the amplification of Aspergillus RNA by the isothermal digoxigenin (DIG)-labeling NASBA process. The DIG-labeled RNA amplicons were hybridized with a specific biotinylated DNA probe immobilized on streptavidin-coated microtiter plate. The hybrids were colorimetrically detected by the addition of an anti-DIG antibodies linked to ALP and substrate (disodium 4-nitrophenyl phosphate). The detection limit of the Aspergillus NABSA-ELISA system was 1 CFU and the RNA in non-target bacteria or fungus was not amplified. The performance of this NASBA-ELISA compared to RT-PCR and galactomannan (GM) was evaluated by testing blood samples from 86 patients at high risk for IA. The sensitivity of NASBA-ELISA, RT-PCR and GM-ELISA was 80.56 % (95 % CI 63.98-91.81), 72.22 % (95 % CI 54.81-85.80), 58.33 % (95 % CI 40.76-74.49), respectively, and the specificity was 80.00 % (95 % CI 66.28-89.97), 84.00 % (95 % CI 70.89-92.83), 82.00 % (95 % CI 68.56-91.42). The efficiency of the three methods in various combinations was also evaluated. Combination of NASBA-ELISA and GM-ELISA testing achieved perfect specificity (100 %; 95 % CI 92.89-100) and perfect positive predictive value (100 %; 95 % CI 83.16-100). The best sensitivity (97.22 %; 95 % CI 85.47-99.93) and the highest Youden index (0.652) were obtained by testing with both NASBA and RT-PCR in parallel. In conclusion, the NASBA-ELISA assay consists of an alternative process for large-scale samples detection with semi-quantitative results and provides good clinical performance without resorting to expensive equipment. This assay makes it possible for the NASBA based RNA diagnosis to become a routine work in laboratories in less developed countries with fewer resources.

Rapid methods for the detection of foodborne bacterial pathogens: principles, applications, advantages and limitations

The incidence of foodborne diseases has increased over the years and resulted in major public health problem globally. Foodborne pathogens can be found in various foods and it is important to detect foodborne pathogens to provide safe food supply and to prevent foodborne diseases. The conventional methods used to detect foodborne pathogen are time consuming and laborious. Hence, a variety of methods have been developed for rapid detection of foodborne pathogens as it is required in many food analyses. Rapid detection methods can be categorized into nucleic acid-based, biosensor-based and immunological-based methods. This review emphasizes on the principles and application of recent rapid methods for the detection of foodborne bacterial pathogens. Detection methods included are simple polymerase chain reaction (PCR), multiplex PCR, real-time PCR, nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP) and oligonucleotide DNA microarray which classified as nucleic acid-based methods; optical, electrochemical and mass-based biosensors which classified as biosensor-based methods; enzyme-linked immunosorbent assay (ELISA) and lateral flow immunoassay which classified as immunological-based methods. In general, rapid detection methods are generally time-efficient, sensitive, specific and labor-saving. The developments of rapid detection methods are vital in prevention and treatment of foodborne diseases.

Rapid methods for the detection of foodborne bacterial pathogens: principles, applications, advantages and limitations

The incidence of foodborne diseases has increased over the years and resulted in major public health problem globally. Foodborne pathogens can be found in various foods and it is important to detect foodborne pathogens to provide safe food supply and to prevent foodborne diseases. The conventional methods used to detect foodborne pathogen are time consuming and laborious. Hence, a variety of methods have been developed for rapid detection of foodborne pathogens as it is required in many food analyses. Rapid detection methods can be categorized into nucleic acid-based, biosensor-based and immunological-based methods. This review emphasizes on the principles and application of recent rapid methods for the detection of foodborne bacterial pathogens. Detection methods included are simple polymerase chain reaction (PCR), multiplex PCR, real-time PCR, nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP) and oligonucleotide DNA microarray which classified as nucleic acid-based methods; optical, electrochemical and mass-based biosensors which classified as biosensor-based methods; enzyme-linked immunosorbent assay (ELISA) and lateral flow immunoassay which classified as immunological-based methods. In general, rapid detection methods are generally time-efficient, sensitive, specific and labor-saving. The developments of rapid detection methods are vital in prevention and treatment of foodborne diseases.

Immuno-capture and in situ detection of Salmonella typhimurium on a novel microfluidic chip

The new method presented in this article achieved the goal of capturing Salmonella typhimurium via immunoreaction and rapid in situ detection of the CdSe/ZnS quantum dots (QDs) labeled S. typhimurium by self-assembly light-emitting diode-induced fluorescence detection (LIF) microsystem on a specially designed multichannel microfluidic chip. CdSe/ZnS QDs were used as fluorescent markers improving detection sensitivity. The microfluidic chip developed in this study was composed of 12 sample channels, 3 mixing zones, and 6 immune reaction zones, which also acted as fluorescence detection zones. QDs-IgG-primary antibody complexes were generated by mixing CdSe/ZnS QDs conjugated secondary antibody (QDs-IgG) and S. typhimurium antibody (primary antibody) in mixing zones. Then, the complexes went into immune reaction zones to label previously captured S. typhimurium in the sandwich mode. The capture rate of S. typhimurium in each detection zone was up to 70%. The enriched QDs-labeled S. typhimurium was detected using a self-assembly LIF microsystem. A good linear relationship was obtained in the range from 3.7×10 to 3.7×10(5) cfu mL(-1) using the equation I=0.1739 log (C)-0.1889 with R(2)=0.9907, and the detection limit was down to 37 cfu mL(-1). The proposed method of online immunolabeling with QDs for in situ fluorescence detection on the designed multichannel microfluidic chip had been successfully used to detect S. typhimurium in pork sample, and it has shown potential advantages in practice.