Methods for detection of viable foodborne pathogens: current state-of-art and future prospects

CRISPR/Cas12a-mediated cyclic signal amplification and electrochemical reporting strategy for rapid and accurate sensing of Vibrio parahaemolyticus in aquatic foods

Rapid and accurate detection of target foodborne pathogenic bacteria is extremely important for preventing and controlling foodborne diseases. Vibrio parahaemolyticus (V. parahaemolyticus, Vp) is considered as a major cause of foodborne diseases, posing severe threat to food safety and public health. The efficiency and sensitivity of traditional protocols for Vp identification is time consuming and of poor precision. In this research, a simple electrochemical sensing method was developed for accurate detection of Vp in aquatic products. Target genes of Vp were rapid amplified with the designed recombinase polymerase amplification, which further activated the designed CRISPR/Cas12a system. The electrochemical active ssDNA probe on the sensing interface would be hydrolyzed by the activated trans-cleavage activity of Cas12a, inducing the release of active electrochemical tags from the sensing interface and the decreased sensing signals. Under the optimized conditions, this proposed RPA-mediated electrochemical-CRISPR (E-CRISPR) biosensor enabled sensitive detection of target Vp over a linear range from 101 to 106 CFU/mL, with limit of detection of 32 CFU/mL. Additionally, this E-CRISPR biosensor realized the successful determination of Vp in spiked fish samples with satisfied sensing performance. The isothermal amplification and the rapid electrochemical response of the E-CRISPR biosensor made it suitable for on-site screening. And this E-CRISPR biosensor could be well integrated with other isothermal protocols and extended to other target pathogens, showing great potential for practical applications in molecular diagnostics and other gene detection related fields.

Poly-L-lysine functionalized silica membrane-enhanced colorimetric loop-mediated isothermal amplification for sensitive and rapid detection of Vibrio parahaemolyticus

Traditional detection of foodborne pathogen relies on advanced analyzers, which is inadequate for the rapid control of infections, particularly in resource-limited regions, highlighting the necessity of developing detection systems for point-of-care testing (POCT). Herein, taking Vibrio parahaemolyticus as a detecting target, we reported poly-L-lysine functionalized silica membrane (PL-SM) based loop-mediated isothermal amplification (pLAMP) platform for sensitive on-site detection. This platform utilized PL-SM for DNA capture driven by the electrostatic attraction between protonated amine groups of poly-L-lysine and negatively charged phosphate groups of DNA, followed by introducing a colorimetric indicator calcein for LAMP amplification. After optimization, the colorimetric mode of pLAMP allowed the screening of V. parahaemolyticus with the visual limit of detection (vLOD) of 1 CFU/mL in 50 min, 1000-fold lower than methods based on commercial kits. Validation was performed using 174 seafoods, which was 97 % concordant to those of real-time PCR. Furthermore, an image processing approach was developed based on the analysis of the RGB under UV light. Paired with a smartphone, the objective analytical method could be readily conducted in the field. Thus, we propose a sensitive and visual detection platform, which may play a crucial role in improving testing efficiency and accuracy in food safety, medical diagnostics, and environmental monitoring.

Real-time Detection of Foodborne Pathogens and Biofilm in the Food Processing Environment with Bactiscan, A Macro-scale Fluorescence Device

Food safety relies on rapid detection methods and rigorous sampling of the food processing environment and is challenged by recurrent biofilm contamination and by sublethally injured bacteria that can evade detection. Bactiscan is investigated as an alternative detection approach, a macro-scale and reagentless device that detects microbial contamination through activating the green fluorescence of glycoproteins in the bacterial cell wall. The detection capability of Bactiscan was tested on foodborne pathogens Escherichia coli, Listeria monocytogenes, Salmonella enterica, and Staphylococcus aureus. Detection by Bactiscan was assessed using 3 independent observers viewing bacterial samples dried on stainless steel, using 3 biological repeats and 5 technical repeats. Detection by Bactiscan was possible to 1.20 * 106 colony forming units (CFU), compared to 1.36 * 104 CFU by ATP swab testing, where Bactiscan detection limits were defined by the concentration at which 50% of the samples were observed under illumination of the device. Heat-killed and chlorine-stressed E. coli and S. enterica caused a 2-log reduction in detection by ATP swab tests (p ≤ 0.05), while detection by Bactiscan was unaffected (p ≥ 0.05). Pathogen biofilms were detectable via Bactiscan with >80% accuracy at 4 days of growth; E. coli and L. monocytogenes biofilms were visible at 2 days of growth. In situ contamination studies determined that Bactiscan can detect microbial contamination on chicken, salmon, and yoghurt samples with stronger fluorescence than a competitor's UV torch. The presence of one of the pathogens on the food samples was confirmed by metagenome sequencing, determining that S. aureus was present in 7 samples out of 9 with a relative abundance of >0.5%. These data demonstrate that Bactiscan can effectively detect bacteria present in the food processing environment and can complement existing technologies to improve food industry cleaning practices and infection prevention.

Preamplification-Free Detection of Viable Microorganisms in Fermentation Using Tandem CRISPR Nuclease Probe

Accurate detection of viable bacteria is crucial for evaluating and monitoring the fermentation process. However, the complexity of fermentation samples presents challenges to developing precise and rapid detection tools. Here, we present a Cas13a-Csm6 tandem nuclease probe capable of the one-pot detection of viable microorganisms during fermentation, eliminating the need for nucleic acid preamplification. The RNA-activated CRISPR-Cas13a generates cleavage substrates that serve as activators for the CRISPR/Cas III-A Csm6 system. Leveraging the high specificity and efficient amplification capacity of the CRISPR cascade, this nuclease probe can detect 1% of viable Lactobacillus and Bacillus, facilitating the monitoring of bacterial populations throughout fermentation. This approach completes detection within 30 min and improves sensitivity for bacterial profiling by 16-fold compared with using Cas13 alone. The Cas13a-Csm6 tandem nuclease probe offers a precise and rapid analytical tool for the on-site quality monitoring of fermented foods.

Pathogen and Spoilage Microorganisms in Meat and Dairy Analogues: Occurrence and Control Strategies

Recent advances in the production of meat and dairy analogues and plant-based products have introduced new food safety challenges, as these foods are susceptible to contamination by both pathogens and spoilage microorganisms originating from raw materials and processing environments. In addition, plant-based analogues often exhibit physicochemical properties such as high water activity, near-neutral pH, and elevated protein and moisture content that favour the survival and growth of microorganisms, as evidenced by the detection of Salmonella sp., Listeria monocytogenes, and Enterobacteriaceae in commercial products. While extrusion and thermal processing effectively reduce microbial loads, these treatments may not inactivate all spores, including spore-forming bacteria like Bacillus cereus and Clostridium spp. Critical findings seem to highlight that some protein isolates are particularly prone to higher microbial contamination, and that outbreaks linked to pathogens such as Salmonella, L. monocytogenes, and E. coli have already occurred in plant-based analogues in Europe and North America. Here we discuss the microbiology and sources of microbial contamination of these products. In addition, we further discuss the integration of non-thermal technologies and biocontrol methods, such as protective cultures, bacteriocins, and bacteriophages, as promising approaches to enhance food safety while addressing clean-label demands.

Rapid and broad-spectrum detection of salmonella in various environments by magnetic enrichment-surface enhanced Raman spectroscopy

Rapid, accurate, and broad-spectrum detection of pathogenic bacteria in food is very important and an emerging need for increasing food safety concerns. Here, we present an ultrasensitive Surface-enhanced Raman spectroscopy (SERS) based aptasensor, which consists of core-shell structure (Ag@Au) and magnetic composites (Fe3O4@Au@Ag). 4-mercaptobenzoic acid (4MBA) as Raman reporter was embedded in Ag@Au nanoparticles (Ag@4MBA@Au) based on an internal standard. The combination of Ag@4MBA@Au and Fe3O4@Au@Ag are used to form the aptasensor with strongest Raman signal. Upon exposure to salmonella, the interaction between the SERS nanotags and the magnetic substrate was disrupted, causing an inverse correlation between the Raman intensity of 4MBA and the salmonella concentration. The result shows a wide linear range from 10 to 108 cfu/mL with five subtypes salmonella (S. Typhimurium, S. Enteritidis, S. Kentucky, S. Indiana, S. NO) and a low limit of detection of 1.782, 1.637, 1.941, 1.632, 1.875 cfu/mL, respectively. When applied to the detection of salmonella in actual samples (lake water, milk, shrimp), no pretreatment is required, and the results show no significant difference compared to the standard.

Application of Bioinformatics and Machine Learning Tools in Food Safety

PURPOSE OF REVIEW

Food safety is a fundamental challenge in public health and sustainable development, facing threats from microbial, chemical, and physical contamination. Innovative technologies improve our capacity to detect contamination early and prevent disease outbreaks, while also optimizing food production and distribution processes.

RECENT FINDINGS

This article discusses the role of new bioinformatics and machine learning technologies in promoting food safety and contamination control, along with various related articles in this field. By analyzing genetic and proteomic data, bioinformatics helps to quickly and accurately identify pathogens and sources of contamination. Machine learning, as a powerful tool for massive data processing, also can discover hidden patterns in the food production and distribution chain, which helps to improve risk prediction and control processes. By reviewing previous research and providing new solutions, this article emphasizes the role of these technologies in identifying, preventing, and improving decisions related to food safety. This study comprehensively shows how the integration of bioinformatics and machine learning can help improve food quality and safety and prevent foodborne disease outbreaks.

Molecular methods for rapid detection and identification of foodborne pathogenic bacteria

Foodborne pathogenic bacteria are one of the main factors causing food safety issues. The rapid and accurate detection of pathogenic bacteria using molecular techniques is an effective and powerful strategy for preventing and controlling outbreaks of foodborne diseases, thereby ensuring food safety. This article summarizes the rapid and efficient molecular diagnostic techniques for detecting pathogenic bacteria, including polymerase chain reaction and its derivatives, isothermal amplification, DNA hybridization, genomic sequencing, and Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPR-associated (CRISPR/Cas)-based detection technique. Through a comparative analysis of the technical principles, advantages, and potential limitations of these diagnostic methods, as well as an outlook on the future development directions for molecular biological detection technology, which will provide a valuable reference for developing more accurate, convenient, and sensitive methods for foodborne pathogens detection, and will help better address the challenges posed by foodborne diseases, thereby ensuring public health and safety.

Effect of Citric Acid on Viability, Membrane Damage, Efflux Pump Activity, and Growth Recovery of Vibrio alginolyticus and Vibrio cholerae Strains

Citric acid, a common food ingredient, can induce cellular stress in foodborne pathogens, potentially affecting their viability and recovery. This study evaluated the physiological responses of Vibrio alginolyticus and Vibrio cholerae cells in logarithmic and stationary growth phases after exposure to citric acid at pH 4.5, 5.0, and 5.5 for 60, 120, and 180 min. After exposure, viability, membrane damage, efflux pump activity, and recovery were evaluated. Culture media type and growth phase had no significant effect on cell viability (p > 0.05). V. cholerae strains were more sensitive to citric acid than V. alginolyticus strains, with a slight reduction (0.5 log CFU/mL) after 180 min of citric acid exposure (p < 0.05). Membrane damage was greater in stationary-phase cells than in logarithmic-phase cells after 60 min, whereas efflux pump activity increased over time and was independent of the growth phase (p < 0.05). Regardless of pH, cells exposed to citric acid for 60 min had longer detection times (7.92 ± 0.7 h) compared to those exposed for 180 min (6.68 ± 1.45 h), and cells grew faster at high pH values and at lower exposure time (p < 0.05). Overall, citric acid induced mild sublethal damage in both V. alginolyticus and V. cholerae, with cell recovery primarily attributed to efflux pump activity. These results provide valuable insights into the risk associated with Vibrio cells under mild citric acid stress, a condition similar to that occurring during the preparation of raw fish dishes marinated in lemon juice.

CRISPR revolution: Unleashing precision pathogen detection to safeguard public health and food safety

Foodborne pathogens represent a significant challenge to global food safety, causing widespread illnesses and economic losses. The growing complexity of food supply chains and the emergence of antimicrobial resistance necessitate rapid, sensitive, and portable diagnostic tools. CRISPR technology has emerged as a transformative solution, offering unparalleled precision and adaptability in pathogen detection. This review explores CRISPR's role in addressing critical gaps in traditional and modern diagnostic methods, emphasizing its advantages in sensitivity, specificity, and scalability. CRISPR-based diagnostics, such as Cas12 and Cas13 systems, enable rapid detection of bacterial and viral pathogens, as well as toxins and chemical hazards, directly in food matrices. Their integration with isothermal amplification techniques and portable biosensors enhances field applicability, making them ideal for decentralized and real-time testing. Additionally, CRISPR's potential extends beyond food safety, contributing to public health efforts by monitoring antimicrobial resistance and supporting One Health frameworks. Despite these advancements, challenges remain, including issues with performance in complex food matrices, scalability, and regulatory barriers. This review highlights future directions, including AI integration for assay optimization, the development of universal CRISPR platforms, and the adoption of sustainable diagnostic solutions. By tackling these challenges, CRISPR has the potential to redefine global food safety standards and create a more resilient food system. Collaborative research and innovation will be critical to fully unlocking its transformative potential in food safety and public health.

Advances in whole genome sequencing for foodborne pathogens: implications for clinical infectious disease surveillance and public health

Foodborne outbreaks affecting millions of people worldwide are a significant and growing global health threat, exacerbated by the emergence of new and increasingly virulent foodborne pathogens. Traditional methods of detecting these outbreaks, including culture-based techniques, serotyping and molecular methods such as real-time PCR, are still widely used. However, these approaches often lack the precision and resolution required to definitively trace the source of an outbreak and distinguish between closely related strains of pathogens. Whole genome sequencing (WGS) has emerged as a revolutionary tool in outbreak investigations, providing high-resolution, comprehensive genetic data that allows accurate species identification and strain differentiation. WGS also facilitates the detection of virulence and antimicrobial resistance (AMR) genes, providing critical insight into the potential pathogenicity, treatment/control options and risks of spreading foodborne pathogens. This capability enhances outbreak surveillance, source tracing and risk assessment, making WGS an increasingly integrated component of public health surveillance systems. Despite its advantages, the widespread implementation of WGS faces several pressing challenges, including high sequencing costs, the need for specialized bioinformatics expertise, limited computational infrastructure in resource-constrained settings, and the standardization of data-sharing frameworks across regulatory and public health agencies. Addressing these barriers is crucial to maximizing the impact of WGS on foodborne disease surveillance. Even so, WGS is emerging as a vital tool in food safety and public health, and its potential to become the gold standard in outbreak detection has been recognized by public health authorities in the USA, the European Union, Australia and China, for example. This review highlights the role of WGS in foodborne outbreak investigations, its implementation challenges, and its impact on public health surveillance.

Development of real-time PCR methods for quality control detection of pathogenic bacteria in cosmetic preparations

Introduction

The preservation of microbial safety in cosmetic products is essential for consumer health and requires rapid and accurate detection strategies… Traditional detection methods, such as quantitative and qualitative tests, are effective but often time-consuming and labor-intensive. Moreover, plate count methods fail to detect viable but non-cultivable cells, which remain alive but cannot grow under standard laboratory conditions. To address these limitations, molecular techniques like PCR, particularly real-time PCR (rt-PCR), multiplex rt-PCR, and viability PCR assays, as well as flow cytometry, have enhanced microbiological analysis by improving detection sensitivity, accuracy, and enabling rapid pathogen identification. ISO standards offer guidelines for reliable and consistent microbial detection methods, to guarantee the effectiveness of traditional and molecular techniques in food and cosmetic safety testing.

Methods

This study evaluates real-time PCR (rt-PCR) as an alternative to the traditional plate-based method for the detection of Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans in cosmetic formulations.

Results and discussion

rt-PCR consistently demonstrated superior sensitivity and reliability, particularly in detecting pathogens at low inoculum levels and within complex matrices. For all pathogens, rt-PCR achieved a 100% detection rate across all replicates, reaching the same or superior results than the classical plate method. rt-PCR's ability to directly target DNA overcomes issues related to colony morphology and microbial competition. The study highlights the necessity of standardized rt-PCR protocols aligned with international ISO guidelines to enhance its applicability in routine quality control programs. In conclusion, rt-PCR represents a significant advancement in microbial safety for food and cosmetics, offering a rapid, sensitive, and reliable alternative to conventional methods. By integrating enrichment strategies, rt-PCR ensures higher accuracy in pathogen detection, reinforcing product safety and regulatory compliance in the cosmetics industry.

Aggregative Sampling Performs Similar to Composite Produce Samples to Recover Quality and Safety Indicators Throughout Romaine Lettuce Production

Aggregative sampling using polymer cloth swabs is a nondestructive, potentially more representative food safety sampling alternative for leafy greens. This study compared aggregative and produce tissue grab sampling to recover aerobic bacteria, total coliforms, and generic Escherichia coli, from commercial romaine grown in 120 m fields, with 5-36 samples at various stages. Aggregative swabs and grab samples were collected preharvest. During harvest, aggregative swabs were collected from romaine exiting the harvester chute, transport bin tops, and as gloves worn by harvesters. Romaine grabs were collected from transport bin tops and trim leftover on the ground. During postharvest, gloves, swabs, and grabs were collected from romaine exteriors, and swabs and grabs from head interiors. In preharvest, swabs had 1.2 log(CFU/g) higher means of aerobic bacteria than romaine tissue grab samples (p < 0.001), but 1.7 log(CFU/g) lower coliforms (p < 0.001). In-harvest, aerobic bacteria means from gloves worn by harvesters and swabs from harvester chute were 0.5 log(CFU/g) higher than romaine samples from leftover trims (p < 0.001) and bin tops (p = 0.01), respectively. Coliform recovery means from gloves was not significantly different from romaine leftover trims (p = 0.99). Swabs from harvester chute and bin tops recovered 1.6 and 1.4 log(CFU/g) lower coliforms means (p < 0.001) than romaine from bin tops, respectively. Generic E. coli was only recovered from one romaine leftover trim grab sample. During postharvest processing, aerobic bacteria (p = 0.25) and total coliforms (p = 0.16) recovery from the exterior of heads was not significantly different between gloves and romaine samples, nor was aerobic bacteria (p = 0.17) and total coliform (p = 0.86) recovery from head interiors. These results suggest that aggregative sampling performs similar to produce grab sampling to recover quality and safety indicators and justifies testing these methods for pathogen sampling in leafy greens.

Morphological and autofluorescence assessment of oocysts differentiate live from dead coccidian parasites

To assess and mitigate foodborne risk, regulatory agencies and produce growers require the means not merely to detect but moreover determine the viability of foodborne eukaryotic pathogens such as Cyclospora cayetanensis. Viability assessment would also aid those employing live attenuated vaccines against coccidiosis, a major problem in poultry production. Therefore, we sought to identify morphological changes differentiating viable from non-viable coccidian oocysts, employing Eimeria acervulina as a tractable model, enabling empirical validation by means of in vivo challenge infections in the natural chicken host. High resolution microscopic examinations identified granular structures that autofluoresce under UV exposure in dead oocysts, greatly intensifying overall autofluorescence in dead oocysts. We harnessed this intensification as a basis to sort live from dead oocysts using a Fluorescence-Activated Cell Sorting (FACS) cell sorter, validating their distinction by documenting infectivity in chickens using the former, and minimal shedding with the latter. Our rapid, sensitive, and robust assay holds promise for application to other species of coccidia, including those important to livestock and public health.

Emerging Initiated Chemical Vapor Deposition Nanocoatings for Sustainable Food and Agriculture

Initiated chemical vapor deposition (iCVD) has emerged as a versatile technique for developing functional nanocoatings that address critical food and agricultural challenges. This review highlights the unique capacities of iCVD nanocoatings, which enable precise engineering of surface properties, such as targeted cellular and molecular interactions, antimicrobial activity, and fouling resistance. In addition, the solvent-free nature of iCVD is particularly advantageous for coating sensitive materials and complex geometries commonly used across food and agriculture applications. This review provides an overview of iCVD's chemistry, deposition mechanisms, and ability to control nanocoating morphology and composition. Key applications discussed include iCVD nanocoatings for food quality monitoring, pathogen detection, antimicrobial food packaging, biomass extraction, and irrigation water purification. By summarizing recent advancements and identifying emerging trends, this review showcases the potential of iCVD as a powerful tool for developing sustainable, nanoenabled solutions in modern food and agriculture production.

Development and Characterization of a Polyvalent Polyclonal Antibody as a Common Capture Antibody for the Detection of Enterotoxigenic Escherichia coli in a Sandwich ELISA

Due to its low cost and simplicity, the sandwich enzyme-linked immunosorbent assay (sELISA) is a traditional technique for identifying foodborne pathogens. However, most sELISAs are designed for single foodborne pathogen detection using two specific antibodies, which capture and detect the target bacteria. This study aimed to produce and characterize a common capture polyclonal antibody for Enterotoxigenic Escherichia coli (ETEC), Salmonella Typhimurium, and Shigella flexneri (S. flexneri) by a sELISA. Rabbit polyclonal antibodies (pAbs) were generated against recombinant proteins of CsgA, FhuA, and OmpA, which we called anti-mix. The recombinant proteins generated are conserved in Escherichia coli (E. coli), Salmonella enterica serovar Typhimurium, and S. flexneri species, but not in Listeria monocytogenes (L. monocytogenes) and Enterococcus faecalis (E. faecalis). The anti-mix serum gave a title higher than 1:32,000 by an indirect ELISA using purified recombinant proteins and whole bacteria cultures of the bacteria expressing the antigens but failed to recognize L. monocytogenes and E. faecalis. In addition, a recombinant protein A was purified and used to orient the capture antibodies (anti-mix) in the sELISA. However, no statistically significant difference was found in the assay sensitivity for ETEC detection in spiked milk samples with or without protein A. The assay linearity of sELISA for ETEC detection in Phosphate-buffered saline (PBS) was from 1 × 108 to 1 × 104 cells/mL, and for spiked milk samples was 1 × 108 to 1 × 105 cells/mL. In spiked milk samples, the detection limit of ETEC was lower than PBS, which suggests a negative effect from the matrix analyzed (milk) compared to PBS.

Nutritional Stress Leads to Persistence and Persister-like Growth in Staphylococcus aureus

Staphylococcus aureus is a versatile zoonotic pathogen capable of causing a wide range of infections. Due to the organism's ability to persist, recalcitrant and recurring infections are a major concern for public and animal health. This study investigated the establishment of persistence using two S. aureus strains-ATCC 29740, a bovine mastitis isolate, and USA300, a human clinical isolate-under substrate depletion. This nutritional stress established a persistence phenotype where the strains remained persistent for >120 days at notable concentrations [>2 log10 CFU/mL] and developed persister-like growth, including small colony variant formations. With RT-qPCR, we found the cell density was higher than represented by the plate count while the intracellular ATP remained constant during the persistence phase. These findings indicate that S. aureus has complex survival strategies to support its persistent state, providing a host-specific perspective when addressing recurrent infections in human and animal infectious diseases.

Review of the detection of pathogenic Escherichia coli based-microchip technology

Escherichia coli (E. coli) is a pathogen that has generated global concern due to the public health challenges it has created. Therefore, the rapid and accurate detection of E. coli is important to public health safety. Microchips have become a popular analytical technique for detecting E. coli due to their automation, high analytical efficiency, and low analyte consumption. Therefore, this paper highlights multiple microchip-based strategies for the detection of E. coli, reviews their limitations, and provides strategies and future perspectives for analyzing E. coli..

Recent developments in waterborne pathogen detection technologies

Waterborne pathogens find their way into water bodies through contamination of fecal discharge, stormwater run-offs, agriculture and industrial activities, and poor water infrastructure. These organisms are responsible for causing diarrheal, gastroenteritis, cholera, and typhoid diseases which raise an alarming sense on public human health due to the high mortality rate, especially in children. Several studies have indicated that these waterborne diseases can be managed by monitoring pathogens in water using traditional culture-based and molecular techniques. However, these methods have shown several setbacks such as the longer duration for detection and the inability to detect pathogens at low concentrations. Effective management of these diseases requires rapid, sensitive, highly selective, fast, and efficient economic methods to monitor pathogens in water. Since the creation of biosensors, these tools have been applied and shown the ability to detect pathogens at low concentrations. The highlights of biosensor systems are that they are fast, portable, easy to use, highly sensitive, and specific. The capabilities of biosensors have given these tools exposure to be widely applied in detecting pharmaceutical pollutants, pesticides, toxins, residues of detergents, and cosmetics from household activities in soil and water. With such difficulties faced for detecting waterborne pathogens, this review evaluates the effectiveness of technologies for waterborne pathogens detection and their drawbacks. It further highlights biosensors as the current reliable method available for detecting pathogens in water and its future capabilities in sustaining safe potable water.

Inhibitory Effects of Nisin and Gallium (III) Nitrate Hydrate on Planktonic and Adhered Cells and Implications for the Viable but Non-Culturable State

Effective antimicrobial and biofilm control strategies require an understanding of the differential effects of antimicrobial agents on the viability and culturability of microbial cells. A viable but non-culturable (VBNC) state, a survival strategy of non-spore-forming bacteria in response to adverse conditions, poses a significant challenge for public health and food safety. In the present study, we investigated the antimicrobial and antibiofilm effects of nisin and gallium (III) nitrate hydrate against the Gram-positive strain Lactiplantibacillus plantarum subsp. plantarum DSM 20174 and the Gram-negative strain Pseudomonas fluorescens ATCC 13525, respectively. Both strains were chosen as model systems for their relevance to food and clinical settings. Culture-based methods and flow cytometry (FCM) were used to evaluate the culturability and viability of both planktonic and sessile cells, providing insights into their physiological response to antimicrobial treatment-induced stress at different concentrations (100, 250, 350, and 500 ppm). The findings highlight the strain-specific action of nisin on L. plantarum and the promising antibiofilm effects of Ga (III) against P. fluorescens. This study underscores the promising potential of FCM as a powerful tool for high-throughput analyses of antimicrobial efficacy, providing valuable insights into developing targeted biofilm control strategies for food safety and clinical applications.

Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce

Foodborne illnesses pose a significant global health threat, often caused by pathogens like Escherichia coli, Listeria monocytogenes, and Salmonella spp. The emergence of antibiotic-resistant strains further exacerbates food safety challenges. This study combines shotgun metagenomics and culture-based approaches to detect foodborne pathogens and antimicrobial resistance genes (ARGs) in Malaysian produce and meats from the Kinta Valley region. A total of 27 samples comprising vegetables, meats, and fruits were analyzed. Metagenomics provided comprehensive microbial profiles, revealing diverse bacterial communities with species-level taxonomic resolution. Culture-based methods complemented these findings by identifying viable pathogens. Key foodborne pathogens were detected, with Listeria monocytogenes identified in meats and vegetables and Shigella flexneri detected inconsistently between the methods. ARGs analysis highlighted significant resistance to cephalosporins and penams, particularly in raw chicken and vegetable samples, underscoring the potential public health risks. While deli meats and fruits exhibited a lower antimicrobial resistance prevalence, resistant genes linked to E. coli and Salmonella strains were identified. Discrepancies between the methods suggest the need for integrated approaches to improve the pathogen detection accuracy. This study demonstrates the potential of metagenomics in advancing food safety research and supports its adoption as a complementary tool alongside culture-based methods for comprehensive foodborne pathogen surveillance and ARG profiling in Malaysian food systems.

Aptamer and DNAzyme Based Colorimetric Biosensors for Pathogen Detection

The detection of pathogens is critical for preventing and controlling health hazards across clinical, environmental, and food safety sectors. Functional nucleic acids (FNAs), such as aptamers and DNAzymes, have emerged as versatile molecular tools for pathogen detection due to their high specificity and affinity. This review focuses on the in vitro selection of FNAs for pathogens, with emphasis on the selection of aptamers for specific biomarkers and intact pathogens, including bacteria and viruses. Additionally, the selection of DNAzymes for bacterial detection is discussed. The integration of these FNAs into colorimetric biosensors has enabled the development of simple, cost-effective diagnostic platforms. Both non-catalytic and catalytic colorimetric biosensors are explored, including those based on gold nanoparticles, polydiacetylenes, protein enzymes, G-quadruplexes, and nanozymes. These biosensors offer visible detection through color changes, making them ideal for point-of-care diagnostics. The review concludes by highlighting current challenges and future perspectives for advancing FNA-based colorimetric biosensing technologies for pathogen detection.

Detection of Viable but Nonculturable E. coli Induced by Low-Level Antimicrobials Using AI-Enabled Hyperspectral Microscopy

Rapid detection of bacterial pathogens is essential for food safety and public health, yet bacteria can evade detection by entering a viable but nonculturable (VBNC) state under sublethal stress, such as antimicrobial residues. These bacteria remain active but undetectable by standard culture-based methods without extensive enrichment, necessitating advanced detection methods. This study developed an AI-enabled hyperspectral microscope imaging (HMI) framework for rapid VBNC detection under low-level antimicrobials. The objectives were to (i) induce the VBNC state in Escherichia coli K-12 by exposure to selected antimicrobial stressors, (ii) obtain HMI data capturing physiological changes in VBNC cells, and (iii) automate the classification of normal and VBNC cells using deep learning image classification. The VBNC state was induced by low-level oxidative (0.01% hydrogen peroxide) and acidic (0.001% peracetic acid) stressors for 3 days, confirmed by live-dead staining and plate counting. HMI provided spatial and spectral data, extracted into pseudo-RGB images using three characteristic spectral wavelengths. An EfficientNetV2-based convolutional neural network architecture was trained on these pseudo-RGB images, achieving 97.1% accuracy of VBNC classification (n = 200), outperforming the model trained on RGB images at 83.3%. The results highlight the potential for rapid, automated VBNC detection using AI-enabled hyperspectral microscopy, contributing to timely intervention to prevent foodborne illnesses and outbreaks.

Ultrasensitive detection of E. coli using bioinspired based platform

Bacterial infections are a leading cause of mortality worldwide, underscoring the urgent need for effective detection methods. This study introduces a novel approach that combines surface-enhanced Raman spectroscopy (SERS) with an electro-optic technique for bacterial detection. The method utilizes a metal-semiconductor substrate that, when activated by an external electric field, significantly amplifies the SERS signal intensity. We validated this approach through a proof-of-concept study, demonstrating that the SERS signal of Gram-negative Escherichia coli can be enhanced tenfold by applying an electric field, confirming the method's efficacy for bacterial detection. Our findings highlight the potential of this rapid, label-free biosensor for pathogen detection with near single-cell sensitivity.

Exploring the Microbial Ecology of Water in Sub-Saharan Africa and the Potential of Bacteriophages in Water Quality Monitoring and Treatment to Improve Its Safety

Access to safe water and food is a critical issue in sub-Saharan Africa, where microbial contamination poses significant health risks. Conventional water treatment and food preservation methods have limitations in addressing water safety, particularly for antibiotic-resistant bacteria and other pathogenic microorganisms. This review explores the potential application of bacteriophages as an innovative solution for water treatment and food safety in the region. Bacteriophages specifically infect bacteria and offer a targeted approach to reducing bacterial load, including multidrug-resistant strains, without the drawbacks of chemical disinfectants. This review also highlights the advantages of phage bioremediation, including its specificity, adaptability, and minimal environmental impact. It also discusses various case studies demonstrating its efficacy in different water systems. Additionally, we underscore the need for further research and the development of region-specific phage applications to improve water quality and public health outcomes in sub-Saharan Africa. By integrating bacteriophage strategies into water treatment and food production, the region can address critical microbial threats, mitigate the spread of antimicrobial resistance, and advance global efforts toward ensuring safe water for all.

Advancements in Detection Methods for Salmonella in Food: A Comprehensive Review

Non-typhoidal Salmonella species are one of the leading causes of gastrointestinal disease in North America, leading to a significant burden on the healthcare system resulting in a huge economic impact. Consequently, early detection of Salmonella species in the food supply, in accordance with food safety regulations, is crucial for protecting public health, preventing outbreaks, and avoiding serious economic losses. A variety of techniques have been employed to detect the presence of this pathogen in the food supply, including culture-based, immunological, and molecular methods. The present review summarizes these methods and highlights recent updates on promising emerging technologies, including aptasensors, Surface Plasmon Resonance (SPR), and Surface Enhanced Raman Spectroscopy (SERS).

Enhancing Ultra-High Temperature Milk Quality: A Novel Approach to Microbial Contamination Detection Using the BD BACTEC™ FX System

The demand for effective detection methods to ensure the safety and quality of Ultra-High Temperature (UHT) milk remains crucial in the food industry. Traditional techniques for detecting microorganisms are time-consuming and labor-intensive, leading to a need for a rapid and sensitive method for detecting microbial growth in UHT milk. This study evaluates the efficacy of the BD BACTEC™ FX system for microbial detection in UHT milk samples. The system utilizes internal fluorescent CO2 sensors to detect the metabolic activity of bacteria growing in the culture broth. The investigation comprises two stages: a controlled laboratory experiment with UHT milk samples spiked with Bacillus spizizenii inoculated at different population levels (from 0 to 4.0 log10 CFU/mL), and an industrial-scale assessment of commercial UHT milk. The microbial detection system detected the lowest B. spizizenii count (0 log CFU/mL) inoculated into UHT milk after 13 h of incubation. The 13-hour incubation period was also sufficient to detect microbial contamination in commercial UHT milk samples. Results indicate that this system offers heightened sensitivity compared to conventional methods, detecting microbial contamination in a significantly shorter time frame (6-13 h). Taxonomic identification of contaminants revealed the presence of Cellulomonas spp. and Enterococcus spp. in UHT commercial samples. The findings emphasize the critical importance of robust detection techniques in ensuring the safety and quality of UHT milk products.

Fully Integrated Microfluidic Digital Chip for Simple and Highly Quantitative Detection of Norovirus

The prevalence of foodborne illnesses is a significant global concern, resulting in numerous illnesses, deaths, and substantial economic losses annually. Traditional detection methods for foodborne pathogens are often slow, limited, and impractical for field use, underscoring the need for rapid, sensitive, and portable assays. Microfluidic technology has emerged as a promising solution for sample preparation, reaction, and detection on a small scale. Our study introduces a novel microfluidic digital loop-mediated isothermal amplification (LAMP) assay platform, which employs digital microfluidic chips for absolute quantitative analysis of nucleic acids. This portable chip utilizes LAMP technology to achieve ultrasensitive detection of target nucleic acids within 30 min and reduces the detection limit to 1 fM without the need for complex instrumentation. By digitizing amplification signals directly from the target sample, our platform offers simplicity, affordability, portability, and quantitative molecular readouts. This innovation represents a crucial step toward the on-site detection of foodborne pathogens, thereby enhancing food safety and mitigating disease outbreaks.

Multispectral pathogens detection in food using multiplex hyperbranched saltatory rolling circle amplification

Foodborne illnesses caused by Salmonella and Staphylococcus aureus are a significant public health concern, leading to societal and economic repercussions. It is important to develop a simple and straightforward bacteria detection and identification method. A triple-probe multiplex rolling circle amplification technique has been developed to simultaneously detect Salmonella Typhimurium and S. aureus. This method utilizes fluorophore-labeled long padlock probes targeting S. Typhimurium invA and S. aureus glnA specific genes, along with a pH-based detection approach for direct visual identification. The multiplex hyperbranched saltatory rolling circle amplification assay at 30 °C has showed promising results with synthetic targets within 30 min and real bacteria within 2 h after establishing the detection settings. The assay is specific for S. aureus and S. Typhimurium, with a limit of detection of 39 μM for fluorescence and 78 μM for colorimetric. In the simulative test of this method for the detection of S. Typhimurium and S. aureus in milk, the limit of detection for the fluorescence signal after 2 h of amplification was 10 CFU/mL and 5 CFU/mL, respectively. The detection method was evaluated to be stable enough to detect pathogen for 3.29 months. Consequently, this triple-probe-multiplex rolling circle amplification method displays notable specificity, sensitivity, as well as ease of interpretation when testing food samples for harmful pathogens.

Salmonella Detection in Food Using a HEK-hTLR5 Reporter Cell-Based Sensor

The development of a rapid, sensitive, specific method for detecting foodborne pathogens is paramount for supplying safe food to enhance public health safety. Despite the significant improvement in pathogen detection methods, key issues are still associated with rapid methods, such as distinguishing living cells from dead, the pathogenic potential or health risk of the analyte at the time of consumption, the detection limit, and the sample-to-result. Mammalian cell-based assays analyze pathogens' interaction with host cells and are responsive only to live pathogens or active toxins. In this study, a human embryonic kidney (HEK293) cell line expressing Toll-Like Receptor 5 (TLR-5) and chromogenic reporter system (HEK dual hTLR5) was used for the detection of viable Salmonella in a 96-well tissue culture plate. This cell line responds to low concentrations of TLR5 agonist flagellin. Stimulation of TLR5 ligand activates nuclear factor-kB (NF-κB)-linked alkaline phosphatase (AP-1) signaling cascade inducing the production of secreted embryonic alkaline phosphatase (SEAP). With the addition of a ρ-nitrophenyl phosphate as a substrate, a colored end product representing a positive signal is quantified. The assay's specificity was validated with the top 20 Salmonella enterica serovars and 19 non-Salmonella spp. The performance of the assay was also validated with spiked food samples. The total detection time (sample-to-result), including shortened pre-enrichment (4 h) and selective enrichment (4 h) steps with artificially inoculated outbreak-implicated food samples (chicken, peanut kernel, peanut butter, black pepper, mayonnaise, and peach), was 15 h when inoculated at 1-100 CFU/25 g sample. These results show the potential of HEK-DualTM hTLR5 cell-based functional biosensors for the rapid screening of Salmonella.

Assessment of the presence of multidrug-resistant Escherichia coli, Salmonella and Staphylococcus in chicken meat, eggs and faeces in Mymensingh division of Bangladesh

The emergence of bacteria that is resistant to several drugs of clinical importance poses a threat to successful treatment, a phenomenon known as multidrug resistance that affects diverse classes of antibiotics. The purpose of this study was to evaluate the prevalence of multidrug-resistant Escherichia coli, Salmonella spp. and Staphylococcus aureus in chicken egg, meat and faeces from four districts of Bangladesh. A total of 120 chicken samples were collected from different poultry farms. Conventional culture and molecular detection methods were used for identification of bacterial isolates from the collected samples followed by antibiotic susceptibility test through the disc diffusion method, finally antibiotic resistant genes were detected by PCR. E. coli, Salmonella spp. and Staphylococcus aureus were detected in meat, egg and faecal samples. Antimicrobial susceptibility results revealed isolates from faeces were 100 % resistant to amoxicillin, while all S. aureus and Salmonella sp. from faeces were resistant to doxycycline, tetracycline and erythromycin. Salmonella spp. isolates from eggs indicated 100 % resistance to erythromycin, amoxycillin, while E. coli were 100 % resistant to erythromycin. E. coli and S. aureus from meat were 100 % resistant to amoxicillin and erythromycin. However, Salmonella spp. from eggs were 100 % susceptible to doxycycline, gentamicin, levofloxacin and tetracycline. The mecA and aac(3)-IV genes were only found in S. aureus and E. coli, respectively. The Sul1, tetB, and aadA1 were highest in Salmonella spp. and S. aureus, while the sul1, tetA and bla SHV were higher in E. coli. Isolates from all samples were multidrug resistant. These findings indicate a high risk of transmission of resistance genes from microbial contamination to food of animal origin. The study emphasizes the need for effective biosecurity measures, responsible antibiotic use, and strict regulations in poultry production to prevent the spread of antibiotic resistance.

Electrostatic microfiltration (EM) enriches and recovers viable microorganisms at low-abundance in large-volume samples and enhances downstream detection

Rapid and sensitive detection of pathogens in various samples is crucial for disease diagnosis, environmental surveillance, as well as food and water safety monitoring. However, the low abundance of pathogens (<10 CFU) in large volume (1 mL-1 L) samples containing vast backgrounds critically limits the sensitivity of even the most advanced techniques, such as digital PCR. Therefore, there is a critical need for sample preparation that can enrich low-abundance pathogens from complex and large-volume samples. This study develops an efficient electrostatic microfiltration (EM)-based sample preparation technique capable of processing ultra-large-volume (≥500 mL) samples at high throughput (≥10 mL min-1). This approach achieves a significant enrichment (>8000×) of extremely-low-abundance pathogens (down to level of 0.02 CFU mL-1, i.e., 10 CFU in 500 mL). Furthermore, EM-enabled sample preparation facilitates digital amplification techniques sensitively detecting broad pathogens, including bacteria, fungi, and viruses from various samples, in a rapid (≤3 h) sample-to-result workflow. Notably, the operational ease, portability, and compatibility/integrability with various downstream detection platforms highlight its great potential for widespread applications across diverse settings.

Bioreceptor modified electrochemical biosensors for the detection of life threating pathogenic bacteria: a review

The lack of reliable and efficient techniques for early monitoring to stop long-term effects on human health is an increasing problem as the pathogenesis effect of infectious bacteria is growing continuously. Therefore, developing an effective early detection technique coupled with efficient and continuous monitoring of pathogenic bacteria is increasingly becoming a global public health prime target. Electrochemical biosensors are among the strategies that can be utilized for accomplishing that goal with promising potential. In recent years, identifying target biological analytes by interacting with bioreceptors modified electrodes is among the most commonly used detection techniques in electrochemical biosensing strategies. The commonly employed bioreceptors are nucleic acid molecules (DNA or RNA), proteins, antibodies, enzymes, organisms, tissues, and biomimetic components such as molecularly imprinted polymers. Despite the advancement in electrochemical biosensing, developing a reliable and effective biosensor for detecting pathogenic bacteria is still in the infancy stage with so much room for growth. A major milestone in addressing some of the issues and improving the detection pathway is the investigation of specific bacterial detection techniques. The present study covers the fundamental concepts of electrochemical biosensors, human PB illnesses, and the latest electrochemical biosensors based on bioreceptor elements that are designed to detect specific pathogenic bacteria. This study aims to assist researchers with the most up-to-date research work in the field of bio-electrochemical pathogenic bacteria detection and monitoring.

Concanavalin A-assisted multiplex digital PCR assay for rapid capture and accurate quantification detection of foodborne pathogens

Multiplex, sensitive, and rapid detection of pathogens is crucial for ensuring food safety and safeguarding human health, however, it remains a significant challenge. This study proposes a concanavalin A-assisted multiplex digital amplification (CAMDA) assay for simultaneous quantitative detection of multiple foodborne bacteria. The CAMDA assay enables the simultaneous detection of six foodborne pathogens within 1.1 h and the limit of detection is 101 CFU/mL. Furthermore, the CAMDA assay exhibits high specificity, with a rate of 97 % for Bacillus cereus and 100 % for other pathogens tested in this study. Moreover, practical application validation using eight milk powder samples demonstrates that the accuracy of the CAMDA assay reaches 100 % when compared to qPCR results. Therefore, our developed CAMDA assay holds great potential for accurate and rapid detection of multiple pathogens in complex food matrices while also promoting the utilization of microfluidic chips in food investigation.

Ultrasensitive detection of Salmonella typhi using a PAM-free Cas14a-based biosensor

The effectiveness of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas14a1, widely utilized for pathogenic microorganism detection, has been limited by the requirement of a protospacer adjacent motif (PAM) on the target DNA strands. To overcome this limitation, this study developed a Single Primer isothermal amplification integrated-Cas14a1 biosensor (SPCas) for detecting Salmonella typhi that does not rely on a PAM sequence. The SPCas biosensor utilizes a novel primer design featuring an RNA-DNA primer and a 3'-biotin-modified primer capable of binding to the same single-stranded DNA (ssDNA) in the presence of the target gene. The RNA-DNA primer undergoes amplification and is blocked at the biotin-modified end. Subsequently, strand replacement is initiated to generate ssDNA assisted by RNase H and Bst enzymes, which activate the trans-cleavage activity of Cas14a1 even in the absence of a PAM sequence. Leveraging both cyclic chain replacement reaction amplification and Cas14a1 trans-cleavage activity, the SPCas biosensor exhibits a remarkable diagnostic sensitivity of 5 CFU/mL. Additionally, in the assessment of 20 milk samples, the SPCas platform demonstrated 100% diagnostic accuracy, which is consistent with the gold standard qPCR. This platform introduces a novel approach for developing innovative CRISPR-Cas-dependent biosensors without a PAM sequence.

Enhancing food safety: A low-cost biosensor for Bacillus licheniformis detection in food products

To enhance food safety, the need for swift and precise detection of B. licheniformis, a bacterium prevalent in various environments, including soil and food products, is paramount. This study presents an innovative and cost-effective bioassay designed to specifically identify the foodborne pathogen, B. licheniformis, utilizing a colorimetric signal approach. The biosensor, featuring a 3D-printed architecture, incorporates a casein-based liquid-proof gelatine film, selectively liquefying in response to the caseinolytic/proteolytic activity of external enzymes from the pathogen. As the sample liquefies, it progresses through a color layer, causing the migration of dye to an absorbent layer, resulting in a distinct positive signal. This bioassay exhibits exceptional sensitivity, detecting concentrations as low as 1 CFU/mL within a 9.3-h assay duration. Notably, this cost-efficient bioassay outperforms conventional methods in terms of efficacy and cost-effectiveness, offering a straightforward solution for promptly detecting B. licheniformis in food samples.

A Rapid Total Bacterial Count Method for Food Samples using Syringe Filters and Lectin-Conjugated Semiconductor Nanorods

Total bacterial count in food is one of important food safety criteria. The current plate count method (Heterotrophic Plate Count) for food analysis requires microbiology lab facilities and at least 2 days turnover time. We developed a rapid fluorescence-based total bacterial count method that utilises semiconductor nanorods (SNRs) conjugated with a lectin Griffonia simplicifolia II (GSII-SNRs) to stain bacterial cells captured on syringe filters, via the common N-acetylglucosamine molecules on bacterial cell wall. This "Filter-and-Stain" detection method has a rapid turnover time of 20 min. The fluorescence emission can be seen under UV light with minimum interference from food sample background. The fluorescence intensity quantified through image analysis is proportional to the bacterial concentration with a limit of detection of 1000 CFU/mL, for total bacterial count assessment in food safety. Moreover, the GSII-SNRs do not bind to heat inactivated bacterial cells, and thus can differentiate live and dead bacteria. Our method has been validated with representative food (coffee powder, raw spinach leaves, and ready-to-eat tomato salsa) to demonstrate its high potential for on-site food safety assessment, especially in places with no immediate access to microbiology labs.

Advances in aptamer-based biosensors for monitoring foodborne pathogens

Biosensors are analytical devices for detecting a wide range of targets, including cells, proteins, DNA, enzymes, and chemical and biological compounds. They mostly rely on using bioprobes with a high binding affinity to the target for specific detection. However, low specificity and effectiveness of the conventional biosensors has led to the search for novel materials, that can specifically detect biomolecules. Aptamers are a group of single-stranded DNA or RNA oligonucleotides, that can bind to their targets with high specificity and serve as effective bioprobes for developing aptamer-based biosensors. Aptamers have a shorter production time, high stability, compared to traditional bioprobes, and possess ability to develop them for specific target molecules for tailored applications. Thus, various aptasensing approaches, including electrochemical, optical, surface plasmon resonance and chip-dependent approaches, have been investigated in recent times for various biological targets, including foodborne pathogens. Hence, this article is an overview of various conventional foodborne pathogen detection methods, their limitations and the ability of aptamer-based biosensors to overcome those limitations and replace them. In addition, the current status and advances in aptamer-based biosensors for the detection of foodborne pathogens to ensure food safety were also discussed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05889-8.

Flow cytometry: Unravelling the real antimicrobial and antibiofilm efficacy of natural bioactive compounds

Flow cytometry (FCM) provides unique information on bacterial viability and physiology, allowing a real-time early warning antimicrobial and antibiofilm monitoring system for preventing the spread risk of foodborne disease. The present work used a combined culture-based and FCM approach to assess the in vitro efficacy of essential oils (EOs) from condiment plants commonly used in Mediterranean Europe (i.e., thyme EO, oregano EO, basil EO, and lemon EO) against planktonic and sessile cells of food-pathogenic Listeria monocytogenes 56 LY, and contaminant and alterative species Escherichia coli ATCC 25922 and Pseudomonas fluorescens ATCC 13525. Evaluation of the bacterial response to the increasing concentrations of natural compounds posed FCM as a crucial technique for the quantification of the live/dead, and viable but non-culturable (VBNC) cells when antimicrobial agents exert no real bactericidal action. Furthermore, the FCM results displayed higher numbers of viable bacteria expressed as Active Fluorescent Units (AFUs) with a greater level of repeatability compared with outcomes of the plate-count method. Overall, accurate counting of viable microbial cells is a critically important parameter in food microbiology, and flow cytometry provides an innovative approach with high-throughput potential for applications in the food industry as "flow microbiology".

A Label-Free Optical Flow Cytometry Based-Method for Rapid Assay of Disinfectants' Bactericidal Activity

Selecting the appropriate disinfectant to control and prevent healthcare-associated infections (HAIs) is a challenging task for environmental health experts due to the large number of available disinfectant products. This study aimed to develop a label-free flow cytometry (FCM) method for the rapid evaluation of bactericidal activity and to compare its efficacy with that of standard qualitative/quantitative suspension tests. The bactericidal efficiency of eight commercial disinfectants containing quaternary ammonium compounds (QACs) was evaluated against four strains recommended by EN 13727 (Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Enterococcus hirae) and four multidrug-resistant pathogens. The proposed FCM protocol measures changes in scattered light and counts following disinfectant exposure, neutralization, and culture steps. Unlike other available FCM-based methods, this approach does not rely on autofluorescence measurements, impedance cytometry, or fluorescent dyes. The FCM scattered light signals revealed both decreased count rates and morphological changes after treatment with minimum inhibitory concentrations (MICs) and higher concentrations for all tested bacteria. The results from the FCM measurements showed excellent correlation with those from standard assays, providing a rapid tool for monitoring the susceptibility profile of clinical, multidrug-resistant pathogens to chemical disinfectants, which could support infection prevention and control procedures for healthcare environments. This label-free FCM protocol offers a novel and rapid tool for environmental health experts, aiding in the optimization of disinfectant selection for the prevention and control of HAIs.

Filling the Knowledge Gap Regarding Microbial Occupational Exposure Assessment in Waste Water Treatment Plants: A Scoping Review

BACKGROUND

Wastewater treatment plants (WWTPs) are crucial in the scope of European Commission circular economy implementation. However, bioaerosol production may be a hazard for occupational and public health. A scoping review regarding microbial contamination exposure assessment in WWTPs was performed.

METHODS

This study was performed through PRISMA methodology in PubMed, Scopus and Web of Science.

RESULTS

28 papers were selected for data extraction. The WWTPs' most common sampled sites are the aeration tank (42.86%), sludge dewatering basin (21.43%) and grit chamber. Air sampling is the preferred sampling technique and culture-based methods were the most frequently employed assays. Staphylococcus sp. (21.43%), Bacillus sp. (7.14%), Clostridium sp. (3.57%), Escherichia sp. (7.14%) and Legionella sp. (3.57%) were the most isolated bacteria and Aspergillus sp. (17.86%), Cladosporium sp. (10.71%) and Alternaria sp. (10.71%) dominated the fungal presence.

CONCLUSIONS

This study allowed the identification of the following needs: (a) common protocol from the field (sampling campaign) to the lab (assays to employ); (b) standardized contextual information to be retrieved allowing a proper risk control and management; (c) the selection of the most suitable microbial targets to serve as indicators of harmful microbial exposure. Filling these gaps with further studies will help to provide robust science to policy makers and stakeholders.

Synthetic phage-based approach for sensitive and specific detection of Escherichia coli O157

Escherichia coli O157 can cause foodborne outbreaks, with infection leading to severe disease such as hemolytic-uremic syndrome. Although phage-based detection methods for E. coli O157 are being explored, research on their specificity with clinical isolates is lacking. Here, we describe an in vitro assembly-based synthesis of vB_Eco4M-7, an O157 antigen-specific phage with a 68-kb genome, and its use as a proof of concept for E. coli O157 detection. Linking the detection tag to the C-terminus of the tail fiber protein, gp27 produces the greatest detection sensitivity of the 20 insertions sites tested. The constructed phage detects all 53 diverse clinical isolates of E. coli O157, clearly distinguishing them from 35 clinical isolates of non-O157 Shiga toxin-producing E. coli. Our efficient phage synthesis methods can be applied to other pathogenic bacteria for a variety of applications, including phage-based detection and phage therapy.

Characterization of viable but nonculturable state of Campylobacter concisus

Campylobacter concisus is an opportunistic bacterial pathogen linked with a range of human diseases. The objective of this study was to investigate the viable but nonculturable (VBNC) state of the bacterium. To induce the VBNC state, C. concisus cells were maintained in sterilized phosphate-buffered saline at 4°C for three weeks. The VBNC cells were monitored using quantitative analysis by propidium monoazide (PMAxx) coupled with quantitative real-time PCR (PMAxx-qPCR), targeting the DNA gyrase subunit B gene. The results demonstrated that C. concisus ATCC 51562 entered the VBNC state in 15 days, while ATCC 51561 entered the VBNC state in 9 days. The viable cell counts, assessed by PMAxx-qPCR, consistently remained close to the initial level of 107 CFU ml-1, indicating a substantial portion of the cell population had entered the VBNC state. Notably, morphological analysis revealed that the VBNC cells became coccoid and significantly smaller. The cells could be resuscitated through a temperature increase in the presence of a highly nutritious growth medium. In conclusion, under environmental stress, most C. concisus cells converted to the VBNC state. The VBNC state of C. concisus may be important for its environmental survival and spread, and the presence of VBNC forms should be considered in environmental and clinical monitoring.

Mesoporous Silica Nanoparticles-Enhanced Microarray Technology for Highly Sensitive Simultaneous Detection of Multiplex Foodborne Pathogens

Ensuring food safety is paramount for the food industry and global health concerns. In this study, we have developed a method for the detection of prevalent foodborne pathogenic bacteria, including Escherichia coli, Salmonella spp., Listeria spp., Shigella spp., Campylobacter spp., Clostridium spp., and Vibrio spp., utilizing antibody-aptamer arrays. To enhance the fluorescence signals on the microarray, the mesoporous silica nanoparticles (MSNs) conjugated with fluorescein, streptavidin, and seven detection antibodies-biotin were employed, forming fluorescein doped mesoporous silica nanoparticles conjugated with detection antibodies (MSNs-Flu-SA-Abs) complexes. The array pattern was designed for easy readability and enabled the simultaneous detection of all seven foodborne pathogens, referred to as the 7FP-biochip. Following the optimization of MSNs-Flu-SA-Abs complexes attachment and enhancement of the detection signal in fluorescent immunoassays, a high level of sensitivity was achieved. The detection limits for the seven pathogens in both buffer and food samples were 102 CFU/mL through visual screening, with fluorescent intensity quantification achieving levels as low as 20-34 CFU/g were achieved on the antibody-aptamer arrays. Our antibody-aptamer array offers several advantages, including significantly reduced nonspecific binding with no cross-reaction between bacteria. Importantly, our platform detection exhibited no cross-reactivity among the tested bacteria in this study. The multiplex detection of foodborne pathogens in canned tuna samples with spiked bacteria was successfully demonstrated in real food measurements. In conclusion, our study presents a promising method for detecting multiple foodborne pathogens simultaneously. With its high sensitivity and specificity, the developed antibody-aptamer array holds great potential for enhancing food safety and public health.

Listeria spp., Listeria monocytogenes

Listeriosis is a disease caused by L. monocytogenes, a relevant microorganism as a causative agent of foodborne diseases - FBD. This study aimed to evaluate the distribution of Listeria spp., and L. monocytogenes in different production areas in two small plants (A and B) and two micro-food processing plants (C and D) producing meat derivatives, located in different cities of Colombia. The methodology implemented was i. The analysis of sampling points is based on a harmonised tool. ii. Four samplings in each production plant between 2019 and 2020. iii. Isolation and identification of microorganisms through conventional microbiology, a semi-automated system, molecular serotyping and clonal characterisation by ERIC-PCR. L. monocytogenes frequency in the production plants belonging to the study ranged between 5.9 and 28.6 %; for Listeria spp., plants A and D had isolated, plant A had the highest proportion, while for L. monocytogenes geno-serotypes found were: 1/2a, 1/2c, 4a-4c, 4b, 4d - 4e, with geno-serotype 4b as the most frequent. Furthermore, possible persistent isolates were detected in plant C as the feasible sources of contamination, based on failures in flow management, raw material contaminated with L. monocytogenes, lack of standardised cooking processes and transfer of the microorganism through equipment and surfaces. Finally, in three of the four production plants assayed, L. monocytogenes or Listeria spp. were present in the packaging area in some of the samples taken during the study, which calls for increased and frequent monitoring, as well as constant technical support for the control of L. monocytogenes in micro and small-scale production plants.

Strain-level characterization of foodborne pathogens without culture enrichment for outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling

Introduction

Shotgun metagenomics has previously proven effective in the investigation of foodborne outbreaks by providing rapid and comprehensive insights into the microbial contaminant. However, culture enrichment of the sample has remained a prerequisite, despite the potential impact on pathogen detection resulting from the growth competition. To circumvent the need for culture enrichment, we explored the use of adaptive sampling using various databases for a targeted nanopore sequencing, compared to shotgun metagenomics alone.

Methods

The adaptive sampling method was first tested on DNA of mashed potatoes mixed with DNA of a Staphylococcus aureus strain previously associated with a foodborne outbreak. The selective sequencing was used to either deplete the potato sequencing reads or enrich for the pathogen sequencing reads, and compared to a shotgun sequencing. Then, living S. aureus were spiked at 105 CFU into 25 g of mashed potatoes. Three DNA extraction kits were tested, in combination with enrichment using adaptive sampling, following whole genome amplification. After data analysis, the possibility to characterize the contaminant with the different sequencing and extraction methods, without culture enrichment, was assessed.

Results

Overall, the adaptive sampling outperformed the shotgun sequencing. While the use of a host removal DNA extraction kit and targeted sequencing using a database of foodborne pathogens allowed rapid detection of the pathogen, the most complete characterization was achieved when using solely a database of S. aureus combined with a conventional DNA extraction kit, enabling accurate placement of the strain on a phylogenetic tree alongside outbreak cases.

Discussion

This method shows great potential for strain-level analysis of foodborne outbreaks without the need for culture enrichment, thereby enabling faster investigations and facilitating precise pathogen characterization. The integration of adaptive sampling with metagenomics presents a valuable strategy for more efficient and targeted analysis of microbial communities in foodborne outbreaks, contributing to improved food safety and public health.

FlashPCR: Revolutionising qPCR by Accelerating Amplification through Low ∆T Protocols

Versatility, sensitivity, and accuracy have made the real-time polymerase chain reaction (qPCR) a crucial tool for research, as well as diagnostic applications. However, for point-of-care (PoC) use, traditional qPCR faces two main challenges: long run times mean results are not available for half an hour or more, and the requisite high-temperature denaturation requires more robust and power-demanding instrumentation. This study addresses both issues and revises primer and probe designs, modified buffers, and low ∆T protocols which, together, speed up qPCR on conventional qPCR instruments and will allow for the development of robust, point-of-care devices. Our approach, called "FlashPCR", uses a protocol involving a 15-second denaturation at 79 °C, followed by repeated cycling for 1 s at 79 °C and 71 °C, together with high Tm primers and specific but simple buffers. It also allows for efficient reverse transcription as part of a one-step RT-qPCR protocol, making it universally applicable for both rapid research and diagnostic applications.

Progress in methods for the detection of viable Escherichia coli

Escherichia coli (E. coli) is a prevalent enteric bacterium and a necessary organism to monitor for food safety and environmental purposes. Developing efficient and specific methods is critical for detecting and monitoring viable E. coli due to its high prevalence. Conventional culture methods are often laborious and time-consuming, and they offer limited capability in detecting potentially harmful viable but non-culturable E. coli in the tested sample, which highlights the need for improved approaches. Hence, there is a growing demand for accurate and sensitive methods to determine the presence of viable E. coli. This paper scrutinizes various methods for detecting viable E. coli, including culture-based methods, molecular methods that target DNAs and RNAs, bacteriophage-based methods, biosensors, and other emerging technologies. The review serves as a guide for researchers seeking additional methodological options and aiding in the development of rapid and precise assays. Moving forward, it is anticipated that methods for detecting E. coli will become more stable and robust, ultimately contributing significantly to the improvement of food safety and public health.