Foodborne pathogens in the omics era

Function and therapeutic prospects of next-generation probiotic Akkermansia muciniphila in infectious diseases

Akkermansia muciniphila is a gram-negative bacterium that colonizes the human gut, making up 3-5% of the human microbiome. A. muciniphila is a promising next-generation probiotic with clinical application prospects. Emerging studies have reported various beneficial effects of A. muciniphila including anti-cancer, delaying aging, reducing inflammation, improving immune function, regulating nervous system function, whereas knowledge on its roles and mechanism in infectious disease is currently unclear. In this review, we summarized the basic characteristics, genome and phenotype diversity, the influence of A. muciniphila and its derived components on infectious diseases, such as sepsis, virus infection, enteric infection, periodontitis and foodborne pathogen induced infections. We also provided updates on mechanisms how A. muciniphila protects intestinal barrier integrity and modulate host immune response. In summary, we believe that A. muciniphila is a promising therapeutic probiotic that may be applied for the treatment of a variety of infectious diseases.

Engineering of an adaptive tandem CRISPR/Cas12a molecular amplifier permits robust analysis of Vibrio parahaemolyticus

Seeking new molecular diagnostic method for pathogenic bacteria detection is of utmost importance for ensuring food safety and protecting human health. Herein, we have engineered an adaptive tandem CRISPR/Cas12a molecular amplifier specifically designed for robust analysis of vibrio parahaemolyticus (V. parahaemolyticus), one of the most harmful pathogens. Our strategy involves the integration of three crucial processes: recombinase polymerase amplification (RPA) for copy number amplification, terminal deoxynucleotidyl transferase (TdT) for template-free strand elongation, and CRISPR/Cas12a-mediated trans-cleavage of a reporter molecule. By combining these processes, the target genomic DNA extracted from V. parahaemolyticus is able to activate many CRISPR/Cas12a units (CRISPR/Cas12an) simultaneously, resulting in a greatly amplified target signal to indicate the presence and concentration of V. parahaemolyticus. This unique model offers more advantages compared to traditional amplification models that use one RPA amplicon to activate one CRISPR/Cas12a unit. Under optimized conditions, our method enables the detection of target V. parahaemolyticus within a linear range of 1 × 102-1 × 107 CFU/mL, with an impressive limit of detection as low as 12.4 CFU/mL. It is conceivable that the adaptive tandem CRISPR/Cas12a molecular amplifier could be adapted as routine diagnostic kits in future for in-field detection of pathogens.

Food Safety-Transcriptomics and Proteomics

Food safety is a critical aspect of public health and involves the handling, preparation, and storage of food to avoid contamination and foodborne illnesses [...].

A high-sucrose diet causes microbiota composition shift and promotes the susceptibility of mice to Salmonella Typhimurium infection

A westernized diet characterized by high fat and sugar is tightly associated with the development of metabolic diseases and inflammatory bowel disease. Although a high-fat diet has been extensively studied for its involvement in various diseases, fewer studies have examined the impact of a high-sugar diet on the development of certain diseases, particularly enteric infections. This study aimed to explore the effect of a high sucrose diet on Salmonella Typhimurium-induced infection. C57BL/6 mice received a normal diet (Control) or a high sucrose diet (HSD) for eight weeks and then were infected by Salmonella Typhimurium. The high-sugar diet profoundly altered the relative abundance of certain microbial taxa. Bacteroidetes and Verrucomicrobiota were more abundant in normal diet-fed mice than in HSD-fed mice. Moreover, short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs) were significantly higher in mice from the control group than the HSD group. More S. Typhimurium counts in feces and other tissues were observed in HSD-fed mice after infection. Tight junction proteins and antimicrobial peptides were significantly decreased in HSD-fed mice. Fecal microbiota transplantation (FMT) demonstrated that mice that received normal fecal microbiota had lower Salmonella Typhimurium burdens compared with mice that received HSD fecal microbiota, indicating that the altered microbial communities are associated with the severity of infection. Together, these findings suggest that the excessive intake of sucrose disturbs intestinal homeostasis and predisposes mice to Salmonella-induced infection.

Prospects for the next generation of artificial enzymes for ensuring the quality of chilled meat: Opportunities and challenges

As living standards rise, the demand for high-quality chilled meat among consumers also grows. Researchers and enterprises have been interested in ensuring the quality of chilled meat in all links of the downstream industry. Nanozyme has shown the potential to address the aforementioned requirements. Reasons and approaches for the application of nanozymes in the freshness assessment or shelf life extension of chilled meat were discussed. The challenges for applying these nanozymes to ensure the quality of chilled meat were also summarized. Finally, this review examined the safety, regulatory status, and consumer attitudes toward nanozymes. This review revealed that the freshness assessment of chilled meat is closely related to mimicking the enzyme activities of nanozymes, whereas the shelf life changes of chilled meat are mostly dependent on the photothermal activities and pseudophotodynamic activities of nanozymes. In contrast, studies regarding the shelf life of chilled meat are more challenging to develop, as excessive heat or reactive oxygen species impair its quality. Notably, meat contains a complex matrix composition that may interact with the nanozyme, reducing its effectiveness. Nanopollution and mass manufacturing are additional obstacles that must be overcome. Therefore, it is vital to choose suitable approaches to ensure meat quality. Furthermore, the safety of nanozymes in meat applications still needs careful consideration owing to their widespread usage.

Hyperspectral imaging and machine learning in food microbiology: Developments and challenges in detection of bacterial, fungal, and viral contaminants

Hyperspectral imaging (HSI) is a robust and nondestructive method that can detect foreign particles such as microbial, chemical, and physical contamination in food. This review summarizes the work done in the last two decades in this field with a highlight on challenges, risks, and research gaps. Considering the challenges of using HSI on complex matrices like food (e.g., the confounding and masking effects of background signals), application of machine learning and modeling approaches that have been successful in achieving better accuracy as well as increasing the detection limit have also been discussed here. Foodborne microbial contaminants such as bacteria, fungi, viruses, yeast, and protozoa are of interest and concern to food manufacturers due to the potential risk of either food poisoning or food spoilage. Detection of these contaminants using fast and efficient methods would not only prevent outbreaks and recalls but will also increase consumer acceptance and demand for shelf-stable food products. The conventional culture-based methods for microbial detection are time and labor-intensive, whereas hyperspectral imaging (HSI) is robust, nondestructive with minimum sample preparation, and has gained significant attention due to its rapid approach to detection of microbial contaminants. This review is a comprehensive summary of the detection of bacterial, viral, and fungal contaminants in food with detailed emphasis on the specific modeling and datamining approaches used to overcome the specific challenges associated with background and data complexity.

Acute Infectious Gastroenteritis: The Causative Agents, Omics-Based Detection of Antigens and Novel Biomarkers

Acute infectious gastroenteritis (AGE) is among the leading causes of mortality in children less than 5 years of age worldwide. There are many causative agents that lead to this infection, with rotavirus being the commonest pathogen in the past decade. However, this trend is now being progressively replaced by another agent, which is the norovirus. Apart from the viruses, bacteria such as Salmonella and Escherichia coli and parasites such as Entamoeba histolytica also contribute to AGE. These agents can be recognised by their respective biological markers, which are mainly the specific antigens or genes to determine the causative pathogen. In conjunction to that, omics technologies are currently providing crucial insights into the diagnosis of acute infectious gastroenteritis at the molecular level. Recent advancement in omics technologies could be an important tool to further elucidate the potential causative agents for AGE. This review will explore the current available biomarkers and antigens available for the diagnosis and management of the different causative agents of AGE. Despite the high-priced multi-omics approaches, the idea for utilization of these technologies is to allow more robust discovery of novel antigens and biomarkers related to management AGE, which eventually can be developed using easier and cheaper detection methods for future clinical setting. Thus, prediction of prognosis, virulence and drug susceptibility for active infections can be obtained. Case management, risk prediction for hospital-acquired infections, outbreak detection, and antimicrobial accountability are aimed for further improvement by integrating these capabilities into a new clinical workflow.

Impact of the aquatic pathobiome in low-income and middle-income countries (LMICs) quest for safe water and sanitation practices

Microbial contamination of surface waters is of particular relevance in low-income and middle-income countries (LMICs) since they often represent the only available source of water for drinking and domestic use. In the recent years, a growing urbanization, profound demographic shifts and drastic climate events have greatly affected LMICs capacity to reach access to safe drinking water and sanitation practices, and to protect citizens' health from risks associated to the exposure and use of contaminated water. Detailed phylogenetic and microbiological information on the exact composition of pathogenic organisms in urban and peri-urban water is scarce, especially in rapidly changing settings of sub-Saharan Africa. In this review we aim to highlight how large-scale water pathobiome studies can support the LMICs challenge to global access to safe water and sanitation practices.

3D-Printed Nanocellulose-Based Cushioning-Antibacterial Dual-Function Food Packaging Aerogel

Cushioning and antibacterial packaging are the requirements of the storage and transportation of fruits and vegetables, which are essential for reducing the irreversible quality loss during the process. Herein, the composite of carboxymethyl nanocellulose, glycerin, and acrylamide derivatives acted as the shell and chitosan/AgNPs were immobilized in the core by using coaxial 3D-printing technology. Thus, the 3D-printed cushioning-antibacterial dual-function packaging aerogel with a shell-core structure (CNGA/C-AgNPs) was obtained. The CNGA/C-AgNPs packaging aerogel had good cushioning and resilience performance, and the average compression resilience rate was more than 90%. Although AgNPs was slowly released, CNGA/C-AgNPs packaging aerogel had an obvious antibacterial effect on E. coli and S. aureus. Moreover, the CNGA/C-AgNPs packaging aerogel was biodegradable. Due to the customization capabilities of 3D-printing technology, the prepared packaging aerogel can be adapted to more application scenarios by accurately designing and regulating the microstructure of aerogels, which provides a new idea for the development of food intelligent packaging.