Foodborne Research Articles

Machine learning reveals the dynamic importance of accessory sequences for Salmonella outbreak clustering.

Gene-by-gene typing is widely used to detect clusters of foodborne illnesses that share a common origin. It remains actively debated whether the inclusion of accessory sequences in bacterial typing schema is informative or deleterious for cluster definitions in outbreak investigations due to the potential confounding effects of horizontal gene transfer. By training machine learning models on a curated set of historical Salmonella outbreaks, we revealed an enriched presence of outbreak distinguishing features in a wide range of mobile genetic elements. Systematic comparison of the efficacy of clustering different accessory elements against standard sequence typing methods led to our cataloging of scenarios where accessory sequence variations were beneficial and uninformative to resolving outbreak clusters. The presented work underscores the complexity of the molecular trends in enteric outbreaks and seeks to inspire novel computational ways to exploit whole-genome sequencing data in enteric disease surveillance and management.

Establishing Reference Genes for Accurate Gene Expression Profiling in Toxigenic Bacillus cereus

Bacillus cereus is a Gram-positive pathogen associated with foodborne illnesses and severe non-gastrointestinal infections. Robust tools for accurate gene transcription analysis are essential for studying toxin gene expression dynamics and deciphering the complex regulatory networks orchestrating the expression of toxin and virulence factors. This study aimed to identify reliable reference genes for normalizing reverse transcription quantitative PCR (RT-qPCR) data in toxigenic B. cereus. An emetic and an enteropathogenic strain were used as model organisms to establish a suitable reference gene set to monitor the dynamics of toxin gene transcription. Ten candidate reference genes were evaluated for their expression stability using geNorm, NormFinder, BestKeeper and the ΔCq method, with the final rankings integrated via RefFinder. Among the tested genes, rho, rpoD and recA were identified as the most stable expressed reference genes across all tested conditions. As shown in this proof-of-principle study, the established reference gene set provides a suitable tool to investigate the influence of extrinsic and intrinsic factors on toxin gene transcription. In conclusion, our newly established reference gene set provides a robust basis for studying toxin gene expression in B. cereus and contributes to a better understanding of its pathogenicity and potential strategies to mitigate its harmful effects.

Risk of Staphylococcus aureus nasal carriage among food handlers: implications for foodborne illnesses

The presence of microorganisms or their toxin in food materials is a predominant problem in the food industry, posing significant hazards to public health. Staphylococcus aureus, a bacterium commonly colonising human skin, nose, and gut, is a leading cause of foodborne infections. Asymptomatic carriers can contaminate food by touching it or through respiratory secretions, leading to staphylococcal food poisoning. This study aims to assess the prevalence and antibiotic resistance patterns of Staphylococcus aureus among food handlers. Nasal swabs from food handlers were analysed using standard microbiological techniques. The study found that 57% of restaurant workers and food handlers had Staphylococcus aureus in their nasal cavities. Among the participants, women had a higher prevalence at 94%, while men had a prevalence rate of 6%. The chi-square analysis revealed no significant differences in the occurrence of Staphylococcus aureus across different genders or age groups, indicating that neither gender nor age significantly influenced the prevalence. The age group with the highest prevalence rate was 23-28 years at 23.5%. Levofloxacin and Rifampicin showed the highest sensitivity rates (87%), while all isolates resisted Norfloxacin. These findings highlight the critical need for enhanced food hygiene education and the use of protective equipment among food handlers to prevent foodborne illnesses. Addressing antibiotic resistance is also fundamental for public health interventions

Evaluation of saline treatments on bacteriological quality of Tiger Nut) Cyperus esculentus L.) for consumption post purchase

Food-borne diseases are usually caused by ingestion of contaminated food. One of such foods susceptible to microbial contamination is Tiger nut (Cyperus esculentus L.). We evaluated the bacteriological quality of Tiger nuts under various consumer treatment conditions post purchase.Three tiger nut samples each from 7 vendors were obtained by convenient sampling in Ho, the capital of the Volta Region of Ghana. The samples were subjected to vigorous washes in 1%, 2% and 3% sterile saline with tap water as control. The resulting liquids were analysed for microbial load and species using specific media and standard microbial methods. Data obtained from the study were analysed by ANOVA, and significant differences among means were defined at p<0.05. The mean bacterial count for the fresh tiger nut in tap water ranged from 1.95×106 to 1.59×107 cfu/mL whilst that in tap water only (control), 1%, 2% and 3% saline solutions recorded a range of 7.08×105 to 1.18×107, 7.31×105 to 1.34×107, 4.0×104 to 1.13×107 and 1.11×105 to 9.62×106 cfu/mL respectively. The higher bacterial load from the tiger nut in the sterile tap water was above the acceptable reference limit of 105 cfu/mL by the National Administration for Food Drugs and Control (NAFDAC). The mean bacterial count of Escherichia coli and Staphylococcus aureus in all the 21 samples was 6.15 log10 and 6.18 log10 cfu/mL respectively, all of which exceeded the acceptable range from 102 to 103 cfu/mL by the International Commission on Microbiological Specifications for Foods (ICMSF).To improve the bacteriological quality of tiger nut, proper farming practices, handling and treatment regimens under hygienic conditions should be employed to reduce or eliminate the occurrence of contaminants to ensure the protection and safety of the consumer.

Dimensionality of food safety and hygiene training programs for food handlers in Lusaka, Zambia

Globally, foodborne illnesses pose a substantial threat to public health, contributing significantly toillness and death. The behaviors, awareness, and attitudes of food handlers are critical determinantsof food safety. This research aimed to investigate the comprehensiveness and scope of food safetyand hygiene training initiatives targeting food handlers in Lusaka, Zambia. To this end, weconducted a two-phase qualitative analysis and evaluation of available training materials. Thisincluded interviews with 18 food establishment managers/ Human resource officers" should not becapitalized unless it is part of a proper noun. The analysis was conducted manually to identifyemerging themes and understanding the materials to assess the entry requirements for participants,duration of training, qualifications of trainers, topics covered and the delivery methods used. Thestudy found no uniform format for the training materials which also lacked important topics on foodsafety systems and Good Agricultural Practices and Good Agricultural Practices topics.Additionally, the study found poor uptake of the training due to a lack of awareness of legalrequirements, high attrition, training costs, and a lack of established institutions offering the trainingon a regular basis. This study recommends the standardization of food safety and hygiene trainingprograms in Zambia, tailored to the local context. Specifically, the development of a Participant'sHandbook and a Facilitator's Manual is recommended. These resources should outline qualificationsand competencies required for trainers, duration and format of training and entry requirements andprerequisites for trainees

Characterization, application and action mechanism of bioactive peptides (BAPs) derived from microbes, plants and recombinant proteins against food borne pathogens; a review

The preventive properties of bioactive peptides (BAPs) derived from microbes and plants have stimulated extensive research and discovery. The antimicrobial properties of BAPs against foodborne pathogens have made them effective and potential alternatives to existing antibiotics. Antitumor, antihypertensive, antioxidant, anti-obesity, and antidiabetic activities are just a few of the other beneficial properties of BAPs. An increasing number of harmful microorganisms, including foodborne pathogens, are developing resistance to various antibiotics. The goal of scientific research is to discover new, innovative and safe antimicrobial agents to fight these infections. Foodborne pathogens are among the many pathogenic microorganisms against which plant and microbial BAPs have shown significant antimicrobial activity. These compounds (BAPs) have the ability to eliminate pathogenic microorganisms by disrupting membrane integrity, inhibiting DNA and RNA synthesis, preventing protein synthesis, blocking protein activity or interacting with specific intracellular targets. In addition, the beneficial effect of BAP consumption includes the regulation of intestinal microbiota and modulation of the balance of reactive oxygen species in the digestive tract. This review article deals with different sources of antipathogen peptides, the food application of peptides from distinct sources, and their Mechanism of action.

Assessment of the Microbial Profile of Selected Commercially Prepared Food Spices in Nigeria

The microbial profiles and antibiogram patterns of some commercially prepared food spices in Nigeria were evaluated in this study. Ten selected food spices (cinnamon, coriander, black pepper, chilli pepper, suya spice, salad cream, paprika, parsley, mint and basil) were purchased from the popular Oja-Oba market in Akure, Nigeria. Standard microbiological assays were used to identify and quantify microorganisms in the spices. The antibiotic sensitivity of bacterial and fungal isolates was tested using the disk diffusion method. Twelve bacterial species (Staphylococcus aureus, Enterococcus faecalis, Lactobacillus plantarum, Escherichia coli, Pseudomonas aeruginosa, Salmonella typhimurium, Proteus mirabilis, Enterobacter aerogenes, Bacillus cereus, Clostridium perfringens, Klebsiella pneumoniae and Citrobacter freundii) were isolated from the food spices. Bacillus cereus and Enterobacter aerogenes were the most prevalent, while Proteus mirabilis, Pseudomonas aeruginosa, and Clostridium perfringens were the least frequently encountered bacterial species. Four Fungal species (Aspergillus niger, Aspergillus fumigatus, Saccharomyces cerevisiae, and Fusarium oxysporum) were also isolated from the food spices, with Aspergillus niger and Saccharomyces cerevisiae the most frequently encountered and Aspergillus fumigatus the least regularly encountered fungal species. The bacterial load of the food spices ranged from 8.0 x 103 to 9.0 x 105 CFU/ml, while the mean fungal count ranged from 2.0 x 103 to 1.2 x 105 SFU/ml. Antibiogram analysis revealed that Pefloxacin had the highest efficacy and Zinacef the least in all isolated bacterial species. At the same time, Ketoconazole exhibited the highest effectiveness in all isolated fungal species, and Nystatin showed the least effectiveness. The high population of pathogenic microorganisms coupled with the presence of Salmonella typhimurium and other enteric microorganisms in the food spices can cause severe foodborne illness to the consumers of such food spices and may lead to foodborne illness outbreaks.

Efficacy Evaluation of Jania rubens Extract Against Four Pathogenic Strains Associated with Foodborne Disease in Iran

This study evaluated the antimicrobial properties of Jania rubens algae extract, obtained via Soxhlet extraction, against food spoilage and pathogenic bacteria. Using response surface methodology and the Box-Behnken design, the research optimized extraction parameters, including solvent type, solvent-to-algae ratio, and extraction duration. Antimicrobial efficacy was assessed through the zone of inhibition (ZOI), Minimum Inhibitory Concentration (MIC), and Minimum Bactericidal Concentration (MBC) against Escherichia coli, Salmonella enteritidis, Staphylococcus aureus, and Bacillus cereus. Results showed MIC and MBC values for E. coli ranged from 0.32–1.5 and 2–3, respectively; for S. enteritidis, 0.98–1.9 and 2.5–3.5; for S. aureus, 0.4–1.5 and 0.8–2.8; and for B. cereus, 0.36–1.35 and 0.85–1.85. Optimal extraction conditions included acetone as the solvent, a 5:1 solvent-to-algae ratio, and extraction durations of 2 or 6 hours. The algae extract significantly extended the lag phase and reduced bacterial growth rates, with effects intensifying at higher concentrations. The study concludes that Jania rubens extract, particularly under optimized Soxhlet extraction conditions, exhibits potent antibacterial activity, making it a promising natural antimicrobial agent for food preservation.

Efficacy Evaluation of Jania rubens Extract Against Four Pathogenic Strains Associated with Foodborne Disease in Iran

This study evaluated the antimicrobial properties of Jania rubens algae extract, obtained via Soxhlet extraction, against food spoilage and pathogenic bacteria. Using response surface methodology and the Box-Behnken design, the research optimized extraction parameters, including solvent type, solvent-to-algae ratio, and extraction duration. Antimicrobial efficacy was assessed through the zone of inhibition (ZOI), Minimum Inhibitory Concentration (MIC), and Minimum Bactericidal Concentration (MBC) against Escherichia coli, Salmonella enteritidis, Staphylococcus aureus, and Bacillus cereus. Results showed MIC and MBC values for E. coli ranged from 0.32–1.5 and 2–3, respectively; for S. enteritidis, 0.98–1.9 and 2.5–3.5; for S. aureus, 0.4–1.5 and 0.8–2.8; and for B. cereus, 0.36–1.35 and 0.85–1.85. Optimal extraction conditions included acetone as the solvent, a 5:1 solvent-to-algae ratio, and extraction durations of 2 or 6 hours. The algae extract significantly extended the lag phase and reduced bacterial growth rates, with effects intensifying at higher concentrations. The study concludes that Jania rubens extract, particularly under optimized Soxhlet extraction conditions, exhibits potent antibacterial activity, making it a promising natural antimicrobial agent for food preservation.

Detection of Foodborne Viruses in Dates Using ISO 15216 Methodology

Foodborne viruses such as human norovirus (HuNoV) and hepatitis A virus (HAV) are the major causes of foodborne illnesses worldwide. These viruses have a low infectious dose and are persistent in the environment and food for weeks. Ready-to-eat (RTE) low moisture foods (LMFs) undergo minimal pathogen reduction processes. In recent years, multiple foodborne HAV outbreaks involving hundreds of individuals were associated with the consumption of dates, indicating that they could be important vehicles for foodborne infection. There is no standard method for the extraction and detection of foodborne viruses from dates, but herein we have compared the efficiency of three different protocols based on the ISO 15216 method in the extraction of murine norovirus (MNV) from whole Medjool dates and successfully employed the best performing method in the extraction of HAV, HuNoV GI, and GII and determined the limit of detection (LOD95) of 61, 148, and 184 genomic equivalent (gEq) per 25 g, respectively. Finally, we tested the adopted method on various varieties of dates including pitted ones and reported the detection of HuNoV GI and GII from four naturally contaminated date varieties. This ISO 15216 protocol could be employed for surveillance purposes and outbreak management related to dates.

Fresh Vegetables as a Source of Multidrug Resistant Pathogens

Background: Global increase of fresh vegetables consumption as a healthy food, often eaten raw, raises concerns about foodborne illnesses and the spread of antimicrobial-resistant pathogens due to contamination through various sources. Objective: To determine the microbial quality of common vegetables in the Gaza Strip and the antimicrobial resistance of bacteria recovered from vegetables samples. Methods: One-hundred and fifty vegetable samples consisting of ten types (10 samples of Cabbage, 20 Red cabbage, 20 Cucumber, 20 Tomato, 10 Parsley, 20 Eruca, 10 Green mint, 10 Lettuce, 20 Radish, and 10 Green onion) were collected from local farms and markets. Standard microbiological techniques were used to quantify (total viable count, coliform, Staphylococcus aureus, Pseudomonas and Enterococcus) and identify bacteria. Antimicrobial susceptibility testing (disk diffusion and microbroth dilution) was performed in accordance to clinical and laboratory standards institute (CLSI document). Results: Most samples (98%) were positive for coliforms, followed by Pseudomonas (94%), Staphylococcus aureus (89.3%), and Enterococcus (81.3%). High levels of antibiotic resistance were observed across various bacterial species. Enterobacteriaceae showed the highest resistance to ceftriaxone (76.2%) and the lowest resistance to amikacin (8.2%). Staphylococcus aureus had the highest resistance to penicillin (92.6%) and the lowest resistance to clarithromycin/levofloxacin (22.8%). Enterococcus spp. displayed the highest resistance to penicillin (94.4%) and the lowest resistance to norfloxacin (21.6%). Finally, Pseudomonas exhibited the highest resistance to ertem (70.9%) and the lowest resistance to amikacin (25.4%). Conclusion: Microbial contamination and antimicrobial resistance in vegetables pose a significant public health threat in the Gaza Strip. Improved agricultural practices, enhanced food safety, responsible antimicrobials use, and continuous monitoring are crucial to mitigate these risks.

Automated Classification of Biscuit Quality Using YOLOv8 Models in Food Industry

Abstract It is of great importance for food safety and consumer satisfaction that industrial food products are durable, hygienic, and flawless. Robust products protect the physical integrity of the product by preventing damage that may occur during the production and transportation processes, which meets the expectations of the consumer. Hygienic production conditions prevent foodborne diseases by minimizing the risk of microbial contamination and protect consumer health. Perfect products strengthen the brand image with their aesthetic and satisfactory features and increase consumer loyalty. In the study conducted in this context, the classification of defect and no defect conditions of biscuits in the food industry was examined using YOLOv8 models. A summary dataset consisting of 4990 biscuit images was created and the biscuits were initially divided into two categories: defect and no defect. Later, defect biscuits were classified into three subcategories: not complete, overcooked, and texture defect. As a result of experiments with YOLOv8 models, binary classification (defect, no defect), the highest accuracy rate was achieved in the YOLOv8-m, YOLOv8-l, and YOLOv8-x models with 96.78%, while the highest accuracy rate in the triple classification (not complete, overcooked, and texture defect) performance was achieved in the YOLOv8-m model with 96.99%.

What was Killing Babies in Sundsvall? A Study of Infant Mortality Patterns Using Individual Level Cause of Death Data, 1860–1892

In this report, we analyse infant mortality in Sundsvall 1860–1892. The focus is on the pattern and development of causes of death with separate analyses of neonatal and post-neonatal mortality. Furthermore, we discuss the development of infant mortality in relation to possible determinants in the historical context in Sundsvall. The results show substantial differences between neonatal and post-neonatal mortality when it comes to causes of death as well as their seasonal pattern. For deaths in the first 28 days, a large proportion of the deaths were diagnosed as unknown disease or given vague and symptom-descriptive diagnoses. For post-neonatal mortality on the other hand, the dominant cause of death categories were water- and food-borne infections and air-borne infections. Water- and food-borne diseases had a very strong seasonal pattern with the peak in late summer — July and August. There is no indication that sanitary improvements in the 1880's led to fewer cases of diarrhoea. Mortality from air-borne diseases on the other hand was lowest during summer, instead peaking in the winter months.

Antibacterial activity and multi-target mechanism of harmane against Escherichia coli O157:H7 and its application on ready-to-eat leafy greens.

Escherichia coli O157:H7 has caused many foodborne disease outbreaks and resulted in unimaginable economic losses. With the evolution of food consumption, people prefer natural preservatives. In this study, the natural agent harmane exhibited potential activity against E. coli O157:H7 (MIC=64μg/mL). It exhibited bacteriostatic mode at 1 X and 2 X MIC treatment, and bactericidal mode at 4 X MIC treatment. Moreover, it showed good in vitro stability in sheep plasma, low in vitro hemolysis and no in vivo acute toxicity with LD50 > 50mg/kg. Moreover, harmane significantly decreased the colony number of E. coli O157:H7 in fresh-cut lettuce samples after 5days of storage without affecting appearance. The mechanism study elucidated that harmane significantly decomposed the mature biofilm by reducing exopolysaccharide contents, and killed the viable bacterial cells in biofilm. The cell wall was damaged by harmane via interacting with peptidoglycan. Fluorescent staining and intracellular macromolecular leakage assays showed that irreversible destruction to membrane permeability and integrity. When entering the cell, harmane could defeat the redox balance, suppress metabolic activity and target to ribosome. These findings not only revealed the application potential of harmane as new natural preservative, but also preliminarily elucidated the multi-target mechanism, providing a new strategy for controlling E. coli O157:H7 in the food industry.

Advancing foodborne pathogen detection: a review of traditional and innovative optical and electrochemical biosensing approaches.

Foodborne diseases are a significant cause of morbidity (600 million cases) and mortality (420,000 deaths) worldwide every year and are mainly associated with pathogens. Besides the direct effects on human health, they have relevant concerns related to financial, logistics, and infrastructure for the food and medical industries. The standard pathogen identification techniques usually require a sample enrichment step, plating, isolation, and biochemical tests. This process involves specific facilities, a long-time analysisprocedures, and skilled personnel. Conversely, biosensors are an emerging innovative approach to detecting pathogens in real time due to their portability, specificity, sensitivity, and low fabrication costs. These advantages can be achieved from the synergistic work between nanotechnology, materials science, and biotechnology for coupling biomolecules in nano-matrices to enhance biosensing performance. This review highlights recent advancements in electrochemical and optical biosensing techniques for detecting bacteria and viruses. Key properties, such as detection limits, are examined, as they depend on factors like the design of the biorecognition molecule, the type of transducer, the target's characteristics, and matrix interferences. Sensitivity levels reported range from 1 to 1 × 10⁸ CFU/mL, with detection times spanning 10min to 8h. Additionally, the review explores innovative approaches, including biosensors capable of distinguishing between live and dead bacteria, multimodal sensing, and the simultaneous detection of multiple foodborne pathogens-emerging trends in biosensor development.

In silico design of an epitope-based vaccine ensemble for fasliolopsiasis

IntroductionFasciolopsiasis, a food-borne intestinal disease is most common in Asia and the Indian subcontinent. Pigs are the reservoir host, and fasciolopsiasis is most widespread in locations where pigs are reared and aquatic plants are widely consumed. Human infection has been most commonly documented in China, Bangladesh, Southeast Asia, and parts of India. It predominates in school-age children, and significant worm burdens are not uncommon. The causal organism is Fasciolopsis buski, a giant intestinal fluke that infects humans and causes diarrhoea, fever, ascites, and intestinal blockage. The increasing prevalence of medication resistance and the necessity for an effective vaccination make controlling these diseases challenging.MethodsOver the last decade, we have achieved major advances in our understanding of intestinal fluke biology by in-depth interrogation and analysis of evolving F. buski omics datasets. The creation of large omics datasets for F. buski by our group has accelerated the discovery of key molecules involved in intestinal fluke biology, toxicity, and virulence that can be targeted for vaccine development. Finding successful vaccination antigen combinations from these huge number of genes/proteins in the available omics datasets is the key in combating these neglected tropical diseases. In the present study, we developed an in silico workflow to select antigens for composing a chimeric vaccine, which could be a significant technique for developing a fasciolopsiasis vaccine that prevents the parasite from causing serious harm.Results and discussionThis chimeric vaccine can now be tested experimentally and compared to other vaccine candidates to determine its potential influence on human health. Although the results are encouraging, additional validation is needed both in vivo and in vitro. Considering the extensive genetic data available for intestinal flukes that has expanded with technological advancements, we may need to reassess our methods and suggest a more sophisticated technique in the future for identifying vaccine molecules.

Clonorchis sinensis and Echinostoma hortense detected by endoscopy and molecular characterization: two case reports and update on diagnosis

Clonorchis sinensis (C. sinensis) and Echinostoma hortense (E. Hortense) infections represent significant food-borne zoonotic parasitic diseases. C. sinensis stands as the primary parasite underlying cholangitis, cholelithiasis, and even cholangiocarcinoma, whereas E. Hortense parasitizes the duodenum. Unfortunately, the non-specific clinical presentations of these two trematodes frequently mislead clinicians, resulting in overlooks or misdiagnoses, and consequently, inadequate treatment. We diagnosed digestive system trematodes through endoscopic observation and molecular methods. Herein, we present a case where C. sinensis was definitively diagnosed through direct observation under duodenoscopy. For the first time, we captured the entire migratory process of the parasite from the common bile duct into the intestinal lumen. In another case, multiple active trematodes were detected on the duodenal wall under duodenoscopy, subsequently extracted using endoscopic forceps. Based on the morphology of the worms and their eggs, an initial diagnosis of Echinostoma was made. To confirm the species, we designed primers targeting the ribosomal ITS (internal transcribed spacer) and mitochondrial COX-1 (cyclooxygenase-1) genes, followed by PCR amplification and sequencing. The results conclusively matched the sequence of E. Hortense, verifying our final diagnosis. Our proposed approach, integrating endoscopy with molecular characteristics, offers novel strategies for diagnosing trematode infections. This methodology represents a significant advancement in the field, enhancing the accuracy and timeliness of treatment interventions.

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.

Association of the PhoQ/PhoP Stress Response System with the Internalization of Escherichia coli O157:H7 in Romaine Lettuce

Foodborne illness associated with Escherichia coli O157:H7 (E. coli O157) and romaine lettuce is a serious and persistent food safety issue. This study investigated the ability and associated genetic traits of five E. coli O157 strains—namely 86-24, 93-111, C7927, MF1847, and 505B—to internalize in romaine lettuce grown in soil and hydroponic systems. The results showed significant variations in the strains’ ability to internalize, with soil cultivation being more susceptible to E. coli O157 internalization relative to hydroponics. Whole-genome comparisons and an analysis of the five E. coli O157 strains revealed insights into the potential genetic traits associated with internalization capacity. A single unique gene, ORF-4296, was found to be present in all four internalizing strains (86-24, 93-111, C7927, and MF1847), but absent in the non-internalizing strain 505B. Immediately downstream of OFR-4296 is the PhoQ/PhoP operon, which regulates the important stress responses of E. coli O157. Our data showed that this operon was identical in the four internalizing strains but different in strain 505B. Specifically, the C-terminal of PhoQ in strain 505B had a distinct amino acid sequence. The inability of 505B to internalize may be linked to its lack of ORF-4296 and its distinctive C-terminal sequence of PhoQ.

Molecular Characterization of Whole Genome Sequencing of Salmonella spp. in Shapingba District, Chongqing, China, 2016-2023.

In recent years, Salmonella infection is a major global public health concern, particularly in food safety. This study analyzed the genomes of 102 Salmonella strains isolated between 2016 and 2023 from food, foodborne disease patients, and food poisoning incidents, focusing on their molecular characteristics, antibiotic resistance genes (ARGs), and virulence genes. S. enterica serovar Enteritidis (37.3%) and S. enterica serovar Typhimurium (21.6%, including its monophasic variant 1,4,[5],12:i:-) were the main strains among 22 serotypes. Multilocus sequence typing revealed 23 sequence types (STs), with ST11, ST19, and ST34 as the most prevalent. All strains carried at least 24 ARGs. Detection rates for aac(6')-Iy, blaTEM-1, and sul2 ranged from 44.1% to 63.7%, mainly in S. Enteritidis and S. Typhimurium. Rates for qnrS1, sul1, and aadA were 12.8% to 16.7%, while mcr-1 appeared in one ST34 S. Typhimurium strain. All strains contained at least 98 virulence genes. The genes pefABCD, mig-5, and spvBCD were in 48.0% of strains, while rck was found in 36.3%, mainly linked to S. Enteritidis and S. Typhimurium. The tssM gene was found in 37.3% of the strains, exclusively in S. Enteritidis. Core genome single nucleotide polymorphisms (cgSNPs) analysis grouped the strains into nine clusters, with 75.5% belonging to three major groups. Food poisoning event 1 was correlated with cluster 3, while events 2 and 3 were linked to cluster 1. Across events, SNP differences among strains were ≤6. Strains with SNP differences ≤10 were also found in other clusters. This method is promising for tracking sporadic cases and identifying potential foodborne safety incidents. Salmonella strains in the region exhibit substantial genetic diversity, demonstrating the efficacy of cgSNPs analysis for source tracking. Ongoing surveillance is essential given the prevalence of ARGs and virulence genes. This study provides a data foundation for local Salmonella epidemiology.