Molecular typing and genome sequencing allow the identification of persistent Listeria monocytogenes strains and the tracking of the contamination source in food environments

Significance of Whole-Genome Sequencing for the Traceability of Foodborne Pathogens: During the Processing of Meat and Dairy Products

The complexity of tracing foodborne pathogens in the food chain has increased significantly due to the long and complicated chain, the involvement of numerous links, and the presence of various types of pathogens at different stages and environments. Traditional typing techniques are not sufficient to meet the requirements of tracing pathogens in the food chain. Whole-Genome Sequencing (WGS) has gradually become an important technological tool for characterizing and tracing pathogens in the food chain due to comprehensive information, speed, and superior discriminatory power. This paper provides an overview of the advantages of WGS and its application in foodborne pathogen traceability. This paper focused on foodborne pathogen contamination pathways during the processing of animal foods in commercial restaurant kitchens and the potential contamination of milk, milk powder, and other dairy products by pathogens during processing in the dairy industry chain and environments. Improper handling practices during meat processing (i.e., using cloths, washing hands without soap, and cleaning boards with knives) were a critical point of foodborne pathogen cross-contamination in commercial kitchen premises. However, in dairy products, contamination of pathogens in raw milk was the main cause of foodborne disease outbreaks. Therefore, preventing the contamination of pathogens in food should not only be focused on hygiene measures during processing and in environments but also on the quality and hygiene of raw materials to prevent the spread of foodborne pathogens throughout the entire production chain. Further, Whole-Metagenome Sequencing and DNA sequence markers are considered to be the future direction of WGS. The purpose of this work is to promote the wider application of WGS during the processing of meat and dairy products and provide theoretical support for the rapid investigation and accurate traceability of foodborne pathogen outbreaks in food.

Inhibitory Effect of DNase-Chitosan-Nisin Nanoparticles on Cell Viability, Motility, and Spatial Structures of Listeria monocytogenes Biofilms

Listeria monocytogenes biofilm contamination on food contact surfaces is a major concern for the food industry. Nanoparticle encapsulation appears as a novel strategy for food surface disinfection to prevent biofilm formation. Chitosan nanoparticles loaded with nisin and DNase I (DNase-CS-N) have been constructed to exhibit antimicrobial activity against L. monocytogenes. This study aimed to investigate their ability to inhibit L. monocytogenes biofilm formation and eliminate preformed biofilms on food contact surfaces (polystyrene, polyurethane, and stainless steel). DNase-CS-N could decrease 99% and 99.5% biofilm cell numbers at 1/2 MIC and MIC, respectively. At sub-MICs, DNase-CS-N could reduce cell motility (swimming and swarming) and slime production of L. monocytogenes. In terms of effect on biofilm elimination, DNase-CS-N at the concentration of 4 MIC led to 3-4 log reduction in biofilm cells in preformed biofilms, performing higher efficiency compared with other treatments (CSNPs, CS-N). Furthermore, the three-dimensional structure of L. monocytogenes biofilms was severely disrupted after DNase-CS-N treatment, with bacterial cells scattered on the surface. The morphology of biofilm cells was also greatly damaged with wrinkled surfaces, disrupted cell membranes, and leakage of intracellular nucleic acids and proteins. These results indicate the potential applicability of DNase-CS-N for inhibiting and eliminating L. monocytogenes biofilms on food contact surfaces.

The Relationship between Biofilm Phenotypes and Biofilm-Associated Genes in Food-Related Listeria monocytogenes Strains

Listeria monocytogenes is an important pathogen responsible for listeriosis, a serious foodborne illness associated with high mortality rates. Therefore, L. monocytogenes is considered a challenge for the food industry due to the ability of some strains to persist in food-associated environments. Biofilm production is presumed to contribute to increased L. monocytogenes resistance and persistence. The aims of this study were to (1) assess the biofilm formation of L. monocytogenes isolates from a meat processing facility and sheep farm previously characterized and subjected to whole-genome sequencing and (2) perform a comparative genomic analysis to compare the biofilm formation and the presence of a known set of biofilm-associated genes and related resistance or persistence markers. Among the 37 L. monocytogenes isolates of 15 sequence types and four serogroups involved in this study, 14%, 62%, and 24% resulted in the formation of weak, moderate, and strong biofilm, respectively. Increased biofilm-forming ability was associated with the presence of the stress survival islet 1 (SSI-1), inlL, and the truncated inlA genes. Combining the phenotypic and genotypic data may contribute to understanding the relationships between biofilm-associated genes and L. monocytogenes biofilm-forming ability, enabling improvement in the control of this foodborne pathogen.

Stress resistant rpsU variants of Listeria monocytogenes can become underrepresented due to enrichment bias

Population heterogeneity is an important component of the survival mechanism of Listeria monocytogenes, leading to cells in a population with diverse stress resistance levels. We previously demonstrated that several ribosomal gene rpsU mutations enhanced the stress resistance of L. monocytogenes and lowered the growth rate at 30 °C and lower temperatures. This study investigated whether these switches in phenotypes could result in a bias in strain detection when standard enrichment-based procedures are applied to a variety of strains. Detailed growth kinetics analysis of L. monocytogenes strains were performed, including the LO28 wild type (WT) and rpsU variants V14 and V15, during two commonly used enrichment-based procedures described in the ISO 11290-1:2017 and the U.S. Food and Drug Administration Bacteriological Analytical Manual (BAM). WT had a higher growth rate than the variants during the enrichment processes. Co-culture growth kinetics predictions for WT and rpsU variants showed that the detection chances of the rpsU mutants were reduced from ∼52 % to less than ∼13 % and ∼ 3 % during ISO and BAM enrichment, respectively, which were further validated through subsequent qPCR experiments. Higher heat stress resistance of rpsU variants did not lead to faster recovery during enrichment after heat treatment, and different pre-culturing temperatures before heat treatment did not significantly affect the growth kinetics of the WT and rpsU variants. Additionally, post-enrichment isolation procedures involving streaking on selective agar plates did not show preferences for isolating WT or rpsU variants nor affect the detection chance of rpsU variants. The difference in detection chance suggests that the selective enrichment procedures inadequately represent the genotypic diversity present in a sample. Hence, the enrichment bias during the L. monocytogenes isolation procedure may contribute to the observed underrepresentation of the rpsU mutation among L. monocytogenes isolates deposited in publicly available genome databases. The underrepresentation of rpsU mutants in our findings suggests that biases introduced by standard isolation and enrichment procedures could inadvertently skew our understanding of genetic diversity when relying on public databases.

Intensive Environmental Sampling and Whole Genome Sequence-based Characterization of Listeria in Small- and Medium-sized Dairy Facilities Reveal Opportunities for Simplified and Size-appropriate Environmental Monitoring Strategies

Small- and medium-sized dairy processing facilities (SMDFs) may face unique challenges with respect to controlling Listeria in their processing environments, e.g., due to limited resources. The aim of this study was to implement and evaluate environmental monitoring programs (EMPs) for Listeria control in eight SMDFs in a ∼1-year longitudinal study; this included a comparison of pre-operation (i.e., after cleaning and sanitation and prior to production) and mid-operation (i.e., at least 4 h into production) sampling strategies. Among 2,072 environmental sponge samples collected across all facilities, 272 (13%) were positive for Listeria. Listeria prevalence among pre- and mid-operation samples (15% and 17%, respectively), was not significantly different. Whole genome sequencing (WGS) performed on select isolates to characterize Listeria persistence patterns revealed repeated isolation of closely related Listeria isolates (i.e., ≤20 high-quality single nucleotide polymorphism [hqSNP] differences) in 5/8 facilities over >6 months, suggesting Listeria persistence and/or reintroduction was relatively common among the SMDFs evaluated here. WGS furthermore showed that for 41 sites where samples collected pre- and mid-operation were positive for Listeria, Listeria isolates obtained were highly related (i.e., ≤10 hqSNP differences), suggesting that pre-operation sampling alone may be sufficient and more effective for detecting sites of Listeria persistence. Importantly, our data also showed that only 1/8 of facilities showed a significant decrease in Listeria prevalence over 1 year, indicating continued challenges with Listeria control in at least some SMDFs. We conclude that options for simplified Listeria EMPs (e.g., with a focus on pre-operation sampling, which allows for more rapid identification of likely persistence sites) may be valuable for improved Listeria control in SMDFs.

Radical species generating technologies for decontamination of Listeria species in food: a recent review report

Foodborne illnesses occur due to the contamination of fresh, frozen, or processed food products by some pathogens. Among several pathogens responsible for the illnesses, Listeria monocytogenes is one of the lethal bacteria that endangers public health. Several preexisting and novel technologies, especially non-thermal technologies are being studied for their antimicrobial effects, particularly toward L. monocytogenes. Some noteworthy emerging technologies include ultraviolet (UV) or light-emitting diode (LED), pulsed light, cold plasma, and ozonation. These technologies are gaining popularity since no heat is employed and undesirable deterioration of food quality, especially texture, and taste is devoided. This review aims to summarize the most recent advances in non-thermal processing technologies and their effect on inactivating L. monocytogenes in food products and on sanitizing packaging materials. These technologies use varying mechanisms, such as photoinactivation, photosensitization, disruption of bacterial membrane and cytoplasm, etc. This review can help food processing industries select the appropriate processing techniques for optimal benefits, in which the structural integrity of food can be preserved while simultaneously destroying L. monocytogenes present in foods. To eliminate Listeria spp., different technologies possess varying mechanisms such as rupturing the cell wall, formation of pyrimidine dimers in the DNA through photochemical effect, excitation of endogenous porphyrins by photosensitizers, generating reactive species, causing leakage of cellular contents and oxidizing proteins and lipids. These technologies provide an alternative to heat-based sterilization technologies and further development is still required to minimize the drawbacks associated with some technologies.

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis K, Allende A, Bolton D, Bover‐Cid S, Chemaly M, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Nonno R, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Fox E, Gosling R(B, Gil BM, Møretrø T, Stessl B, da Silva Felício MT, Messens W, Simon AC, Alvarez‐Ordóñez A. Persistence of microbiological hazards in food and feed production and processing environments

Listeria monocytogenes (in the meat, fish and seafood, dairy and fruit and vegetable sectors), Salmonella enterica (in the feed, meat, egg and low moisture food sectors) and Cronobacter sakazakii (in the low moisture food sector) were identified as the bacterial food safety hazards most relevant to public health that are associated with persistence in the food and feed processing environment (FFPE). There is a wide range of subtypes of these hazards involved in persistence in the FFPE. While some specific subtypes are more commonly reported as persistent, it is currently not possible to identify universal markers (i.e. genetic determinants) for this trait. Common risk factors for persistence in the FFPE are inadequate zoning and hygiene barriers; lack of hygienic design of equipment and machines; and inadequate cleaning and disinfection. A well-designed environmental sampling and testing programme is the most effective strategy to identify contamination sources and detect potentially persistent hazards. The establishment of hygienic barriers and measures within the food safety management system, during implementation of hazard analysis and critical control points, is key to prevent and/or control bacterial persistence in the FFPE. Once persistence is suspected in a plant, a 'seek-and-destroy' approach is frequently recommended, including intensified monitoring, the introduction of control measures and the continuation of the intensified monitoring. Successful actions triggered by persistence of L. monocytogenes are described, as well as interventions with direct bactericidal activity. These interventions could be efficient if properly validated, correctly applied and verified under industrial conditions. Perspectives are provided for performing a risk assessment for relevant combinations of hazard and food sector to assess the relative public health risk that can be associated with persistence, based on bottom-up and top-down approaches. Knowledge gaps related to bacterial food safety hazards associated with persistence in the FFPE and priorities for future research are provided.

Environmental persistence of Listeria monocytogenes and its implications in dairy processing plants

Listeriosis, an invasive illness with a fatality rate between 20% and 30%, is caused by the ubiquitous bacterium Listeria monocytogenes. Human listeriosis has long been associated with foods. This is because the ubiquitous nature of the bacteria renders it a common food contaminant, posing a significant risk to the food processing sector. Although several sophisticated stress coping mechanisms have been identified as significant contributing factors toward the pathogen's persistence, a complete understanding of the mechanisms underlying persistence across various strains remains limited. Moreover, aside from genetic aspects that promote the ability to cope with stress, various environmental factors that exist in food manufacturing plants could also contribute to the persistence of the pathogen. The objective of this review is to provide insight into the challenges faced by the dairy industry because of the pathogens' environmental persistence. Additionally, it also aims to emphasize the diverse adaptation and response mechanisms utilized by L. monocytogenes in food manufacturing plants to evade environmental stressors. The persistence of L. monocytogenes in the food processing environment poses a serious threat to food safety and public health. The emergence of areas with high levels of L. monocytogenes contamination could facilitate Listeria transmission through aerosols, potentially leading to the recontamination of food, particularly from floors and drains, when sanitation is implemented alongside product manufacturing. Hence, to produce safe dairy products and reduce the frequency of outbreaks of listeriosis, it is crucial to understand the factors that contribute to the persistence of this pathogen and to implement efficient control strategies.

DegU-mediated suppression of carbohydrate uptake in Listeria monocytogenes increases adaptation to oxidative stress

The foodborne bacterial pathogen Listeria monocytogenes exhibits remarkable survival capabilities under challenging conditions, severely threatening food safety and human health. The orphan regulator DegU is a pleiotropic regulator required for bacterial environmental adaptation. However, the specific mechanism of how DegU participates in oxidative stress tolerance remains unknown in L. monocytogenes. In this study, we demonstrate that DegU suppresses carbohydrate uptake under stress conditions by altering global transcriptional profiles, particularly by modulating the transcription of the phosphoenolpyruvate-carbohydrate phosphotransferase system (PTS)-related genes, such as ptsH, ptsI, and hprK. Specifically, in the absence of degU, the transcripts of ptsI are significantly upregulated and those of hprK are significantly downregulated in response to copper ion-induced stress. Overexpression of ptsI significantly increases bacterial growth in vitro, while overexpression of hprK leads to a decrease in growth. We further demonstrate that DegU directly senses oxidative stress, downregulates ptsI transcription, and upregulates hprK transcription. Additionally, through an electrophoretic mobility shift assay, we demonstrate that DegU directly regulates the transcription of ptsI and hprK by binding to specific regions within their respective promoter sequences. Notably, the putative pivotal DegU binding sequence for ptsI is located from 38 to 68 base pairs upstream of the ptsH transcription start site (TSS), whereas for hprK, it is mapped from 36 to 124 base pairs upstream of the hprK TSS. In summary, we elucidate that DegU plays a significant role in suppressing carbohydrate uptake in response to oxidative stress through the direct regulation of ptsI and hprK.ImportanceUnderstanding the adaptive mechanisms employed by Listeria monocytogenes in harsh environments is of great significance. This study focuses on investigating the role of DegU in response to oxidative stress by examining global transcriptional profiles. The results highlight the noteworthy involvement of DegU in this stress response. Specifically, DegU acts as a direct sensor of oxidative stress, leading to the modulation of gene transcription. It downregulates ptsI transcription while it upregulates hprK transcription through direct binding to their promoters. Consequently, these regulatory actions impede bacterial growth, providing a defense mechanism against stress-induced damage. These findings gained from this study may have broader implications, serving as a reference for studying adaptive mechanisms in other pathogenic bacteria and aiding in the development of targeted strategies to control L. monocytogenes and ensure food safety.

Listeria monocytogenes GshF contributes to oxidative stress tolerance via regulation of the phosphoenolpyruvate-carbohydrate phosphotransferase system

Glutathione (GSH) is an essential component of the glutaredoxin (Grx) system, and it is synthesized by the enzyme glutathione synthase GshF in Listeria monocytogenes. GSH plays a crucial role in regulating Listeria virulence by modifying the virulence factors LLO and PrfA. In this study, we investigated the involvement of L. monocytogenes GshF in oxidative tolerance and intracellular infection. Our findings revealed that the deletion of gshF resulted in a significant reduction in bacterial growth in vitro when exposed to diamide and copper ions stress. More importantly, this deletion also impaired the efficiency of invasion and proliferation in macrophages and mice organs. Furthermore, GshF influenced global transcriptional profiles, including carbohydrate and amino acid metabolism, particularly those related to the phosphoenolpyruvate-carbohydrate phosphotransferase system (PTS) genes lmo1997-lmo2004, under oxidative stress conditions. In the wild-type strain, the transcription of lmo1997-lmo2004 was notably downregulated in response to copper ions and diamide stress compared to normal conditions. However, in the absence of gshF, the transcripts of lmo1997-lmo2004 were upregulated in response to these stress conditions. Notably, the deletion of iiBman (lmo2002) enhanced oxidative stress tolerance to copper ions, whereas overexpression of iiBman reduced this resistance. In conclusion, our study provides the first evidence that L. monocytogenes GshF plays a crucial role in bacterial antioxidation through the regulation of iiBman.IMPORTANCEListeria monocytogenes has developed various mechanisms to withstand oxidative stress, including the thioredoxin and glutaredoxin systems. However, the specific role of the glutathione synthase GshF, responsible for synthesizing GSH in L. monocytogenes, in oxidative tolerance remains unclear. This study aimed to elucidate the relationship between GshF and oxidative tolerance in L. monocytogenes by examining the efficiency of invasion and proliferation in macrophages and mice organs, as well as analyzing global transcriptional profiles under oxidative stress conditions. The results revealed that GshF plays a significant role in L. monocytogenes' response to oxidative stress. Notably, GshF acts to suppress the transcription of phosphoenolpyruvate-carbohydrate phosphotransferase system genes lmo1997-lmo2004, among which iiBman (lmo2002) was identified as the most critical gene for resisting oxidative stress. These findings enhance our understanding of how L. monocytogenes adapts to its environment and provide valuable insights for investigating the environmental adaptation mechanisms of other pathogenic bacteria.

Risk factor-based clustering of Listeria monocytogenes in food processing environments using principal component analysis

Listeria monocytogenes has a range of strategies that allow it to persist as biofilms in food processing environments (FPE), making it a pathogen of concern to the food industry. The properties of these biofilms are highly variable among strains, and this significantly affects the risk of food contamination. The present study therefore aims to conduct a proof-of-concept study to cluster strains of L. monocytogenes by risk potential using principal component analysis, a multivariate approach. A set of 22 strains, isolated from food processing environments, were typed by serogrouping and pulsed-field gel electrophoresis, showing a relatively high diversity. They were characterized in terms of several biofilm properties that might pose a potential risk of food contamination. The properties studied were tolerance to benzalkonium chloride (BAC), the structural parameters of biofilms (biomass, surface area, maximum and average thickness, surface to biovolume ratio and roughness coefficient) measured by confocal laser scanning microscopy and (3) transfer of biofilm cells to smoked salmon. The PCA correlation circle revealed that the tolerance of biofilms to BAC was positively correlated with roughness, but negatively with biomass parameters. On the contrary, cell transfers were not related to three-dimensional structural parameters, which suggests the role of other variables yet unexplored. Additionally, hierarchical clustering grouped strains into three different clusters. One of them included the strains with high tolerance to BAC and roughness. Another one consisted of strains with enhanced transfer ability, whereas the third cluster contained those that stood out for the thickness of biofilms. The present study represents a novel and effective way to classify L. monocytogenes strains according to biofilm properties that condition the potential risk of reaching the consumer through food contamination. It would thus allow the selection of strains representative of different worst-case scenarios for future studies in support of QMRA and decision-making analysis.