Transcriptomic Analysis of the Adaptation of Listeria monocytogenes to Lagoon and Soil Matrices Associated with a Piggery Environment: Comparison of Expression Profiles

Gene expression changes throughout the life cycle allow a bacterial plant pathogen to persist in diverse environmental habitats

Bacterial pathogens exhibit a remarkable ability to persist and thrive in diverse ecological niches. Understanding the mechanisms enabling their transition between habitats is crucial to control dissemination and potential disease outbreaks. Here, we use Ralstonia solanacearum, the causing agent of the bacterial wilt disease, as a model to investigate pathogen adaptation to water and soil, two environments that act as bacterial reservoirs, and compare this information with gene expression in planta. Gene expression in water resembled that observed during late xylem colonization, with an intriguing induction of the type 3 secretion system (T3SS). Alkaline pH and nutrient scarcity-conditions also encountered during late infection stages-were identified as the triggers for this T3SS induction. In the soil environment, R. solanacearum upregulated stress-responses and genes for the use of alternate carbon sources, such as phenylacetate catabolism and the glyoxylate cycle, and downregulated virulence-associated genes. We proved through gain- and loss-of-function experiments that genes associated with the oxidative stress response, such as the regulator OxyR and the catalase KatG, are key for bacterial survival in soil, as their deletion cause a decrease in culturability associated with a premature induction of the viable but non culturable state (VBNC). This work identifies essential factors necessary for R. solanacearum to complete its life cycle and is the first comprehensive gene expression analysis in all environments occupied by a bacterial plant pathogen, providing valuable insights into its biology and adaptation to unexplored habitats.

Occurrence and Multidrug Resistance in Strains of Listeria monocytogenes Recovered from the Anaerobic Co-Digestion Sludge Contained in a Single Stage Steel Biodigester: Implications for Antimicrobial Stewardship

L. monocytogenes is a zoonotic foodborne pathogen with inherent adaptability to tolerate environmental and physiological stresses, thereby causing severe disease outbreaks. Antibiotic resistant foodborne pathogens are a challenge to the food industry. A total of 18 samples were pooled from a bio-digester co-digesting swine manure/pinewood sawdust, and evaluated for the occurrence of bacterium plus total viable counts using the spread plate method. The recovered bacterial isolates were presumptively identified by growth on selective medium and confirmed by biochemical characterisation, leading to the isolation of 43 L. monocytogenes. The isolates were characterized based on their susceptibility to antibiotics via the Kirby-Bauer disc diffusion technique against a panel of 14 antibiotics. Equally, the multiple antibiotic resistance (MAR) index was calculated, and MAR phenotypes generated. The bacterial counts were between 102 and104 cfu/mL. Complete susceptibility (100%) was demonstrated to ampicillin, gentamicin and sulfamethoxazole, which are the drugs of choice in the treatment of listeriosis. In addition, intermediate sensitivity occurred at 25.58% to cefotaxime, and the highest resistance (51.16%) was exhibited against nalidixic acid. The MAR index ranged from 0 to 0.71. Overall, 41.86% of the Listeria isolates displayed multidrug resistance, with 18 different MAR phenotypes, demonstrating CIP, E, C, TET, AUG, S, CTX, NA, AML, NI as the greatest MAR phenotype. It can be concluded that the isolates yielding MAR > 0.2 originated from the farm, where antibiotics had been in routine use. Therefore, strict monitoring of antibiotics use in the farm is crucial to mitigate further increase in antibiotic resistance amongst these bacterial isolates.

Comparative analysis of Listeria monocytogenes plasmid transcriptomes reveals common and plasmid‐specific gene expression patterns and high expression of noncoding RNAs

Recent research demonstrated that some Listeria monocytogenes plasmids contribute to stress survival. However, only a few studies have analyzed gene expression patterns of L. monocytogenes plasmids. In this study, we identified four previously published stress‐response‐associated transcriptomic data sets which studied plasmid‐harboring L. monocytogenes strains but did not include an analysis of the plasmid transcriptomes. The four transcriptome data sets encompass three distinct plasmids from three different L. monocytogenes strains. Differential gene expression analysis of these plasmids revealed that the number of differentially expressed (DE) L. monocytogenes plasmid genes ranged from 30 to 45 with log₂ fold changes of −2.2 to 6.8, depending on the plasmid. Genes often found to be DE included the cadmium resistance genes cadA and cadC, a gene encoding a putative NADH peroxidase, the putative ultraviolet resistance gene uvrX, and several uncharacterized noncoding RNAs (ncRNAs). Plasmid‐encoded ncRNAs were consistently among the highest expressed genes. In addition, one of the data sets utilized the same experimental conditions for two different strains harboring distinct plasmids. We found that the gene expression patterns of these two L. monocytogenes plasmids were highly divergent despite the identical treatments. These data suggest plasmid‐specific gene expression responses to environmental stimuli and differential plasmid regulation mechanisms between L. monocytogenes strains. Our findings further our understanding of the dynamic expression of L. monocytogenes plasmid‐encoded genes in diverse environmental conditions and highlight the need to expand the study of L. monocytogenes plasmid genes' functions.

Listeria monocytogenes: Investigation of Fitness in Soil Does Not Support the Relevance of Ecotypes

Listeria monocytogenes (Lm) is a ubiquitous bacterium that causes the serious foodborne illness listeriosis. Although soil is a primary reservoir and a central habitat for Lm, little information is available on the genetic features underlying the fitness of Lm strains in this complex habitat. The aim of this study was to identify (i) correlations between the strains fitness in soil, their origin and their phylogenetic position (ii) identify genetic markers allowing Lm to survive in the soil. To this end, we assembled a balanced panel of 216 Lm strains isolated from three major ecological compartments (outdoor environment, animal hosts, and food) and from 33 clonal complexes occurring worldwide. The ability of the 216 strains to survive in soil was tested phenotypically. Hierarchical clustering identified three phenotypic groups according to the survival rate (SR): phenotype 1 “poor survivors” (SR < 2%), phenotype 2 “moderate survivors” (2% < SR < 5%) and phenotype 3 “good survivors” (SR > 5%). Survival in soil depended neither on strains’ origin nor on their phylogenetic position. Genome-wide-association studies demonstrated that a greater number of genes specifically associated with a good survival in soil was found in lineage II strains (57 genes) than in lineage I strains (28 genes). Soil fitness was mainly associated with variations in genes (i) coding membrane proteins, transcription regulators, and stress resistance genes in both lineages (ii) coding proteins related to motility and (iii) of the category “phage-related genes.” The cumulative effect of these small genomic variations resulted in significant increase of soil fitness.

The Saprophytic Lifestyle of Listeria monocytogenes and Entry Into the Food-Processing Environment

Listeria monocytogenes is an environmentally adapted saprophyte that can change into a human and animal bacterial pathogen with zoonotic potential through several regulatory systems. In this review, the focus is on the occurrence of Listeria sensu stricto and sensu lato in different ecological niches, the detection methods, and their analytical limitations. It also highlights the occurrence of L. monocytogenes genotypes in the environment (soil, water, and wildlife), reflects on the molecular determinants of L. monocytogenes for the saprophytic lifestyle and the potential for antibiotic resistance. In particular, the strain-specific properties with which some genotypes circulate in wastewater, surface water, soil, wildlife, and agricultural environments are of particular interest for the continuously updating risk analysis.

The Fate of Foodborne Pathogens in Manure Treated Soil

The aim of this review was to provide an update on the complex relationship between manure application, altered pathogen levels and antibiotic resistance. This is necessary to protect health and improve the sustainability of this major farming practice in agricultural systems based on high levels of manure production. It is important to consider soil health in relation to environment and land management practices in the context of the soil microflora and the introduction of pathogens on the health of the soil microbiome. Viable pathogens in manure spread on agricultural land may be distributed by leaching, surface run-off, water source contamination and contaminated crop removal. Thus it is important to understand how multiple pathogens can persist in manures and on soil at farm-scale and how crops produced under these conditions could be a potential transfer route for zoonotic pathogens. The management of pathogen load within livestock manure is a potential mechanism for the reduction and prevention of outbreaks infection with Escherichia coli, Listeria Salmonella, and Campylobacter. The ability of Campylobacter, E. coli, Listeria and Salmonella to combat environmental stress coupled with their survival on food crops and vegetables post-harvest emphasizes the need for further study of these pathogens along with the emerging pathogen Providencia given its link to disease in the immunocompromised and its’ high levels of antibiotic resistance. The management of pathogen load within livestock manure has been widely recognized as a potential mechanism for the reduction and prevention of outbreaks infection but any studies undertaken should be considered as region specific due to the variable nature of the factors influencing pathogen content and survival in manures and soil. Mediocre soils that require nutrients could be one template for research on manure inputs and their influence on soil health and on pathogen survival on grassland and in food crops.

Foodborne pathogens in the omics era

Outbreaks and deaths related to Foodborne Diseases (FBD) occur constantly in the world, as a result of the consumption of contaminated foodstuffs with pathogens such as Listeria monocytogenes, Escherichia coli, Staphylococcus aureus, Salmonella spp, Clostridium spp. and Campylobacter spp. The purpose of this review is to discuss the main omic techniques applied in foodborne pathogen and to demonstrate their functionalities through the food chain and to guarantee the food safety. The main techniques presented are genomic, transcriptomic, secretomic, proteomic, and metabolomic, which together, in the field of food and nutrition, are known as "Foodomics." This review had highlighted the potential of omics to integrate variables that contribute to food safety and to enable us to understand their application on foodborne diseases. The appropriate use of these techniques had driven the definition of critical parameters to achieve successful results in the improvement of consumers health, costs and to obtain safe and high-quality products.

LisRK is required for optimal fitness of Listeria monocytogenes in soil

Listeria monocytogenes is a food-borne pathogen responsible for the disease listeriosis. It is ubiquitously found in the environment and soil is one of its natural habitats. Listeria monocytogenes is highly capable of coping with various stressful conditions. We hypothesized that stress-responsive two-component systems such as LisRK might contribute to the adaptation of L. monocytogenes to the soil environment. Indeed, investigations of the population dynamics of wild-type and mutant strains suggest an important role of LisRK for optimal fitness of L. monocytogenes in sterile soil. Results from non-sterile soil showed that the parental strain was capable of surviving longer than mutant strains lacking lisRK or genes encoding the LisRK-regulated LhrC small RNAs (sRNAs), suggesting that LisRK as well as the LhrC sRNAs were important for survival. Transcription of five LisRK-regulated genes was assessed after 1 h incubation in sterile soil. We observed that LisRK and the LhrC sRNAs contribute to the upregulation of lmo2522 in the soil environment. Notably, lmo2522 encodes an equivalent of the resuscitation promoting factors, Rpfs, in actinobacteria. Collectively, our study demonstrates that LisRK is important for growth and survival in sterile and non-sterile soil and suggests a role for LisRK-regulation of Lmo2522 in resuscitation from dormancy in the soil environment.

Habitat Disturbances Modulate the Barrier Effect of Resident Soil Microbiota on Listeria monocytogenes Invasion Success

Microbial communities are continuously exposed to the arrival of alien species. In complex environments such as soil, the success of invasion depends on the characteristics of the habitat, especially the diversity and structure of the residing bacterial communities. While most data available on microbial invasion relies on experiments run under constant conditions, the fate of invading species when the habitat faces disturbances has not yet been addressed. Here, we designed experiments to assess the consequences of habitat disturbance on the success of ongoing microbial invasion. We investigated (i) if disturbance-induced alterations in resident microbial communities could mitigate or facilitate invasion of Listeria monocytogenes, (ii) if disturbance itself could either improve or reduce the invader's fitness and (iii) if the invading species alters the structure of indigenous microbial communities. Our data show that environmental disturbances affect invasion patterns of L. monocytogenes in soils. Intriguingly, successful invasion was recorded in a regimen of disturbances that triggered small changes in microbial community structure while maintaining high bacterial diversity. On the opposite, dramatic decline of the invader was recorded when disturbance resulted in emergence of specific communities albeit concomitant with a diversity loss. This suggests that community composition is more important than its diversity when it comes to prevent the establishment of an invading species. Finally, shifts in bacterial communities during the disturbance event were strengthened by the presence of the invader indicating a major impact of invasion on microbial diversity when the habitat faces disturbance.

Lagoon water quality monitoring based on digital image analysis and machine learning estimators

Lagoon has been widely used to treat animal wastewater. However, because lagoon effluent often fluctuates in water quality, land application of the effluent may pose a risk to the environment and/or public health. It is necessary to monitor the quality of lagoon water to reduce the risk of its land application. This paper proposes an innovative monitoring method for animal wastewater in lagoons. We implemented spectral processing techniques to analyze the reflectivity of wastewater samples from lagoons, and applied machine learning methods to estimate the water quality parameters of the effluents, including the levels of nitrogen, phosphorus, bacteria (total coliform and E. Coli), and total solids. This study found significant correlations between the spectral rate of emission and above water quality parameters. We used machine learning to train three types of estimators, normal equation linear regression (LR), stochastic gradient descent (SGD), and Ridge regression to quantify these relations. The model performance was evaluated by weight coefficient, function intercept, and mean squared error (MSE). The model showed that TS level and the blue band of spectral reflectance of samples have a relatively good linear relationship, and the MSE of prediction set and decision coefficient were 0.57 and 0.98, respectively. For bacteria level, the MSE of prediction set was 0.63, and coefficient R² was 0.96. The results from this study could provide a versatile method for remote sensing of animal waste water.

Initial Transcriptomic Response and Adaption of Listeria monocytogenes to Desiccation on Food Grade Stainless Steel

The foodborne pathogen Listeria monocytogenes survives exposure to a variety of stresses including desiccation in the food industry. Strand-specific RNA sequencing was applied to analyze changes in the transcriptomes of two strains of L. monocytogenes (Lm 568 and Lm 08-5578) during desiccation [15°C, 43% relative humidity (RH)] on food grade stainless steel surfaces over 48 h to simulate a weekend with no food production. Both strains showed similar survival during desiccation with a 1.8-2 Log CFU/cm2 reduction after 48 h. Analysis of differentially expressed (DE) genes (>twofold, adjusted p-value <0.05) revealed that the initial response to desiccation was established after 6 h and remained constant with few new genes being DE after 12, 24, and 48 h. A core of 81 up- and 73 down-regulated DE genes were identified as a shared, strain independent response to desiccation. Among common upregulated genes were energy and oxidative stress related genes e.g., qoxABCD (cytochrome aa3) pdhABC (pyruvate dehydrogenase complex) and mntABCH (manganese transporter). Common downregulated genes related to anaerobic growth, proteolysis and the two component systems lmo1172/lmo1173 and cheA/cheY, which are involved in cold growth and flagellin production, respectively. Both strains upregulated additional genes involved in combatting oxidative stress and reactive oxygen species (ROS), including sod (superoxide dismutase), kat (catalase), tpx (thiol peroxidase) and several thioredoxins including trxAB, lmo2390 and lmo2830. Osmotic stress related genes were also upregulated in both strains, including gbuABC (glycine betaine transporter) and several chaperones clpC, cspA, and groE. Significant strain differences were also detected with the food outbreak strain Lm 08-5578 differentially expressing 1.9 × more genes (726) compared to Lm 568 (410). Unique to Lm 08-5578 was a significant upregulation of the expression of the alternative transcription factor σB and its regulon. A number of long antisense transcripts (lasRNA) were upregulated during desiccation including anti0605, anti0936, anti1846, and anti0777, with the latter controlling flagellum biosynthesis and possibly the downregulation of motility genes observed in both strains. This exploration of the transcriptomes of desiccated L. monocytogenes provides further understanding of how this bacterium encounters and survives the stress faced when exposed to dry conditions in the food industry.

Metabolism of the Gram-Positive Bacterial Pathogen Listeria monocytogenes

Bacterial metabolism represents the biochemical space that bacteria can manipulate to produce energy, reducing equivalents and building blocks for replication. Gram-positive pathogens, such as Listeria monocytogenes, show remarkable flexibility, which allows for exploitation of diverse biological niches from the soil to the intracytosolic space. Although the human host represents a potentially rich source for nutrient acquisition, competition for nutrients with the host and hostile host defenses can constrain bacterial metabolism by various mechanisms, including nutrient sequestration. Here, we review metabolism in the model Gram-positive bacterium, L. monocytogenes, and highlight pathways that enable the replication, survival, and virulence of this bacterial pathogen.

Role and regulation of the stress activated sigma factor sigma B (σB) in the saprophytic and host-associated life stages of Listeria monocytogenes

The stress activated sigma factor sigma B (σ^B) plays a pivotal role in allowing the food-borne bacterial pathogen Listeria monocytogenes to modulate its transcriptional landscape in order to survive in a variety of harsh environments both outside and within the host. While we have a comparatively good understanding of the systems under the control of this sigma factor much less is known about how the activity of σ^B is controlled. In this review, we present a current model describing how this sigma factor is thought to be controlled including an overview of what is known about stress sensing and the early signal transduction events that trigger its activation. We discuss the known regulatory overlaps between σ^B and other protein and RNA regulators in the cell. Finally, we describe the role of σ^B in surviving both saprophytic and host-associated stresses. The complexity of the regulation of this sigma factor reflects the significant role that it plays in the persistence of this important pathogen in the natural environment, the food chain as well as within the host during the early stages of an infection. Understanding its regulation will be a critical step in helping to develop rational strategies to prevent its growth and survival in the food destined for human consumption and in the prevention of listeriosis.

Sources and survival of Listeria monocytogenes on fresh, leafy produce

Listeria monocytogenes is an intracellular human pathogen which enters the body through contaminated food stuffs and is known to contaminate fresh leafy produce such as spinach, lettuce and rocket. Routinely, fresh leafy produce is grown and processed on a large scale before reaching the consumer through various products such as sandwiches and prepared salads. From farm to fork, the fresh leafy produce supply chain (FLPSC) is complex and contains a diverse range of environments where L. monocytogenes is sporadically detected during routine sampling of produce and processing areas. This review describes sources of the bacteria in the FLPSC and outlines the physiological and molecular mechanisms behind its survival in the different environments associated with growing and processing fresh produce. Finally, current methods of source tracking the bacteria in the context of the food supply chain are discussed with emphasis on how these methods can provide additional, valuable information on the risk that L. monocytogenes isolates pose to the consumer.