Colonization outwith the colon: plants as an alternative environmental reservoir for human pathogenic enterobacteria

Monitoring the Bioprotective Potential of Lactiplantibacillus pentosus Culture on Pathogen Survival and the Shelf-Life of Fresh Ready-to-Eat Salads Stored under Modified Atmosphere Packaging

Globally, fresh vegetables or minimally processed salads have been implicated in several foodborne disease outbreaks. This work studied the effect of Lactiplantibacillus pentosus FMCC-B281 cells (F) and its supernatant (S) on spoilage and on the fate of Listeria monocytogenes and Escherichia coli O157:H7 on fresh-cut ready-to-eat (RTE) salads during storage. Also, Fourier transform infrared (FTIR) and multispectral imaging (MSI) analysis were used as rapid and non-destructive techniques to estimate the microbiological status of the samples. Fresh romaine lettuce, rocket cabbage, and white cabbage were used in the present study and were inoculated with L. pentosus and the two pathogens. The strains were grown at 37 °C for 24 h in MRS and BHI broths, respectively, and then were centrifuged to collect the supernatant and the pellet (cells). Cells (F, ~5 log CFU/g), the supernatant (S), and a control (C, broth) were used to spray the leaves of each fresh vegetable that had been previously contaminated (sprayed) with the pathogen (3 log CFU/g). Subsequently, the salads were packed under modified atmosphere packaging (10%CO2/10%O2/80%N2) and stored at 4 and 10 °C until spoilage. During storage, microbiological counts and pH were monitored in parallel with FTIR and MSI analyses. The results showed that during storage, the population of the pathogens increased for lettuce and rocket independent of the treatment. For cabbage, pathogen populations remained stable throughout storage. Regarding the spoilage microbiota, the Pseudomonas population was lower in the F samples, while no differences in the populations of Enterobacteriaceae and yeasts/molds were observed for the C, F, and S samples stored at 4 °C. According to sensory evaluation, the shelf-life was shorter for the control samples in contrast to the S and F samples, where their shelf-life was elongated by 1-2 days. Initial pH values were ca. 6.0 for the three leafy vegetables. An increase in the pH of ca. 0.5 values was recorded until the end of storage at both temperatures for all cases of leafy vegetables. FTIR and MSI analyses did not satisfactorily lead to the estimation of the microbiological quality of salads. In conclusion, the applied bioprotective strain (L. pentosus) can elongate the shelf-life of the RTE salads without an effect on pathogen growth.

A Review on Microbiological Source Attribution Methods of Human Salmonellosis: From Subtyping to Whole-Genome Sequencing

Salmonella is one of the main causes of human foodborne illness. It is endemic worldwide, with different animals and animal-based food products as reservoirs and vehicles of infection. Identifying animal reservoirs and potential transmission pathways of Salmonella is essential for prevention and control. There are many approaches for source attribution, each using different statistical models and data streams. Some aim to identify the animal reservoir, while others aim to determine the point at which exposure occurred. With the advance of whole-genome sequencing (WGS) technologies, new source attribution models will greatly benefit from the discriminating power gained with WGS. This review discusses some key source attribution methods and their mathematical and statistical tools. We also highlight recent studies utilizing WGS for source attribution and discuss open questions and challenges in developing new WGS methods. We aim to provide a better understanding of the current state of these methodologies with application to Salmonella and other foodborne pathogens that are common sources of illness in the poultry and human sectors.

Colonization of Raphanus sativus by human pathogenic microorganisms

Contamination of vegetables with human pathogenic microorganisms (HPMOs) is considered one of the most important problems in the food industry, as current nutritional guidelines include increased consumption of raw or minimally processed organic vegetables due to healthy lifestyle promotion. Vegetables are known to be potential vehicles for HPMOs and sources of disease outbreaks. In this study, we tested the susceptibility of radish (Raphanus sativus) to colonization by different HPMOs, including Escherichia coli PCM 2561, Salmonella enterica subsp. enterica PCM 2565, Listeria monocytogenes PCM 2191 and Bacillus cereus PCM 1948. We hypothesized that host plant roots containing bactericidal compounds are less prone to HPMO colonization than shoots and leaves. We also determined the effect of selected pathogens on radish growth to check host plant-microbe interactions. We found that one-week-old radish is susceptible to colonization by selected HPMOs, as the presence of the tested HPMOs was demonstrated in all organs of R. sativus. The differences were noticed 2 weeks after inoculation because B. cereus was most abundant in roots (log10 CFU - 2.54), S. enterica was observed exclusively in stems (log10 CFU - 3.15), and L. monocytogenes and E. coli were most abundant in leaves (log10 CFU - 4.80 and 3.23, respectively). The results suggest that E. coli and L. monocytogenes show a higher ability to colonize and move across the plant than B. cereus and S. enterica. Based on fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM) approach HPMOs were detected in extracellular matrix and in some individual cells of all analyzed organs. The presence of pathogens adversely affected the growth parameters of one-week-old R. sativus, especially leaf and stem fresh weight (decreased by 47-66 and 17-57%, respectively). In two-week-old plants, no reduction in plant biomass development was noted. This observation may result from plant adaptation to biotic stress caused by the presence of HPMOs, but confirmation of this assumption is needed. Among the investigated HPMOs, L. monocytogenes turned out to be the pathogen that most intensively colonized the aboveground part of R. sativus and at the same time negatively affected the largest number of radish growth parameters.

Intraspecies competition among Salmonella enterica isolates in the lettuce leaf apoplast

Multiple Salmonella enterica serovars and strains have been reported to be able to persist inside the foliar tissue of lettuce (Lactuca sativa L.), potentially resisting washing steps and reaching the consumer. Intraspecies variation of the bacterial pathogen and of the plant host can both significantly affect the outcome of foliar colonization. However, current understanding of the mechanisms underlying this phenomenon is still very limited. In this study, we evaluated the foliar fitness of 14 genetically barcoded S. enterica isolates from 10 different serovars, collected from plant and animal sources. The S. enterica isolates were vacuum-infiltrated individually or in pools into the leaves of three- to four-week-old lettuce plants. To estimate the survival capacity of individual isolates, we enumerated the bacterial populations at 0- and 10- days post-inoculation (DPI) and calculated their net growth. The competition of isolates in the lettuce apoplast was assessed through the determination of the relative abundance change of barcode counts of each isolate within pools during the 10 DPI experimental period. Isolates exhibiting varying apoplast fitness phenotypes were used to evaluate their capacity to grow in metabolites extracted from the lettuce apoplast and to elicit the reactive oxygen species burst immune response. Our study revealed that strains of S. enterica can substantially differ in their ability to survive and compete in a co-inhabited lettuce leaf apoplast. The differential foliar fitness observed among these S. enterica isolates might be explained, in part, by their ability to utilize nutrients available in the apoplast and to evade plant immune responses in this niche.

Sporadic Detection of Escherichia coli O104:H4 Strain C227/11Φcu in the Edible Parts of Lamb's Lettuce Cultured in Contaminated Agricultural Soil Samples

In the current study, we demonstrate that E. coli O104:H4 strain C227/11Φcu, a derivative of the 2011 enterohemorrhagic/enteroaggregative (EHEC/EAEC) E. coli outbreak strain, migrated into the edible portion of lamb's lettuce plants upon contamination of the surrounding soil. Seeds were surface-sterilized and cultivated on Murashige-Skoog agar or in autoclaved agricultural soil. Migration into the edible portions was investigated by inoculating the agar or soil close to the plants with 108 colony-forming units (CFU). The edible parts, which did not come into contact with the contaminated medium or soil, were quantitatively analyzed for the presence of bacteria after 2, 4 and 8 weeks. Strain C227/11Φcu could colonize lamb's lettuce when contamination of medium or soil occurs. The highest recovery rate (27%) was found for lettuce cultivated in agar, and up to 1.6 × 103 CFU/g lettuce was detected. The recovery rate was lower for the soil samples (9% and 13.5%). Although the used contamination levels were high, migration of C227/11Φcu from the soil into the edible parts was demonstrated. This study further highlights the risk of crop plant contamination with pathogenic E. coli upon soil contamination.

Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System

Tomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for healthier and environmentally friendly vegetables. However, organic tomato production under SCSs has been associated with low crop performance and fruit quality defects. These agricultural deficiencies could be linked to alterations in tomato plant microbiota; nonetheless, this issue has not been sufficiently addressed. Thus, the main goal of the present study was to characterize the rhizosphere and phyllosphere of tomato plants cultivated under conventional and organic SCSs. To accomplish this goal, tomato plants grown in commercial greenhouses under conventional or organic SCSs were tested at 8, 26, and 44 weeks after seedling transplantation. Substrate (n = 24), root (n = 24), and fruit (n = 24) composite samples were subjected to DNA extraction and high-throughput 16S rRNA gene sequencing. The present study revealed that the tomato core microbiota was predominantly constituted by Proteobacteria, Actinobacteria, and Firmicutes. Remarkably, six bacterial families, Bacillaceae, Microbacteriaceae, Nocardioidaceae, Pseudomonadaceae, Rhodobacteraceae, and Sphingomonadaceae, were shared among all substrate, rhizosphere, and fruit samples. Importantly, it was shown that plants under organic SCSs undergo a dysbiosis characterized by significant changes in the relative abundance of Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Enterobacteriaceae, Erythrobacteraceae, Flavobacteriaceae, Nocardioidaceae, Rhodobacteraceae, and Streptomycetaceae. These results suggest that microbial alterations in substrates, roots, and fruits could be potential factors in contributing to the crop performance and fruit quality deficiencies observed in organic SCSs.

[Health risks from crop irrigation with treated wastewater containing antibiotic residues, resistance genes, and resistant microorganisms]

This review describes the effects and potential health risks of resistant microorganisms, resistance genes, and residues of drugs and biocides that occur when re-using wastewater for crop irrigation. It focusses on specific aspects of these contaminants and their interactions, but does not provide a general risk assessment of the microbial load when using reclaimed water.Antimicrobial residues, antimicrobial resistant microorganisms, and resistance genes are frequently detected in treated wastewater. They have effects on the soil and plant-associated microbiota (total associated microorganisms) and can be taken up by plants. An interaction of residues with microorganisms is mainly expected before using the water for irrigation. However, it may also occur as a combined effect on the plant microbiome and all the abundant resistance genes (resistome). Special concerns are raised as plants are frequently consumed raw, that is, without processing that might reduce the bacterial load. Washing fruits and vegetables only has minor effects on the plant microbiome. On the other hand, cutting and other processes may support growth of microorganisms. Therefore, after such process steps, cooling of the foods is required.Further progress has to be made in the treatment of wastewater that will be used for crop irrigation with respect to removing micropollutants and microorganisms to minimize the risk of an increased exposure of consumers to transferable resistance genes and resistant bacteria.

Adaptation of Commensal Escherichia coli in Tomato Fruits: Motility, Stress, Virulence

Food contamination can be a serious concern for public health because it can be related to the severe spreading of pathogens. This is a main issue, especially in the case of fresh fruits and vegetables; indeed, they have often been associated with gastrointestinal outbreak events, due to contamination with pathogenic bacteria. However, little is known about the physiological adaptation and bacterial response to stresses encountered in the host plant. Thus, this work aimed to investigate the adaptation of a commensal E. coli strain while growing in tomato pericarp. Pre-adapted and non-adapted cells were compared and used to contaminate tomatoes, demonstrating that pre-adaptation boosted cell proliferation. DNA extracted from pre-adapted and non-adapted cells was sequenced, and their methylation profiles were compared. Hence, genes involved in cell adhesion and resistance against toxic compounds were identified as genes involved in adaptation, and their expression was compared in these two experimental conditions. Finally, pre-adapted and non-adapted E. coli were tested for their ability to resist the presence of toxic compounds, demonstrating that adaptation exerted a protective effect. In conclusion, this work provides new information about the physiological adaptation of bacteria colonizing the tomato fruit pericarp.

Minimally processed fruits as vehicles for foodborne pathogens

The consumption of minimally processed fruit (MPF) has increased over the last decade due to a novel trend in the food market along with the raising consumers demand for fresh, organic, convenient foods and the search for healthier lifestyles. Although represented by one of the most expanded sectors in recent years, the microbiological safety of MPF and its role as an emergent foodborne vehicle has caused great concern to the food industry and public health authorities. Such food products may expose consumers to a risk of foodborne infection as they are not subjected to prior microbial lethal methods to ensure the removal or destruction of pathogens before consumption. A considerable number of foodborne disease cases linked to MPF have been reported and pathogenic strains of Salmonella enterica, Escherichia coli, Listeria monocytogenes, as well as Norovirus accounted for the majority of cases. Microbial spoilage is also an issue of concern as it may result in huge economic losses among the various stakeholders involved in the manufacturing and commercialization of MPF. Contamination can take place at any step of production/manufacturing and identifying the nature and sources of microbial growth in the farm-to-fork chain is crucial to ensure appropriate handling practices for producers, retailers, and consumers. This review aims to summarize information about the microbiological hazards associated with the consumption of MPF and also highlight the importance of establishing effective control measures and developing coordinated strategies in order to enhance their safety.

Cross-Over Pathogenic Bacteria Detected in Infected Tomatoes (Solanum lycopersicum L.) and Peppers (Capsicum annuum L.) in Bulgaria

The ability of certain human pathogens to adapt to plants without losing their virulence toward people is a major concern today. Thus, the aim of the present work was the investigation of the presence of cross-over pathogenic bacteria in infected tomato and pepper plants. The objects of the study were 21 samples from seven different parts of the plants and three from tomato rhizosphere. In total, 26 strains were isolated, identified by MALDI-TOF, and phenotypically characterized. The PCR amplification of the rpoB gene was applied as an approach for the rapid detection of cross-over pathogens in plant samples. A great bacterial diversity was revealed from tomato samples as nine species were identified (Leclercia adecarboxylata, Pseudesherichia vulneris, Enterobacter cancerogenus, Enterobacter cloacae, Enterobacter bugandensis, Acinetobacter calcoaceticus, Pantoea agglomerans, Pantoea ananatis, and Pectobacterium carotovorum). Polymicrobial contaminations were observed in samples T2 (tomato flower) and T10 (tomato fruit). Five species were identified from pepper samples (P. agglomerans, L. adecarboxylata, Pseudomonas sp., Pseudomonas putida, and Enterococcus sp.). Antibiotic resistance patterns were assigned in accordance with EFSA recommendations. All isolates showed varying resistance to the tested antibiotics. The genetic basis for the phenotypic antibiotic resistance was not revealed. No genes for the virulence factors were found among the population. To our knowledge, this is the first overall investigation of tomato and pepper cross-over pathogenic bacterial populations in Bulgaria.

Plant species-dependent transmission of Escherichia coli O157:H7 from the spermosphere to cotyledons and first leaves

The colonization of six edible plant species: alfalfa, broccoli, coriander, lettuce, parsley and rocket, by the human pathogen Shigatoxigenic Escherichia coli was investigated following two modes of artificial inoculation of seeds, by soaking or watering. The frequency and extent of colonization of cotyledons depended on the mode of inoculation, with three, rapidly germinating species being successfully colonized after overnight soaking, but slower germinating species requiring prolonged exposure to bacteria by watering of the surrounding growth media. Separate analysis of the cotyledons and leaves from individual plants highlighted that successful colonization of the true leaves was also species dependent. For three species, failure of transfer, or lack of nutrients or suitable microhabitat on the leaf surface resulted in infrequent bacterial colonization. Colonization of leaves was lower and generally in proportion to that in cotyledons, if present. The potential risks associated with consumption of leafy produce are discussed.

Flagellar Phenotypes Impact on Bacterial Transport and Deposition Behavior in Porous Media: Case of Salmonella enterica Serovar Typhimurium

Bacterial contamination of groundwater has always been an ecological problem worthy of attention. In this study, Salmonella enterica serovar Typhimurium with different flagellar phenotypes mainly characterized during host-pathogen interaction were analyzed for their transport and deposition behavior in porous media. Column transport experiments and a modified mobile-immobile model were applicated on different strains with flagellar motility (wild-type) or without motility (ΔmotAB), without flagella (ΔflgKL), methylated and unmethylated flagellin (ΔfliB), and different flagella phases (fliC^ON, fljB^ON). Results showed that flagella motility could promote bacterial transport and deposition due to their biological advantages of moving and attaching to surfaces. We also found that the presence of non-motile flagella improved bacterial adhesion according to a higher retention rate of the ΔmotAB strain compared to the ΔflgKL strain. This indicated that bacteria flagella and motility both had promoting effects on bacterial deposition in sandy porous media. Flagella phases influenced the bacterial movement; the fliC^ON strain went faster through the column than the fljB^ON strain. Moreover, flagella methylation was found to favor bacterial transport and deposition. Overall, flagellar modifications affect Salmonella enterica serovar Typhimurium transport and deposition behavior in different ways in environmental conditions.

Microbe Profile: Pectobacterium atrosepticum: an enemy at the door

Pectobacterium atrosepticum is part of a larger family of soft rot bacteria (Pectobacteriaceae) that cause disease on a wide range of crops worldwide. They are closely related to members of the Enterobacteriaceae and, as the plant pathogens and plant associated members of the group, form part of a continuum towards opportunistic and more devastating animal and human pathogens. Many of the horizontally acquired islands present in the genome of P. atrosepticum are directly responsible for life on plants. These include genes for a plethora of plant cell wall degrading enzymes, plant toxins, siderophores etc., which are exported by multiple secretion systems under a highly coordinated regulation system.

Applications of Essential Oils as Antibacterial Agents in Minimally Processed Fruits and Vegetables—A Review

Microbial foodborne diseases are a major health concern. In this regard, one of the major risk factors is related to consumer preferences for “ready-to-eat” or minimally processed (MP) fruits and vegetables. Essential oil (EO) is a viable alternative used to reduce pathogenic bacteria and increase the shelf-life of MP foods, due to the health risks associated with food chlorine. Indeed, there has been increased interest in using EO in fresh produce. However, more information about EO applications in MP foods is necessary. For instance, although in vitro tests have defined EO as a valuable antimicrobial agent, its practical use in MP foods can be hampered by unrealistic concentrations, as most studies focus on growth reductions instead of bactericidal activity, which, in the case of MP foods, is of utmost importance. The present review focuses on the effects of EO in MP food pathogens, including the more realistic applications. Overall, due to this type of information, EO could be better regarded as an “added value” to the food industry.

Analysis of Salmonella enterica Adhesion to Leaves of Corn Salad or Lettuce

Human infections by gastrointestinal bacterial pathogens are commonly associated with the consumption of contaminated food of animal origin (e.g., chicken, fish, eggs) or contaminated water. However, further contamination sources must be considered since number of Salmonella enterica infections associated with the consumption of food of non-animal origin (e.g., vegetables, fruits, nuts) are increasing. This gives raise to interest in understanding the interaction of S. enterica with leafy produce, such as various salads. Especially adhesion as initial step of contamination of salad by S. enterica deserves further investigation. Here we introduce methods to analyse Salmonella adhesion to various salads that provide insights into bacterial factors involved in Salmonella colonization of plants.

Dual transcriptomic analysis reveals metabolic changes associated with differential persistence of human pathogenic bacteria in leaves of Arabidopsis and lettuce

Understanding the molecular determinants underlying the interaction between the leaf and human pathogenic bacteria is key to provide the foundation to develop science-based strategies to prevent or decrease the pathogen contamination of leafy greens. In this study, we conducted a dual RNA-sequencing analysis to simultaneously define changes in the transcriptomic profiles of the plant and the bacterium when they come in contact. We used an economically relevant vegetable crop, lettuce (Lactuca sativa L. cultivar Salinas), and a model plant, Arabidopsis thaliana Col-0, as well as two pathogenic bacterial strains that cause disease outbreaks associated with fresh produce, Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium 14028s (STm 14028s). We observed commonalities and specificities in the modulation of biological processes between Arabidopsis and lettuce and between O157:H7 and STm 14028s during early stages of the interaction. We detected a larger alteration of gene expression at the whole transcriptome level in lettuce and Arabidopsis at 24 h post inoculation with STm 14028s compared to that with O157:H7. In addition, bacterial transcriptomic adjustments were substantially larger in Arabidopsis than in lettuce. Bacterial transcriptome was affected at a larger extent in the first 4 h compared to the subsequent 20 h after inoculation. Overall, we gained valuable knowledge about the responses and counter-responses of both bacterial pathogen and plant host when these bacteria are residing in the leaf intercellular space. These findings and the public genomic resources generated in this study are valuable for additional data mining.

Survival of Enterohemorrhagic Escherichia coli O104:H4 Strain C227/11Φcu in Agricultural Soils Depends on rpoS and Environmental Factors

The consumption of contaminated fresh produce caused outbreaks of enterohemorrhagic (EHEC) Escherichia coli. Agricultural soil might be a reservoir for EHEC strains and represent a contamination source for edible plants. Furthermore, the application of manure as fertilizer is an important contamination route. Thus, the German fertilizer ordinance prohibits the use of manure 12 weeks before crop harvest to avoid pathogen transmission into the food chain. In this study, the survival of E. coli O104:H4 strain C227/11Φcu in soil microenvironments with either diluvial sand or alluvial loam at two temperatures was investigated for more than 12 weeks. It was analyzed whether the addition of cattle manure extends EHEC survival in these microenvironments. The experiments were additionally performed with isogenic ΔrpoS and ΔfliC deletion mutants of C227/11Φcu. The survival of C227/11Φcu was highest at 4 °C, whereas the soil type had a minor influence. The addition of cattle manure increased the survival at 22 °C. Deletion of rpoS significantly decreased the survival period under all cultivation conditions, whereas fliC deletion did not have any influence. The results of our study demonstrate that EHEC C227/11Φcu is able to survive for more than 12 weeks in soil microenvironments and that RpoS is an important determinant for survival.

Phyllosphere microbiome: Diversity and functions

Phyllosphere or aerial surface of plants represents the globally largest and peculiar microbial habitat that inhabits diverse and rich communities of bacteria, fungi, viruses, cyanobacteria, actinobacteria, nematodes, and protozoans. These hyperdiverse microbial communities are related to the host's specific functional traits and influence the host's physiology and the ecosystem's functioning. In the last few years, significant advances have been made in unravelling several aspects of phyllosphere microbiology, including diversity and microbial community composition, dynamics, and functional interactions. This review highlights the current knowledge about the assembly, structure, and composition of phyllosphere microbial communities across spatio-temporal scales, besides functional significance of different microbial communities to the plant host and the surrounding environment. The knowledge will help develop strategies for modelling and manipulating these highly beneficial microbial consortia for furthering scientific inquiry into their interactions with the host plants and also for their useful and economic utilization.

Nematicidal effects of 2-methyl-aconitate isomerase from the phytopathogen Pseudomonas syringae MB03 on the model nematode Caenorhabditis elegans

The pathogenicity of a common phytopathogenic bacterium, Pseudomonas syringae, against animal model hosts, such as mice and Caenorhabditis elegans, has been recently revealed. However, most of the virulence determinants associated with pathogenesis remain elusive. In the current study, we performed predictive analysis of virulence factors against C. elegans in the genome of the wild-type P. syringae strain MB03. Nine predicted nematicidal proteins were expressed and purified in recombinant Escherichia coli strains and were evaluated to define their toxicity against C. elegans in liquid killing assays. Next, we focused on one essential 2-methyl citrate cycle protein, PrpF03, which showed the highest lethal activity against C. elegans compared to the other tested proteins with a half lethal concentration (LC₅₀) of 155.3 (123.4-176.6) µg mL^-1 and a half lethal time (LT₅₀) of 3.72 (1.64-4.85) days. Purified PrpF03 also caused adverse effects on the brood size, growth, and motility of C. elegans. Moreover, the PrpF03 protein exhibited pathological activity towards the intestinal tract of C. elegans. We surmise that the PrpF03 protein functions as a virulence factor when it blocks the average circulation of the 2-methyl citrate cycle of C. elegans by accumulating 2-methyl citrate in the gut of C. elegans, which damages and restrains the growth of intestinal tissues that ultimately kill C. elegans. The discovery of specific nematicidal activities of PrpF03 provides a better understanding of the mechanisms of phytopathogenic P. syringae against nematodes and could aid in developing nematode pest-controlling agents in agriculture.

The role of l-arabinose metabolism for Escherichia coli O157:H7 in edible plants

Arabinose is a major plant aldopentose in the form of arabinans complexed in cell wall polysaccharides or glycoproteins (AGP), but comparatively rare as a monosaccharide. l-arabinose is an important bacterial metabolite, accessed by pectolytic micro-organisms such as Pectobacterium atrosepticum via pectin and hemicellulose degrading enzymes. However, not all plant-associated microbes encode cell-wall-degrading enzymes, yet can metabolize l-arabinose, raising questions about their use of and access to the glycan in plants. Therefore, we examined l-arabinose metabolism in the food-borne pathogen Escherichia coli O157:H7 (isolate Sakai) during its colonization of plants. l-arabinose metabolism (araBA) and transport (araF) genes were activated at 18 °C in vitro by l-arabinose and expressed over prolonged periods in planta. Although deletion of araBAD did not impact the colonization ability of E. coli O157:H7 (Sakai) on spinach and lettuce plants (both associated with STEC outbreaks), araA was induced on exposure to spinach cell-wall polysaccharides. Furthermore, debranched and arabinan oligosaccharides induced ara metabolism gene expression in vitro, and stimulated modest proliferation, while immobilized pectin did not. Thus, E. coli O157:H7 (Sakai) can utilize pectin/AGP-derived l-arabinose as a metabolite. Furthermore, it differs fundamentally in ara gene organization, transport and regulation from the related pectinolytic species P. atrosepticum, reflective of distinct plant-associated lifestyles.

Horizontal transfer of domains in ssrA gene among Enterobacteriaceae

The tmRNA (transfer messenger RNA), encoded by ssrA gene, is involved in rescuing of stalled ribosomes by a process called trans-translation. Additionally, regions of the ssrA gene (coding for tmRNA) were reported to serve as integration sites for various bacteriophages. Though variations in ssrA genes were reported, their functional relevance is less studied. In this study, we investigated the horizontal gene transfer (HGT) of ssrA among the members of Enterobacteriaceae. This was done by predicting recombination signals in ssrA gene (belonging to Enterobacteriaceae) using RDP5 (Recombination Detection Program 5). Our results revealed 7 recombination signals in ssrA gene belonging to different species. We further showed that the recombination signals were more in the domains present in the 3' end than 5' end of tmRNA. Of note, the mRNA region was reported in many recombination signals. Further, members belonging to genera Yersinia, Erwinia, Dickeya and Enterobacter were highly represented in the recombination signals. Sequence analysis revealed the presence of integration sites for different class of bacteriophages in ssrA gene. The locations of phage recognition sites are comparable with recombination signals. Taken together, our results revealed a diverse nature of HGT and recombination which possibly due to transduction mediated by phages.

The Changing Face of the Family Enterobacteriaceae (Order: "Enterobacterales"): New Members, Taxonomic Issues, Geographic Expansion, and New Diseases and Disease Syndromes

The family Enterobacteriaceae has undergone significant morphogenetic changes in its more than 85-year history, particularly during the past 2 decades (2000 to 2020). The development and introduction of new and novel molecular methods coupled with innovative laboratory techniques have led to many advances. We now know that the global range of enterobacteria is much more expansive than previously recognized, as they play important roles in the environment in vegetative processes and through widespread environmental distribution through insect vectors. In humans, many new species have been described, some associated with specific disease processes. Some established species are now observed in new infectious disease settings and syndromes. The results of molecular taxonomic and phylogenetics studies suggest that the current family Enterobacteriaceae should possibly be divided into seven or more separate families. The logarithmic explosion in the number of enterobacterial species described brings into question the relevancy, need, and mechanisms to potentially identify these taxa. This review covers the progression, transformation, and morphogenesis of the family from the seminal Centers for Disease Control and Prevention publication (J. J. Farmer III, B. R. Davis, F. W. Hickman-Brenner, A. McWhorter, et al., J Clin Microbiol 21:46-76, 1985, https://doi.org/10.1128/JCM.21.1.46-76.1985) to the present.

Size Matters: Biological and Food Safety Relevance of Leaf Damage for Colonization of Escherichia coli O157:H7 gfp

This study examined the biological and food safety relevance of leaf lesions for potential invasion of food pathogens into the plant tissue (internalization). This was done by determining the role of artificial leaf damage in terms of damaged leaf area on proliferation of E. coli O157:H7 gfp+. In a two-factorial experiment, unwashed fresh baby leaf spinach (Spinacia oleracea L.) was subjected to four damage levels (undamaged, low, moderate, high damage; factor 1) and three incubation intervals (0, 1, 2 days post-inoculation; factor 2). Individual leaves were immersed for 15 s in a suspension loaded with E. coli O157:H7 gfp+ (10⁶ CFU × mL^–1). The leaves were analyzed individually using image analysis tools to quantify leaf area and number and size of lesions, and using confocal laser scanning and scanning electron microscopy to visualize leaf lesions and presence of the introduced E. coli strain on and within the leaf tissue. Prevalence of E. coli O157:H7 gfp+ was assessed using a culture-dependent technique. The results showed that size of individual lesions and damaged leaf area affected depth of invasion into plant tissue, dispersal to adjacent areas, and number of culturable E. coli O157:H7 gfp+ directly after inoculation. Differences in numbers of the inoculant retrieved from leaf macerate evened out from 2 days post-inoculation, indicating rapid proliferation during the first day post-inoculation. Leaf weight was a crucial factor, as lighter spinach leaves (most likely younger leaves) were more prone to harbor E. coli O157:H7 gfp+, irrespective of damage level. At the high inoculum density used, the risk of consumers’ infection was almost 100%, irrespective of incubation duration or damage level. Even macroscopically intact leaves showed a high risk for infection. These results suggest that the risk to consumers is correlated with how early in the food chain the leaves are contaminated, and the degree of leaf damage. These findings should be taken into account in different steps of leafy green processing. Further attention should be paid to the fate of viable, but non-culturable, shiga-toxigenic E. coli on and in ready-to-eat leafy vegetables.

Taxonomic and Functional Shifts in the Sprout Spent Irrigation Water Microbiome in Response to Salmonella Contamination of Alfalfa Seeds

Despite recent advances in Salmonella-sprout research, little is known about the relationship between Salmonella and the sprout microbiome during sprouting. Sprout spent irrigation water (SSIW) provides an informative representation of the total microbiome of this primarily aquaponic crop. This study was designed to characterize the function and taxonomy of the most actively transcribed genes in SSIW from Salmonella enterica serovar Cubana-contaminated alfalfa seeds throughout the sprouting process. Genomic DNA and total RNA from SSIW was collected at regular intervals and sequenced using Illumina MiSeq and NextSeq platforms. Nucleic acid data were annotated using four different pipelines. Both metagenomic and metatranscriptomic analyses revealed a diverse and highly dynamic SSIW microbiome. A "core" SSIW microbiome comprised Klebsiella, Enterobacter, Pantoea, and Cronobacter The impact, however, of Salmonella contamination on alfalfa seeds influenced SSIW microbial community dynamics not only structurally but also functionally. Changes in genes associated with metabolism, genetic information processing, environmental information processing, and cellular processes were abundant and time dependent. At time points of 24 h, 48 h, and 96 h, totals of 541, 723, and 424 S Cubana genes, respectively, were transcribed at either higher or lower levels than at 0 h in SSIW during sprouting. An array of S Cubana genes (107) were induced at all three time points, including genes involved in biofilm formation and modulation, stress responses, and virulence and tolerance to antimicrobials. Taken together, these findings expand our understanding of the effect of Salmonella seed contamination on the sprout crop microbiome and metabolome.IMPORTANCE Interactions of human enteric pathogens like Salmonella with plants and plant microbiomes remain to be elucidated. The rapid development of next-generation sequencing technologies provides powerful tools enabling investigation of such interactions from broader and deeper perspectives. Using metagenomic and metatranscriptomic approaches, this study identified not only changes in microbiome structure of SSIW associated with sprouting but also changes in the gene expression patterns related to the sprouting process in response to Salmonella contamination of alfalfa seeds. This study advances our knowledge on Salmonella-plant (i.e., sprout) interaction.

Factors influencing the persistence of enteropathogenic bacteria in wetland habitats and implications for water quality

AIMS

To better understand the persistence dynamics of enteropathogenic bacteria in freshwater wetland habitats, we constructed lab-scale mesocosms planted with two different wetland plant species using a subsurface flow wetland design. Mesocosms were treated with either a high-quality or a poor-quality water source to examine the effects of water quality exposure and plant species on Escherichia coli, Salmonella spp. and Enterococcus spp. in the rhizoplane, rhizosphere and water of wetland habitats.

METHODS AND RESULTS

Quantities of study micro-organisms were detected using real-time PCR in wetland mesocosms. A combination of molecular and culture-based methods was also used to enumerate these organisms from surface water and plant material at high, medium and poor water quality sites in the field. We found that all three enteropathogenic micro-organisms were influenced by microhabitat type and plant species. Organisms differed with respect to their predominant microhabitat and the extent of persistence associated with wetland plant species in the mesocosm study. Of the monitored pathogens, only E. coli was influenced by both water quality treatment and plant species. Salmonella spp. quantities in the rhizoplane consistently increased in all treatments over the course of the mesocosm experiment.

CONCLUSIONS

Plant species selection appears to be an overlooked aspect of constructed wetland design with respect to the removal of enteropathogenic micro-organisms. Escherichia coli and Enterococcus concentrations in wetland outflow were significantly different between the two plant species tested, with Enterococcus concentrations being significantly higher in mesocosms planted with Phalaris arundinaceae and E. coli concentrations being higher in mesocosms planted with Veronica anagallis-aquatica. Furthermore, there is evidence that the rhizoplane is a significant reservoir for Salmonella spp. within wetland habitats.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first time that Salmonella spp. has been shown to proliferate under natural conditions within the rhizoplane. This will contribute to our understanding of wetland removal mechanisms for enteropathogenic bacteria. This study identifies the rhizoplane as a potentially important reservoir for human pathogenic micro-organisms and warrants additional study to establish whether this finding is applicable in non-wetland habitats.

The Impact of Plasma Membrane Lipid Composition on Flagellum-Mediated Adhesion of Enterohemorrhagic Escherichia coli

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a major cause of foodborne gastrointestinal illness. The adhesion of EHEC to host tissues is the first step enabling bacterial colonization. Adhesins such as fimbriae and flagella mediate this process. Here, we studied the interaction of the bacterial flagellum with the host cell's plasma membrane using giant unilamellar vesicles (GUVs) as a biologically relevant model. Cultured cell lines contain many different molecular components, including proteins and glycoproteins. In contrast, with GUVs, we can characterize the bacterial mode of interaction solely with a defined lipid part of the cell membrane. Bacterial adhesion on GUVs was dependent on the presence of the flagellar filament and its motility. By testing different phospholipid head groups, the nature of the fatty acid chains, or the liposome curvature, we found that lipid packing is a key parameter to enable bacterial adhesion. Using HT-29 cells grown in the presence of polyunsaturated fatty acid (α-linolenic acid) or saturated fatty acid (palmitic acid), we found that α-linolenic acid reduced adhesion of wild-type EHEC but not of a nonflagellated mutant. Finally, our results reveal that the presence of flagella is advantageous for the bacteria to bind to lipid rafts. We speculate that polyunsaturated fatty acids prevent flagellar adhesion on membrane bilayers and play a clear role for optimal host colonization. Flagellum-mediated adhesion to plasma membranes has broad implications for host-pathogen interactions.IMPORTANCE Bacterial adhesion is a crucial step to allow bacteria to colonize their hosts, invade tissues, and form biofilm. Enterohemorrhagic Escherichia coli O157:H7 is a human pathogen and the causative agent of diarrhea and hemorrhagic colitis. Here, we use biomimetic membrane models and cell lines to decipher the impact of lipid content of the plasma membrane on enterohemorrhagic E. coli flagellum-mediated adhesion. Our findings provide evidence that polyunsaturated fatty acid (α-linolenic acid) inhibits E. coli flagellar adhesion to the plasma membrane in a mechanism separate from its antimicrobial and anti-inflammatory functions. In addition, we confirm that cholesterol-enriched lipid microdomains, often called lipid rafts, are important in bacterial adhesion. These findings demonstrate that plasma membrane adhesion via bacterial flagella play a significant role for an important human pathogen. This mechanism represents a promising target for the development of novel antiadhesion therapies.

The Role of Pea (Pisum sativum) Seeds in Transmission of Entero-Aggregative Escherichia coli to Growing Plants

Crop plants can become contaminated with human pathogenic bacteria in agro-production systems. Some of the transmission routes of human pathogens to growing plants are well explored such as water, manure and soil, whereas others are less explored such as seeds. Fenugreek seeds contaminated with the entero-hemorrhagic Escherichia coli O104:H4 were suspected to be the principle vectors for transmission of the pathogen to sprouts at the food-borne disease outbreak in Hamburg and surrounding area in 2011. In this study we raised the questions of whether cells of the entero-aggregative E. coli O104:H4 strain 55989 is capable of colonizing developing plants from seeds and if it would be possible that, via plant internalization, these cells can reach the developing embryonic tissue of the next generation of seeds. To address these questions, we followed the fate of strain 55989 and of two other E. coli strains from artificially contaminated seeds to growing plants, and from developing flower tissue to mature seeds upon proximate introductions to the plant reproductive organs. Escherichia coli strains differing in origin, adherence properties to epithelial cells, and virulence profile were used in our experimentation to relate eventual differences in seed and plant colonization to typical E. coli properties. Experiments were conducted under realistic growth circumstances in greenhouse and open field settings. Entero-aggregative E. coli strain 55989 and the two other E. coli strains were able to colonize the root compartment of pea plants from inoculated seeds. In roots and rhizosphere soil, the strains could persist until the senescent stage of plant growth, when seeds had ripened. Colonization of the above-soil parts was only temporary at the start of plant growth for all three E. coli strains and, therefore, the conclusion was drawn that translocation of E. coli cells via the vascular tissue of the stems to developing pea seeds seems unlikely under circumstances realistic for agricultural practices. Proximate introductions of cells of E. coli strains to developing flowers also did not result in internal seed contamination, indicating that internal seed contamination with E. coli is an unlikely event. The fact that all three E. coli strains showed stronger preference for the root-soil zones of growing pea plants than for the above soil plant compartments, in spite of their differences in clinical behaviour and origin, indicate that E. coli in general will colonize root compartments of crop plants in production systems.

Diversity and Composition of the Gut Microbiota in the Developmental Stages of the Dung Beetle Copris incertus Say (Coleoptera, Scarabaeidae)

Dung beetles are holometabolous insects that feed on herbivorous mammal dung and provide services to the ecosystem including nutrient cycling and soil fertilization. It has been suggested that organisms developing on incomplete diets such as dungs require the association with microorganisms for the synthesis and utilization of nutrients. We describe the diversity and composition of the gut-microbiota during the life cycle of the dung beetle Copris incertus using 16S rRNA gene sequencing. We found that C. incertus gut contained a broad diversity of bacterial groups (1,699 OTUs and 302 genera). The taxonomic composition varied during the beetle life cycle, with the predominance of some bacterial genera in a specific developmental stage (Mothers: Enterobacter and Serratia; Eggs: Nocardioides and Hydrogenophaga; Larval and pupal stages: Dysgonomonas and Parabacteroides; offspring: Ochrobactrum). The beta diversity evidenced similarities among developmental stages, clustering (i) the adult stages (mother, male and female offsprings), (ii) intermediate developmental (larvae and pupa), and (iii) initial stage (egg). Microbiota differences could be attributed to dietary specialization or/and morpho-physiological factors involved in the transition from a developmental stage to the next. The predicted functional profile (PICRUSt2 analysis) for the development bacterial core of the level 3 categories, indicated grouping by developmental stage. Only 36 categories were significant in the SIMPER analysis, including the metabolic categories of amino acids and antibiotic synthesis, which were enriched in the larval and pupal stages; both categories are involved in the metamorphosis process. At the gene level, we found significant differences only in the KOs encoding functions related to nitrogen fixation, uric acid metabolism, and plant cell wall degradation for all developmental stages. Nitrogen fixation and plant cell wall degradation were enriched in the intermediate stages and uric acid metabolism was enriched in mothers. The data reported here suggested the influence of the maternal microbiota in the composition and diversity of the gut microbiota of the offspring.

Factors Required for Adhesion of Salmonella enterica Serovar Typhimurium to Corn Salad (Valerianella locusta)

Salmonella enterica is a foodborne pathogen often leading to gastroenteritis and is commonly acquired by consumption of contaminated food of animal origin. However, frequency of outbreaks linked to the consumption of fresh or minimally processed food of nonanimal origin is increasing. New infection routes of S. enterica by vegetables, fruits, nuts, and herbs have to be considered. This leads to special interest in S. enterica interactions with leafy products, e.g., salads, that are mainly consumed in a minimally processed form. The attachment of S. enterica to salad is a crucial step in contamination, but little is known about the bacterial factors required and mechanisms of adhesion. S. enterica possesses a complex set of adhesive structures whose functions are only partly understood. Potentially, S. enterica may deploy multiple adhesive strategies for adhering to various salad species and other vegetables. In this study, we systematically analyzed the contributions of the complete adhesiome, of lipopolysaccharide (LPS), and of flagellum-mediated motility of S. enterica serovar Typhimurium (STM) in adhesion to Valerianella locusta (corn salad). We deployed a reductionist, synthetic approach to identify factors involved in the surface binding of STM to leaves of corn salad, with particular regard to the expression of all known adhesive structures, using the Tet-on system. This work reveals the contribution of Saf fimbriae, type 1 secretion system-secreted BapA, an intact LPS, and flagellum-mediated motility of STM in adhesion to corn salad leaves.IMPORTANCE Transmission of gastrointestinal pathogens by contaminated fresh produce is of increasing relevance to human health. However, the mechanisms of contamination of, persistence on, and transmission by fresh produce are poorly understood. We investigated the contributions of the various adhesive structures of STM to the initial event in transmission, i.e., binding to the plant surface. A reductionist system was used that allowed experimentally controlled surface expression of individual adhesive structures and analyses of the contribution to binding to leave surfaces of corn salad under laboratory conditions. The model system allowed the determination of the relative contributions of fimbrial and nonfimbrial adhesins, the type 3 secretion systems, the O antigen of lipopolysaccharide, the flagella, and chemotaxis of STM to binding to corn salad leaves. Based on these data, future work could reveal the mechanism of binding and the relevance of interaction under agricultural conditions.

Variability in growth responses of non-O157 EHEC isolates in leafy vegetables, sprouted seeds and soil extracts occurs at the isolate level

Foods of plant origin are recognised as a major source of foodborne pathogens, in particular for Shigatoxigenic Escherichia coli (STEC). Most work for STEC and plant-based fresh produce has focused on the most prevalent outbreak serogroup, O157. However, non-O157 STEC is an emerging hazard, and as such it is important to characterise aspects within this group that reflect their ability to colonise alternative hosts and habitats relevant to horticultural production. Growth kinetics were quantified for a diverse set of clinical enterohaemorrhagic E. coli isolates in extracts made from different tissues of spinach, lettuce or sprouted seeds, or from soil, to represent association with ready-to-eat fresh produce production. For leafy vegetables, spinach apoplast supported the fastest rates of growth and lettuce root extracts generated the slowest growth rates. Growth rates were similar for the majority of isolates in fenugreek or alfalfa sprouted seed extracts. Monosaccharides were the major driver of bacterial growth. No correlations were found for growth rates between different serotypes or for Shigatoxin gene carriage. Thus, growth rates varied in a plant-dependent and isolate-dependent manner, for all plant or soil extracts tested, indicative of isolate-specific differences in metabolic flexibility. These findings are relevant for risk assessment of non-O157 STEC.

Abundance of human pathogen genes in the phyllosphere of four landscape plants

The surface of leaf, also known as phyllosphere, harbors diverse microbial communities which include both beneficial microorganisms promoting plants growth and harmful microorganisms, such as plant pathogens and human pathogens. Several studies have investigated the interaction between plants and human pathogens, while few works have focused on the quantitative analysis of pathogenic bacteria. On the basis of real-time polymerase chain reaction (qPCR), this study aimed to evaluate the abundance of following genes: the nuc and pvl of Staphylococcus aureus, the lytA and psaA of Streptococcus pneumoniae, and the ttr and invA of Salmonella enterica in the phyllosphere of four landscape plants (Nandina domestica, Rhododendron pulchrum, Photinia serrulata, and Cinnamomum camphora) growing in two habitats. Our results indicated that the relative abundance of pathogenic genes in the phyllosphere ranged from 10^-9 to 10^-6. The specific genes of S. aureus, S. pneumoniae and S. enterica in landscape plants were pvl, lytA and ttr, respectively. The two pathogenic genes of S. pneumoniae and the 16S rRNA gene were mainly affected by habitats, host species, and habitats-species interaction. Moreover, for the abundance of lytA and 16S rRNA, results showed that plants present in roadside with traffic pollution were relatively higher than that of campus with less pollution. The N. domestica and C. camphora were recommended for planting along the roadsides due to lower abundance of pathogenic genes. However, we have observed no significant difference in the abundance of pathogenic genes among four plants in the campus. Thereby, this study provided a valuable reference for selecting landscape plants in view of human health.

Differential transcriptome analysis of enterohemorrhagic Escherichia coli strains reveals differences in response to plant-derived compounds

BACKGROUND

Several serious vegetable-associated outbreaks of enterohemorrhagic Escherichia coli (EHEC) infections have occurred during the last decades. In this context, vegetables have been suggested to function as secondary reservoirs for EHEC strains. Increased knowledge about the interaction of EHEC with plants including gene expression patterns in response to plant-derived compounds is required. In the current study, EHEC O157:H7 strain Sakai, EHEC O157:H- strain 3072/96, and the EHEC/enteroaggregative E. coli (EAEC) hybrid O104:H4 strain C227-11φcu were grown in lamb's lettuce medium and in M9 minimal medium to study the differential transcriptional response of these strains to plant-derived compounds with RNA-Seq technology.

RESULTS

Many genes involved in carbohydrate degradation and peptide utilization were similarly upregulated in all three strains, suggesting that the lamb's lettuce medium provides sufficient nutrients for proliferation. In particular, the genes galET and rbsAC involved in galactose metabolism and D-ribose catabolism, respectively, were uniformly upregulated in the investigated strains. The most prominent differences in shared genome transcript levels were observed for genes involved in the expression of flagella. Transcripts of all three classes of the flagellar hierarchy were highly abundant in strain C227-11φcu. Strain Sakai expressed only genes encoding the basal flagellar structure. In addition, both strains showed increased motility in presence of lamb's lettuce extract. Moreover, strain 3072/96 showed increased transcription activity for genes encoding the type III secretion system (T3SS) including effectors, and was identified as a powerful biofilm-producer in M9 minimal medium.

CONCLUSION

The current study provides clear evidence that EHEC and EHEC/EAEC strains are able to adjust their gene expression patterns towards metabolization of plant-derived compounds, demonstrating that they may proliferate well in a plant-associated environment. Moreover, we propose that flagella and other surface structures play a fundamental role in the interaction of EHEC and EHEC/EAEC with plants.

Influence of Plant Species, Tissue Type, and Temperature on the Capacity of Shiga-Toxigenic Escherichia coli To Colonize, Grow, and Be Internalized by Plants

Contamination of fresh produce with pathogenic Escherichia coli, including Shiga-toxigenic E. coli (STEC), represents a serious risk to human health. Colonization is governed by multiple bacterial and plant factors that can impact the probability and suitability of bacterial growth. Thus, we aimed to determine whether the growth potential of STEC for plants associated with foodborne outbreaks (two leafy vegetables and two sprouted seed species) is predictive of the colonization of living plants, as assessed from growth kinetics and biofilm formation in plant extracts. The fitness of STEC isolates was compared to that of environmental E. coli isolates at temperatures relevant to plant growth. Growth kinetics in plant extracts varied in a plant-dependent and isolate-dependent manner for all isolates, with spinach leaf lysates supporting the highest rates of growth. Spinach extracts also supported the highest levels of biofilm formation. Saccharides were identified to be the major driver of bacterial growth, although no single metabolite could be correlated with growth kinetics. The highest level of in planta colonization occurred on alfalfa sprouts, though internalization was 10 times more prevalent in the leafy vegetables than in sprouted seeds. Marked differences in in planta growth meant that the growth potential of STEC could be inferred only for sprouted seeds. In contrast, biofilm formation in extracts related to spinach colonization. Overall, the capacity of E. coli to colonize, grow, and be internalized within plants or plant-derived matrices was influenced by the isolate type, plant species, plant tissue type, and temperature, complicating any straightforward relationship between in vitro and in planta behaviors.IMPORTANCE Fresh produce is an important vehicle for STEC transmission, and experimental evidence shows that STEC can colonize plants as secondary hosts, but differences in the capacity to colonize occur between different plant species and tissues. Therefore, an understanding of the impact that these plant factors have on the ability of STEC to grow and establish is required for food safety considerations and risk assessment. Here, we determined whether growth and the ability of STEC to form biofilms in plant extracts could be related to specific plant metabolites or could predict the ability of the bacteria to colonize living plants. Growth rates for sprouted seeds (alfalfa and fenugreek) but not those for leafy vegetables (lettuce and spinach) exhibited a positive relationship between plant extracts and living plants. Therefore, the detailed variations at the level of the bacterial isolate, plant species, and tissue type all need to be considered in risk assessment.

Functional and Genetic Diversity of Bacteria Associated with the Surfaces of Agronomic Plants

The main objective of this study was to evaluate the genetic diversity and agricultural significance of bacterial communities associated with the surfaces of selected agronomic plants (carrot, cabbage and turnip). The bacterial diversity of fresh agricultural produce was targeted to identify beneficial plant microflora or opportunistic human pathogens that may be associated with the surfaces of plants. Bacterial strains were screened in vitro for auxin production, biofilm formation and antibiotic resistance. 16S rRNA gene sequencing confirmed the presence of several bacterial genera including Citrobacter, Pseudomonas, Pantoea, Bacillus, Kluyvera, Lysinibacillus, Acinetobacter, Enterobacter, Serratia, Staphylococcus, Burkholderia, Exiguobacterium, Stenotrophomonas, Arthrobacter and Klebsiella. To address the biosafety issue, the antibiotic susceptibility pattern of strains was determined against different antibiotics. The majority of the strains were resistant to amoxicillin (25 µg) and nalidixic acid (30 µg). Strains were also screened for plant growth-promoting attributes to evaluate their positive interaction with colonized plants. Maximum auxin production was observed with Stenotrophomonas maltophilia MCt-1 (101 µg mL⁻¹) and Bacillus cereus PCt-1 (97 µg mL⁻¹). Arthrobacter nicotianae Lb-41 and Exiguobacterium mexicanum MCb-4 were strong biofilm producers. In conclusion, surfaces of raw vegetables were inhabited by different bacterial genera. Potential human pathogens such as Bacillus cereus, Bacillus anthracis, Enterobacter cloacae, Enterobacter amnigenus and Klebsiella pneumoniae were also isolated, which makes the biosafety of these vegetable a great concern for the local community. Nevertheless, these microbes also harbor beneficial plant growth-promoting traits that indicated their positive interaction with their host plants. In particular, bacterial auxin production may facilitate the growth of agronomic plants under natural conditions. Moreover, biofilm formation may help bacteria to colonize plant surfaces to show positive interactions with host plants.

Green Technology: Bacteria-Based Approach Could Lead to Unsuspected Microbe⁻Plant⁻Animal Interactions

The recent and massive revival of green strategies to control plant diseases, mainly as a consequence of the Integrated Pest Management (IPM) rules issued in 2009 by the European Community and the increased consumer awareness of organic products, poses new challenges for human health and food security that need to be addressed in the near future. One of the most important green technologies is biocontrol. This approach is based on living organisms and how these biocontrol agents (BCAs) directly or indirectly interact as a community to control plant pathogens and pest. Although most BCAs have been isolated from plant microbiomes, they share some genomic features, virulence factors, and trans-kingdom infection abilities with human pathogenic microorganisms, thus, their potential impact on human health should be addressed. This evidence, in combination with the outbreaks of human infections associated with consumption of raw fruits and vegetables, opens new questions regarding the role of plants in the human pathogen infection cycle. Moreover, whether BCAs could alter the endophytic bacterial community, thereby leading to the development of new potential human pathogens, is still unclear. In this review, all these issues are debated, highlighting that the research on BCAs and their formulation should include these possible long-lasting consequences of their massive spread in the environment.

Plant health: feedback effect of root exudates-rhizobiome interactions

The well-being of the microbial community that densely populates the rhizosphere is aided by a plant's root exudates. Maintaining a plant's health is a key factor in its continued existence. As minute as rhizospheric microbes are, their importance in plant growth cannot be overemphasized. They depend on plants for nutrients and other necessary requirements. The relationship between the rhizosphere-microbiome (rhizobiome) and plant hosts can be beneficial, non-effectual, or pathogenic depending on the microbes and the plant involved. This relationship, to a large extent, determines the fate of the host plant's survival. Modern molecular techniques have been used to unravel rhizobiome species' composition, but the interplay between the rhizobiome root exudates and other factors in the maintenance of a healthy plant have not as yet been thoroughly investigated. Many functional proteins are activated in plants upon contact with external factors. These proteins may elicit growth promoting or growth suppressing responses from the plants. To optimize the growth and productivity of host plants, rhizobiome microbial diversity and modulatory techniques need to be clearly understood for improved plant health.

Understanding the Complexities of Food Safety Using a "One Health" Approach

The philosophy of One Health is growing in concept and clarity. The interdependence of human, animal, and environmental health is the basis for the concept of One Health. One Health is a comprehensive approach to ensure the health of people, animals, and the environment through collaborative efforts. Preharvest food safety issues align with the grand concept of One Health. Imagine any food production system, and immediately, parallel images from One Health emerge: for example, transmission of zoonotic diseases, antibiotic residues, or resistance genes in the environment; environmental and animal host reservoirs of disease; challenges with rearing animals and growing fresh produce on the same farm; application and transport of manure or diseased animals. During a recent celebration of #OneHealthDay, information was shared around the globe concerning scientists dedicated to One Health research systems. An ever-growing trade and global commerce system mixed with our incessant desire for food products during the whole year makes it all the more important to take a global view through the One Health lens to solve these growing challenges. The recent explosion of Zika virus around the globe renewed the need for assessing transmissible diseases through the eyes of One Health. It is not good enough to know how a disease affects the human population without a thorough understanding of the environment and vector reservoirs. If 60 to 75% of infectious diseases affecting humans are of animal origin, the need for better One Health research strategies and overdue solutions is imperative.

Microbiological Parameters in the Primary Production of Berries: A Pilot Study

The primary production of fresh soft fruits was considered to be a suspected critical point for the contamination of frozen berries that were responsible for the large 2013⁻2014 Hepatitis A virus (HAV) outbreak in Europe. In this study, an Italian berries’ production area was studied for its agro-technical characteristics, and the fresh fruits were analyzed for the presence of enteric viruses (HAV and Norovirus (NoV) genogroup I and genogroup II (GGI and GGII)), the enumeration of hygienic quality parameters, and the prevalence of bacterial pathogens. A total of 50 producers were sampled, who specialized in the exclusive or shared cultivation of berries. Escherichia coli was detected in two blackberry samples, whereas HAV and Norovirus were not detected. The samples were negative for Salmonella spp., Listeria monocytogenes, and Shiga toxin-producing Escherichia coli (STEC). The farms’ attributes were not associated with positive samples, apart from the presence of E. coli and the aerobic mesophilic bacteria for blackberry that were statistically correlated. In blueberries, the high aerobic mesophilic count could likely be associated with the resistance of the outer layer to handling. However, the two pathogens (Salmonella spp. and STEC) and the targeted viruses (HAV, NoV GGI and GGII) were not detected, highlighting the low risk of foodborne pathogens and viral contamination at the primary production stage of the berry food chain in the area considered in this pilot study.

[Persistence, internalization and translocation of Escherichia coli O157:H7, O157:H16 and O105ab in plants and tomato fruits (Solanum lycopersicum L.)]

The presence of pathogenic bacteria, such as Escherichia coli affects the quality and safety of vegetables that are consumed fresh and is associated with serious health problems. The objective of this study was to determine if three different strains of E. coli can penetrate and remain in plants and tomato fruits. A completely randomized experimental design was followed for which a tomato crop ("Cid" variety) was established under greenhouse conditions and three treatments were evaluated, T1 (E. coli O157:H7), T2 (E. coli from tomato cultivation [EcT] O157:H16), T3 (E. coli from spinach cultivation [EcH] O105ab) and a T4 control, with 100 plants each and four forms of inoculation: in the substrate, steam, petiole and the peduncle. Samples were carried out in vegetative stage, flowering, fruiting and physiological maturity to quantify in petri dish CFU/g and know if the bacteria managed to move around and recover in root, stem, flower and fruit. The phylogenetic groups that corresponded to the bacteria recovered were confirmed by biochemical tests, serotyping and PCR. At 120 days the recovery of bacteria in the plant was 23% (E. coli O157:H7), 28% (EcT O157:H16) and 55% (EcH O105ab) whit inoculation to the substrate while the inoculation by puncture the recovery was (in the same order) of 5%, 3%, and 4% at 30 days; 37%, 35% and 30% at 90 days; and 42%, 39% and 13% at 65 days. The strains submit the ability to enter the tomato plant and to stay in it and transported to the fruit, without producing that indicate their presence.

Phenotypic and virulence traits of Escherichia coli and Salmonella strains isolated from vegetables and fruits from India

AIMS

The present study was designed to assess the phenotypic traits and virulence determinants of vegetable-/fruit-origin Escherichia coli and Salmonella strains.

METHODS AND RESULTS

A total of 520 fresh vegetables/fruits samples were analysed for the presence of E. coli, including Shiga toxin-producing E. coli (STEC), and Salmonella. The vegetable-/fruit-origin E. coli and Salmonella strains were further assessed for antimicrobial resistance, biofilm formation, extracellular matrix production and in vitro invasion/intracellular survivability assays. A total of 73 E. coli, including four STEC, and 26 Salmonella strains were recovered from vegetables/fruits in the present study. Most of the E. coli and Salmonella isolates were able to form biofilm with higher production of cellulose/curli-fimbriae. Furthermore, more resistance was observed in E. coli isolates (61·6%) than in Salmonella isolates (38·5%) against tested antimicrobials. Additionally, invasion/intracellular survival results showed that majority of the E. coli and Salmonella isolates were able to efficiently invade/replicate intracellularly in the human epithelial cells.

CONCLUSIONS

Our results demonstrate that vegetable-/fruit-origin E. coli and Salmonella significantly exhibited distinct phenotypic/virulence traits which could be linked to their plant-associated lifestyle with food safety issues.

SIGNIFICANCE AND IMPACT OF THE STUDY

The present study provides valuable baseline information that E. coli and Salmonella may use plants as an alternative host with significant clinical importance.

Human Norovirus and Its Surrogates Induce Plant Immune Response in Arabidopsis thaliana and Lactuca sativa

Human norovirus is the leading cause of foodborne illness worldwide with the majority of outbreaks linked to fresh produce and leafy greens. It is essential that we thoroughly understand the type of relationship and interactions that take place between plants and human norovirus to better utilize control strategies to reduce transmission of norovirus in the field onto plants harvested for human consumption. In this study the expression of gene markers for the salicylic acid (SA) and jasmonic acid (JA) plant defense pathways was measured and compared in romaine lettuce (Lactuca sativa) and Arabidopsis thaliana Col-0 plants that were inoculated with Murine Norovirus-1, Tulane Virus, human norovirus GII.4, or Hank's Balanced Salt Solution (control). Genes involving both the SA and JA pathways were expressed in both romaine lettuce and A. thaliana for all three viruses, as well as controls. Studies, including gene expression of SA- and JA-deficient A. thaliana mutant lines, suggest that the JA pathway is more likely involved in the plant immune response to human norovirus. This research provides the first pieces of information regarding how foodborne viruses interact with plants in the preharvest environment.

Salmonella virulence plasmid: pathogenesis and ecology

A current view on the role of the Salmonella virulence plasmid in the pathogenesis of animal and human hosts is discussed; including the possible relevance in secondary ecological niches. Various strategies towards further studies in this respect are proposed within the One Health Concept.

Differences in internalization and growth of Escherichia coli O157:H7 within the apoplast of edible plants, spinach and lettuce, compared with the model species Nicotiana benthamiana

Internalization of food-borne bacteria into edible parts of fresh produce plants represents a serious health risk. Therefore, internalization of verocytotoxigenic E. coli O157:H7 isolate Sakai was assessed in two species associated with outbreaks, spinach (Spinacia oleracea) and lettuce (Lactuca sativa) and compared to the model species Nicotiana benthamiana. Internalization occurred in the leaves and roots of spinach and lettuce throughout a 10 day time-course. The plant species, tissue type and inoculum dose all impacted the outcome. A combination of low inoculum dose (~102 CFU) together with light microscopy imaging highlighted marked differences in the fate of endophytic E. coli O157:H7 Sakai. In the fresh produce species, bacterial growth was restricted but viable cells persisted over 20 days, whereas there was > 400-fold (~2.5 Log10 ) increase in growth in N. benthamiana. Colony formation occurred adjacent to epidermal cells and mesophyll cells or close to vascular bundles of N. benthamiana and contained components of a biofilm matrix, including curli expression and elicitation, extracellular DNA and a limited presence of cellulose. Together the data show that internalization is a relevant issue in crop production and that crop species and tissue need to be considered as food safety risk parameters.

Microorganisms and heavy metals associated with atmospheric deposition in a congested urban environment of a developing country: Sri Lanka

The presence of bacteria and heavy metals in atmospheric deposition were investigated in Kandy, Sri Lanka, which is a typical city in the developing world with significant traffic congestion. Atmospheric deposition samples were analyzed for Al, Cr, Mn, Fe, Ni, Cu, Zn, Cd and Pb which are heavy metals common to urban environments. Al and Fe were found in high concentrations due to the presence of natural sources, but may also be re-suspended by vehicular traffic. Relatively high concentrations of toxic metals such as Cr and Pb in dissolved form were also found. High Zn loads can be attributed to vehicular emissions and the wide use of Zn coated roofing materials. The metal loads in wet deposition showed higher concentrations compared to dry deposition. The metal concentrations among the different sampling sites significantly differ from each other depending on the traffic conditions. Industrial activities are not significant in Kandy City. Consequently, the traffic exerts high influence on heavy metal loadings. As part of the bacterial investigations, nine species of culturable bacteria, namely; Sphingomonas sp., Pseudomonas aeruginosa, Pseudomonas monteilii, Klebsiella pneumonia, Ochrobactrum intermedium, Leclercia adecarboxylata, Exiguobacterium sp., Bacillus pumilus and Kocuria kristinae, which are opportunistic pathogens, were identified. This is the first time Pseudomonas monteilii and Ochrobactrum intermedium has been reported from a country in Asia. The culturable fraction constituted ~0.01 to 10%. Pigmented bacteria and endospore forming bacteria were copious in the atmospheric depositions due to their capability to withstand harsh environmental conditions. The presence of pathogenic bacteria and heavy metals creates potential human and ecosystem health risk.